WorldWideScience

Sample records for biomolecular chromophores role

  1. Chromophore

    Directory of Open Access Journals (Sweden)

    Roxana Gabriela Zgârian

    2017-02-01

    Full Text Available The paper presents the main results of our study on preparation and characterization of conducting biomembranes to be used as solid polymer electrolytes (SPEs. It bases on deoxyribonucleic acid (DNA, glycerol (GLY and photosensitive chromophores, like Prussian Blue (PB. Its primary application is in fabrication of electrochromic windows. The new SPEs were characterized by UV-VIS and FTIR spectroscopy. They were used in preparation of small electrochromic devices (ECDs. The obtained devices were evaluated by cyclic voltammetry and also by spectroscopic methods. The results show their color change from blue pale to intense blue after application of a direct current (DC electric field, making the composites very interesting for industrial applications in smart windows.

  2. THE ROLE OF NITROGEN IN CHROMOPHORIC AND FLUORESCENT DISSOLVED ORGANIC MATTER FORMATION

    Science.gov (United States)

    Microbial and photochemical processes affect chromophoric dissolved organic matter (CDOM) dynamics in the ocean. Some evidence suggests that dissolved nitrogen plays a role in CDOM formation, although this has received little systematic attention in marine ecosystems. Coastal sea...

  3. Role of biomolecular logic systems in biosensors and bioactuators

    Science.gov (United States)

    Mailloux, Shay; Katz, Evgeny

    2014-09-01

    An overview of recent advances in biosensors and bioactuators based on biocomputing systems is presented. Biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce an output in the form of a YES/NO response. Compared to traditional single-analyte sensing devices, the biocomputing approach enables high-fidelity multianalyte biosensing, which is particularly beneficial for biomedical applications. Multisignal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert medical personnel of medical emergencies together with immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly as exemplified for liver injury. Wide-ranging applications of multianalyte digital biosensors in medicine, environmental monitoring, and homeland security are anticipated. "Smart" bioactuators, for signal-triggered drug release, for example, were designed by interfacing switchable electrodes with biocomputing systems. Integration of biosensing and bioactuating systems with biomolecular information processing systems advances the potential for further scientific innovations and various practical applications.

  4. Molecular Polygons Probe the Role of Intramolecular Strain in the Photophysics of π-Conjugated Chromophores.

    Science.gov (United States)

    Wilhelm, Philipp; Vogelsang, Jan; Poluektov, Georgiy; Schönfelder, Nina; Keller, Tristan J; Jester, Stefan-Sven; Höger, Sigurd; Lupton, John M

    2017-01-24

    π-Conjugated segments, chromophores, are the electronically active units of polymer materials used in organic electronics. To elucidate the effect of the bending of these linear moieties on elementary electronic properties, such as luminescence color and radiative rate, we introduce a series of molecular polygons. The π-system in these molecules becomes so distorted in bichromophores (digons) that these absorb and emit light of arbitrary polarization: any part of the chain absorbs and emits radiation with equal probability. Bending leads to a cancellation of transition dipole moment (TDM), increasing excited-state lifetime. Simultaneously, fluorescence shifts to the red as radiative transitions require mixing of the excited state with vibrational modes. However, strain can become so large that excited-state localization on shorter units of the chain occurs, compensating TDM cancellation. The underlying correlations between shape and photophysics can only be resolved in single molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Role of microgel formation in scavenging of chromophoric dissolved organic matter and heavy metals in a river-sea system.

    Science.gov (United States)

    Shiu, Ruei-Feng; Lee, Chon-Lin

    2017-04-15

    We use riverine and marine dissolved organic carbon (DOC) polymers to examine their aggregation behavior, and to evaluate the roles of microgel formation in scavenging of chromophoric dissolved organic matter (CDOM) and heavy metals in a river-sea system. Our results indicate that riverine and marine microgels did not exhibit very much difference in size and self-assembly curve; however, the assembly effectiveness ([microgel]/DOC) of marine samples was much higher than riverine. Instead of concentration of DOC, other factors such as types and sources of DOC polymers may control the microgel abundance in aquatic environments. After filtering water samples (microgels removed), the CDOM and selected metals (Cu, Ni, Mn) in the filtrate were quantified. CDOM and metals were concurrently removed to an extent via DOC polymer re-aggregation, which also suggested that the microgels had sequestering capability in CDOM and metals. This finding provides an alternative route for CDOM and heavy metals removal from the water column. As such the process of re-aggregation into microgels should then be considered besides traditional phase partitioning in the assessment of the ecological risk and fate of hazardous materials. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Role of microgel formation in scavenging of chromophoric dissolved organic matter and heavy metals in a river-sea system

    Energy Technology Data Exchange (ETDEWEB)

    Shiu, Ruei-Feng [Department of Marine Environment and Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan (China); Lee, Chon-Lin, E-mail: linnohc@fac.nsysu.edu.tw [Department of Marine Environment and Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan (China); Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung, Taiwan (China); Asia-Pacific Ocean Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan (China); Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan (China)

    2017-04-15

    Highlights: • Different types of DOC polymers forming microgel were compared. • The assembly effectiveness of marine DOC was much higher than riverine DOC. • Types and sources of DOC polymers may control the aquatic microgel abundance. • An alternative route for CDOM and heavy metals removal is presented. • Ecological risk and fate assessments of pollutants may consider the microgel phase. - Abstract: We use riverine and marine dissolved organic carbon (DOC) polymers to examine their aggregation behavior, and to evaluate the roles of microgel formation in scavenging of chromophoric dissolved organic matter (CDOM) and heavy metals in a river-sea system. Our results indicate that riverine and marine microgels did not exhibit very much difference in size and self-assembly curve; however, the assembly effectiveness ([microgel]/DOC) of marine samples was much higher than riverine. Instead of concentration of DOC, other factors such as types and sources of DOC polymers may control the microgel abundance in aquatic environments. After filtering water samples (microgels removed), the CDOM and selected metals (Cu, Ni, Mn) in the filtrate were quantified. CDOM and metals were concurrently removed to an extent via DOC polymer re-aggregation, which also suggested that the microgels had sequestering capability in CDOM and metals. This finding provides an alternative route for CDOM and heavy metals removal from the water column. As such the process of re-aggregation into microgels should then be considered besides traditional phase partitioning in the assessment of the ecological risk and fate of hazardous materials.

  7. Role of microgel formation in scavenging of chromophoric dissolved organic matter and heavy metals in a river-sea system

    International Nuclear Information System (INIS)

    Shiu, Ruei-Feng; Lee, Chon-Lin

    2017-01-01

    Highlights: • Different types of DOC polymers forming microgel were compared. • The assembly effectiveness of marine DOC was much higher than riverine DOC. • Types and sources of DOC polymers may control the aquatic microgel abundance. • An alternative route for CDOM and heavy metals removal is presented. • Ecological risk and fate assessments of pollutants may consider the microgel phase. - Abstract: We use riverine and marine dissolved organic carbon (DOC) polymers to examine their aggregation behavior, and to evaluate the roles of microgel formation in scavenging of chromophoric dissolved organic matter (CDOM) and heavy metals in a river-sea system. Our results indicate that riverine and marine microgels did not exhibit very much difference in size and self-assembly curve; however, the assembly effectiveness ([microgel]/DOC) of marine samples was much higher than riverine. Instead of concentration of DOC, other factors such as types and sources of DOC polymers may control the microgel abundance in aquatic environments. After filtering water samples (microgels removed), the CDOM and selected metals (Cu, Ni, Mn) in the filtrate were quantified. CDOM and metals were concurrently removed to an extent via DOC polymer re-aggregation, which also suggested that the microgels had sequestering capability in CDOM and metals. This finding provides an alternative route for CDOM and heavy metals removal from the water column. As such the process of re-aggregation into microgels should then be considered besides traditional phase partitioning in the assessment of the ecological risk and fate of hazardous materials.

  8. Theoretical description of protein field effects on electronic excitations of biological chromophores

    International Nuclear Information System (INIS)

    Varsano, Daniele; Caprasecca, Stefano; Coccia, Emanuele

    2017-01-01

    Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show

  9. Theoretical description of protein field effects on electronic excitations of biological chromophores

    Science.gov (United States)

    Varsano, Daniele; Caprasecca, Stefano; Coccia, Emanuele

    2017-01-01

    Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show

  10. Removal of Chromophoric Dissolved Organic Matter and Heavy Metals in a River-Sea System: Role of Aquatic Microgel Formation

    Science.gov (United States)

    Shiu, R. F.; Lee, C. L.

    2016-12-01

    Dissolved organic carbon (DOC) polymers are complex and poorly understood mixture of organic macromolecules in environment system. Portions of these polymers spontaneously form microgels that play key roles in many biogeochemical reactions, including mediating aggregation processes, element cycling, and pollutant mobility. However, the detailed interaction of microgels-heterogeneous materials in aquatic systems is still lacking. Insight into the interaction between surrounding materials and microgels from different types of aquatic DOC polymers are extremely important, as it is crucial in determining the fate and transport of these materials. Here, we use riverine and marine DOC polymers to examine their aggregation behavior, and to evaluate the roles of microgel formation in scavenging of chromophoric dissolved organic matter (CDOM) and heavy metals in a river-sea system. Our results indicate that riverine and marine microgels did not exhibit too much difference in size ( 3-5 μm) and self-assembly curve; however, the assembly effectiveness ([microgel]/DOC) of marine samples was much higher than riverine. Instead of concentration of DOC, other factors such as types and sources of DOC polymers may control the microgel abundance in aquatic environments. After filtering water samples (microgels removed), the CDOM and selected metals (Cu, Ni, Mn) in the filtrate were quantified. CDOM and metals were concurrently removed to an extent via DOC polymer re-aggregation, which also suggested that the microgels had the sequestering capability in CDOM and metals. This finding provides an alternative route for CDOM and heavy metals removal from the water column. As such the process of re-aggregation into microgels should then be considered besides traditional phase partitioning in the assessment of the ecological risk and fate of pollutant.

  11. Biomolecular Science (Fact Sheet)

    Energy Technology Data Exchange (ETDEWEB)

    2012-04-01

    A brief fact sheet about NREL Photobiology and Biomolecular Science. The research goal of NREL's Biomolecular Science is to enable cost-competitive advanced lignocellulosic biofuels production by understanding the science critical for overcoming biomass recalcitrance and developing new product and product intermediate pathways. NREL's Photobiology focuses on understanding the capture of solar energy in photosynthetic systems and its use in converting carbon dioxide and water directly into hydrogen and advanced biofuels.

  12. Biomolecular simulation: historical picture and future perspectives.

    Science.gov (United States)

    van Gunsteren, Wilfred F; Dolenc, Jozica

    2008-02-01

    Over the last 30 years, computation based on molecular models is playing an increasingly important role in biology, biological chemistry and biophysics. Since only a very limited number of properties of biomolecular systems are actually accessible to measurement by experimental means, computer simulation complements experiments by providing not only averages, but also distributions and time series of any definable, observable or non-observable, quantity. Biomolecular simulation may be used (i) to interpret experimental data, (ii) to provoke new experiments, (iii) to replace experiments and (iv) to protect intellectual property. Progress over the last 30 years is sketched and perspectives are outlined for the future.

  13. Prediction of Biomolecular Complexes

    KAUST Repository

    Vangone, Anna

    2017-04-12

    Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

  14. Prediction of Biomolecular Complexes

    KAUST Repository

    Vangone, Anna; Oliva, Romina; Cavallo, Luigi; Bonvin, Alexandre M. J. J.

    2017-01-01

    Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

  15. Programming in biomolecular computation

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

    2011-01-01

    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem...... conspicuously absent from the literature on biomolecular computing; to partially redress this absence, we introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined...... by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways...

  16. Thermodynamic properties of water solvating biomolecular surfaces

    Science.gov (United States)

    Heyden, Matthias

    Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

  17. Biomolecular Sciences: uniting Biology and Chemistry

    NARCIS (Netherlands)

    Vrieling, Engel

    2017-01-01

    Biomolecular Sciences: uniting Biology and Chemistry www.rug.nl/research/gbb The scientific discoveries in biomolecular sciences have benefitted enormously from technological innovations. At the Groningen Biomolecular Science and Biotechnology Institute (GBB) we now sequence a genome in days,

  18. Biomolecular modelling and simulations

    CERN Document Server

    Karabencheva-Christova, Tatyana

    2014-01-01

    Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series is the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics. Describes advances in biomolecular modelling and simulations Chapters are written by authorities in their field Targeted to a wide audience of researchers, specialists, and students The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables.

  19. Biomolecular EPR spectroscopy

    CERN Document Server

    Hagen, Wilfred Raymond

    2008-01-01

    Comprehensive, Up-to-Date Coverage of Spectroscopy Theory and its Applications to Biological SystemsAlthough a multitude of books have been published about spectroscopy, most of them only occasionally refer to biological systems and the specific problems of biomolecular EPR (bioEPR). Biomolecular EPR Spectroscopy provides a practical introduction to bioEPR and demonstrates how this remarkable tool allows researchers to delve into the structural, functional, and analytical analysis of paramagnetic molecules found in the biochemistry of all species on the planet. A Must-Have Reference in an Intrinsically Multidisciplinary FieldThis authoritative reference seamlessly covers all important bioEPR applications, including low-spin and high-spin metalloproteins, spin traps and spin lables, interaction between active sites, and redox systems. It is loaded with practical tricks as well as do's and don'ts that are based on the author's 30 years of experience in the field. The book also comes with an unprecedented set of...

  20. Photoresponse of the protonated Schiff-base retinal chromophore in the gas phase

    DEFF Research Database (Denmark)

    Toker, Jonathan; Rahbek, Dennis Bo; Kiefer, H V

    2013-01-01

    The fragmentation, initiated by photoexcitation as well as collisionally-induced excitation, of several retinal chromophores was studied in the gas phase. The chromophore in the protonated Schiff-base form (RPSB), essential for mammalian vision, shows a remarkably selective photoresponse. The sel......The fragmentation, initiated by photoexcitation as well as collisionally-induced excitation, of several retinal chromophores was studied in the gas phase. The chromophore in the protonated Schiff-base form (RPSB), essential for mammalian vision, shows a remarkably selective photoresponse...... modifications of the chromophore. We propose that isomerizations play an important role in the photoresponse of gas-phase retinal chromophores and guide internal conversion through conical intersections. The role of protein interactions is then to control the specificity of the photoisomerization in the primary...

  1. Search for Singlet Fission Chromophores

    Energy Technology Data Exchange (ETDEWEB)

    Havlas, Z.; Akdag, A.; Smith, M. B.; Dron, P.; Johnson, J. C.; Nozik, A. J.; Michl, J.

    2012-01-01

    Singlet fission, in which a singlet excited chromophore shares its energy with a ground-state neighbor and both end up in their triplet states, is of potential interest for solar cells. Only a handful of compounds, mostly alternant hydrocarbons, are known to perform efficiently. In view of the large number of conditions that a successful candidate for a practical cell has to meet, it appears desirable to extend the present list of high performers to additional classes of compounds. We have (i) identified design rules for new singlet fission chromophores and for their coupling to covalent dimers, (ii) synthesized them, and (iii) evaluated their performance as neat solids or covalent dimers.

  2. Smartphones for cell and biomolecular detection.

    Science.gov (United States)

    Liu, Xiyuan; Lin, Tung-Yi; Lillehoj, Peter B

    2014-11-01

    Recent advances in biomedical science and technology have played a significant role in the development of new sensors and assays for cell and biomolecular detection. Generally, these efforts are aimed at reducing the complexity and costs associated with diagnostic testing so that it can be performed outside of a laboratory or hospital setting, requiring minimal equipment and user involvement. In particular, point-of-care (POC) testing offers immense potential for many important applications including medical diagnosis, environmental monitoring, food safety, and biosecurity. When coupled with smartphones, POC systems can offer portability, ease of use and enhanced functionality while maintaining performance. This review article focuses on recent advancements and developments in smartphone-based POC systems within the last 6 years with an emphasis on cell and biomolecular detection. These devices typically comprise multiple components, such as detectors, sample processors, disposable chips, batteries, and software, which are integrated with a commercial smartphone. One of the most important aspects of developing these systems is the integration of these components onto a compact and lightweight platform that requires minimal power. Researchers have demonstrated several promising approaches employing various detection schemes and device configurations, and it is expected that further developments in biosensors, battery technology and miniaturized electronics will enable smartphone-based POC technologies to become more mainstream tools in the scientific and biomedical communities.

  3. Integrative NMR for biomolecular research

    International Nuclear Information System (INIS)

    Lee, Woonghee; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R.; Tonelli, Marco; Westler, William M.; Butcher, Samuel E.; Henzler-Wildman, Katherine A.; Markley, John L.

    2016-01-01

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download-packages.html http://pine.nmrfam.wisc.edu/download_packages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html http://pine.nmrfam.wisc.edu/integrative.html ).

  4. Integrative NMR for biomolecular research

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R.; Tonelli, Marco; Westler, William M.; Butcher, Samuel E.; Henzler-Wildman, Katherine A.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

    2016-04-15

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download-packages.html http://pine.nmrfam.wisc.edu/download{sub p}ackages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html http://pine.nmrfam.wisc.edu/integrative.html ).

  5. Physics at the biomolecular interface fundamentals for molecular targeted therapy

    CERN Document Server

    Fernández, Ariel

    2016-01-01

    This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood w...

  6. Stochastic Simulation of Biomolecular Reaction Networks Using the Biomolecular Network Simulator Software

    National Research Council Canada - National Science Library

    Frazier, John; Chusak, Yaroslav; Foy, Brent

    2008-01-01

    .... The software uses either exact or approximate stochastic simulation algorithms for generating Monte Carlo trajectories that describe the time evolution of the behavior of biomolecular reaction networks...

  7. Conducting polymer based biomolecular electronic devices

    Indian Academy of Sciences (India)

    Conducting polymers; LB films; biosensor microactuators; monolayers. ... have been projected for applications for a wide range of biomolecular electronic devices such as optical, electronic, drug-delivery, memory and biosensing devices.

  8. Heterocyclic Nonlinear Optical Chromophores Composed of Phenothiazine or Carbazole Donor and 2-Cyanomethylene-3-cyano-4,5,5- trimethyl-2,5-dihydrofuran Acceptor

    International Nuclear Information System (INIS)

    Cho, Min Ju; Kim, Ja Youn; Kim, Jae Hong; Lee, Seung Hwan; Choi, Dong Hoon; Dalton, Larry R.

    2005-01-01

    We prepared the new nonlinear optical chromophores that show fairly high microscopic nonlinearity through intramolecular charge transfer. Phenothiazine and carbazole units played an important role to contribute high electron donability and connect the resonance pathway via conjugative effect in the cyclized ring beside the aromatic ring. Theoretical calculation, electrochemical analysis, and absorption spectroscopic study gave us useful information about the energy states and microscopic nonlinearities of two serial chromophores. We compared the microscopic nonlinearities of four chromophores with the conjugation length and electron donability in the push-pull type NLO chromophores. The effect of gradient donability and lengthening the conjugation were investigated on the electronic state and microscopic nonlinearity

  9. Biomolecular condensates: organizers of cellular biochemistry.

    Science.gov (United States)

    Banani, Salman F; Lee, Hyun O; Hyman, Anthony A; Rosen, Michael K

    2017-05-01

    Biomolecular condensates are micron-scale compartments in eukaryotic cells that lack surrounding membranes but function to concentrate proteins and nucleic acids. These condensates are involved in diverse processes, including RNA metabolism, ribosome biogenesis, the DNA damage response and signal transduction. Recent studies have shown that liquid-liquid phase separation driven by multivalent macromolecular interactions is an important organizing principle for biomolecular condensates. With this physical framework, it is now possible to explain how the assembly, composition, physical properties and biochemical and cellular functions of these important structures are regulated.

  10. Molecular Selectivity of Brown Carbon Chromophores

    Energy Technology Data Exchange (ETDEWEB)

    Laskin, Julia; Laskin, Alexander; Nizkorodov, Sergey; Roach, Patrick J.; Eckert, Peter A.; Gilles, Mary K.; Wang, Bingbing; Lee, Hyun Ji; Hu, Qichi

    2014-10-21

    Complementary methods of high-resolution mass spectrometry and micro-spectroscopy were utilized for molecular analysis of secondary organic aerosol (SOA) generated from ozonolysis of two structural monoterpene isomers: D-limonene (LSOA) and a-pinene (PSOA). Laboratory simulated aging of LSOA and PSOA, through conversion of carbonyls into imines mediated by NH3 vapors in humid air, resulted in selective browning of the LSOA sample, while the PSOA sample remained white. Comparative analysis of the reaction products in the aged LSOA and PSOA samples provided insights into chemistry relevant to formation of brown carbon chromophores. A significant fraction of carbonyl-imine conversion products with identical molecular formulas were detected in both samples. This reflects the high level of similarity in the molecular composition of these two closely related SOA materials. Several highly conjugated products were detected exclusively in the brown LSOA sample and were identified as potential chromophores responsible for the observed color change. The majority of the unique products in the aged LSOA sample with the highest number of double bonds contain two nitrogen atoms. We conclude that chromophores characteristic of the carbonyl- imine chemistry in LSOA are highly conjugated oligomers of secondary imines (Schiff bases) present at relatively low concentrations. Formation of this type of conjugated compounds in PSOA is hindered by the structural rigidity of the a-pinene oxidation products. Our results suggest that the overall light-absorbing properties of SOA may be determined by trace amounts of strong brown carbon chromophores.

  11. Biomolecular engineering for nanobio/bionanotechnology

    Science.gov (United States)

    Nagamune, Teruyuki

    2017-04-01

    Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.

  12. The role of many-body effects in describing low-lying excited states of pi-conjugated chromophores: high-level equation-of-motion coupled-cluster studies of fused porphyrin systems

    Energy Technology Data Exchange (ETDEWEB)

    Kowalski, Karol [Pacific Northwest National Laboratory (PNNL); Olson, Ryan M [Cray, Inc.; Krishnamoorthy, Sriram [Pacific Northwest National Laboratory (PNNL); Tipparaju, Vinod [ORNL; Apra, Edoardo [ORNL

    2011-01-01

    The unusual photophysical properties of the {pi}-conjugated chromophores make them potential building blocks of various molecular devices. In particular, significant narrowing of the HOMO-LUMO gaps can be observed as an effect of functionalization chromophores with polycyclic aromatic hydrocarbons (PAHs). In this paper we present equation-of-motion coupled cluster (EOMCC) calculations for vertical excitation energies of several functionalized forms of porphyrins. The results for free-base porphyrin (FBP) clearly demonstrate significant differences between functionalization of FBP with one- (anthracene) and two-dimensional (coronene) structures. We also compare the EOMCC results with the experimentally available results for anthracene fused zinc-porphyrin. The impact of various types of correlation effects is illustrated on several benchmark models, where the comparison with the experiment is possible. In particular, we demonstrate that for all excited states considered in this paper, all of them being dominated by single excitations, the inclusion of triply excited configurations is crucial for attaining qualitative agreement with experiment. We also demonstrate the parallel performance of the most computationally intensive part of the completely renormalized EOMCCSD(T) approach (CR-EOMCCSD(T)) across 120000 cores.

  13. Biomolecular ions in superfluid helium nanodroplets

    International Nuclear Information System (INIS)

    Gonzalez Florez, Ana Isabel

    2016-01-01

    The function of a biological molecule is closely related to its structure. As a result, understanding and predicting biomolecular structure has become the focus of an extensive field of research. However, the investigation of molecular structure can be hampered by two main difficulties: the inherent complications that may arise from studying biological molecules in their native environment, and the potential congestion of the experimental results as a consequence of the large number of degrees of freedom present in these molecules. In this work, a new experimental setup has been developed and established in order to overcome the afore mentioned limitations combining structure-sensitive gas-phase methods with superfluid helium droplets. First, biological molecules are ionised and brought into the gas phase, often referred to as a clean-room environment, where the species of interest are isolated from their surroundings and, thus, intermolecular interactions are absent. The mass-to-charge selected biomolecules are then embedded inside clusters of superfluid helium with an equilibrium temperature of ∝0.37 K. As a result, the internal energy of the molecules is lowered, thereby reducing the number of populated quantum states. Finally, the local hydrogen bonding patterns of the molecules are investigated by probing specific vibrational modes using the Fritz Haber Institute's free electron laser as a source of infrared radiation. Although the structure of a wide variety of molecules has been studied making use of the sub-Kelvin environment provided by superfluid helium droplets, the suitability of this method for the investigation of biological molecular ions was still unclear. However, the experimental results presented in this thesis demonstrate the applicability of this experimental approach in order to study the structure of intact, large biomolecular ions and the first vibrational spectrum of the protonated pentapeptide leu-enkephalin embedded in helium

  14. Biomolecular ions in superfluid helium nanodroplets

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez Florez, Ana Isabel

    2016-07-01

    The function of a biological molecule is closely related to its structure. As a result, understanding and predicting biomolecular structure has become the focus of an extensive field of research. However, the investigation of molecular structure can be hampered by two main difficulties: the inherent complications that may arise from studying biological molecules in their native environment, and the potential congestion of the experimental results as a consequence of the large number of degrees of freedom present in these molecules. In this work, a new experimental setup has been developed and established in order to overcome the afore mentioned limitations combining structure-sensitive gas-phase methods with superfluid helium droplets. First, biological molecules are ionised and brought into the gas phase, often referred to as a clean-room environment, where the species of interest are isolated from their surroundings and, thus, intermolecular interactions are absent. The mass-to-charge selected biomolecules are then embedded inside clusters of superfluid helium with an equilibrium temperature of ∝0.37 K. As a result, the internal energy of the molecules is lowered, thereby reducing the number of populated quantum states. Finally, the local hydrogen bonding patterns of the molecules are investigated by probing specific vibrational modes using the Fritz Haber Institute's free electron laser as a source of infrared radiation. Although the structure of a wide variety of molecules has been studied making use of the sub-Kelvin environment provided by superfluid helium droplets, the suitability of this method for the investigation of biological molecular ions was still unclear. However, the experimental results presented in this thesis demonstrate the applicability of this experimental approach in order to study the structure of intact, large biomolecular ions and the first vibrational spectrum of the protonated pentapeptide leu-enkephalin embedded in helium

  15. Converting biomolecular modelling data based on an XML representation.

    Science.gov (United States)

    Sun, Yudong; McKeever, Steve

    2008-08-25

    Biomolecular modelling has provided computational simulation based methods for investigating biological processes from quantum chemical to cellular levels. Modelling such microscopic processes requires atomic description of a biological system and conducts in fine timesteps. Consequently the simulations are extremely computationally demanding. To tackle this limitation, different biomolecular models have to be integrated in order to achieve high-performance simulations. The integration of diverse biomolecular models needs to convert molecular data between different data representations of different models. This data conversion is often non-trivial, requires extensive human input and is inevitably error prone. In this paper we present an automated data conversion method for biomolecular simulations between molecular dynamics and quantum mechanics/molecular mechanics models. Our approach is developed around an XML data representation called BioSimML (Biomolecular Simulation Markup Language). BioSimML provides a domain specific data representation for biomolecular modelling which can effciently support data interoperability between different biomolecular simulation models and data formats.

  16. The role of the [CpM(CO)2](-) chromophore in the optical properties of the [Cp2ThMCp(CO)2](+) complexes, where M = Fe, Ru and Os. A theoretical view.

    Science.gov (United States)

    Cantero-López, Plinio; Le Bras, Laura; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro

    2015-12-14

    The chemical bond between actinide and the transition metal unsupported by bridging ligands is not well characterized. In this paper we study the electronic properties, bonding nature and optical spectra in a family of [Cp2ThMCp(CO)2](+) complexes where M = Fe, Ru, Os, based on the relativistic two component density functional theory calculations. The Morokuma-Ziegler energy decomposition analysis shows an important ionic contribution in the Th-M interaction with around 25% of covalent character. Clearly, charge transfer occurs on Th-M bond formation, however the orbital term most likely represents a strong charge rearrangement in the fragments due to the interaction. Finally the spin-orbit-ZORA calculation shows the possible NIR emission induced by the [FeCp(CO)2](-) chromophore accomplishing the antenna effect that justifies the sensitization of the actinide complexes.

  17. Selected topics in solution-phase biomolecular NMR spectroscopy

    Science.gov (United States)

    Kay, Lewis E.; Frydman, Lucio

    2017-05-01

    Solution bio-NMR spectroscopy continues to enjoy a preeminent role as an important tool in elucidating the structure and dynamics of a range of important biomolecules and in relating these to function. Equally impressive is how NMR continues to 'reinvent' itself through the efforts of many brilliant practitioners who ask increasingly demanding and increasingly biologically relevant questions. The ability to manipulate spin Hamiltonians - almost at will - to dissect the information of interest contributes to the success of the endeavor and ensures that the NMR technology will be well poised to contribute to as yet unknown frontiers in the future. As a tribute to the versatility of solution NMR in biomolecular studies and to the continued rapid advances in the field we present a Virtual Special Issue (VSI) that includes over 40 articles on various aspects of solution-state biomolecular NMR that have been published in the Journal of Magnetic Resonance in the past 7 years. These, in total, help celebrate the achievements of this vibrant field.

  18. An Overview of Biomolecular Event Extraction from Scientific Documents.

    Science.gov (United States)

    Vanegas, Jorge A; Matos, Sérgio; González, Fabio; Oliveira, José L

    2015-01-01

    This paper presents a review of state-of-the-art approaches to automatic extraction of biomolecular events from scientific texts. Events involving biomolecules such as genes, transcription factors, or enzymes, for example, have a central role in biological processes and functions and provide valuable information for describing physiological and pathogenesis mechanisms. Event extraction from biomedical literature has a broad range of applications, including support for information retrieval, knowledge summarization, and information extraction and discovery. However, automatic event extraction is a challenging task due to the ambiguity and diversity of natural language and higher-level linguistic phenomena, such as speculations and negations, which occur in biological texts and can lead to misunderstanding or incorrect interpretation. Many strategies have been proposed in the last decade, originating from different research areas such as natural language processing, machine learning, and statistics. This review summarizes the most representative approaches in biomolecular event extraction and presents an analysis of the current state of the art and of commonly used methods, features, and tools. Finally, current research trends and future perspectives are also discussed.

  19. An Overview of Biomolecular Event Extraction from Scientific Documents

    Directory of Open Access Journals (Sweden)

    Jorge A. Vanegas

    2015-01-01

    Full Text Available This paper presents a review of state-of-the-art approaches to automatic extraction of biomolecular events from scientific texts. Events involving biomolecules such as genes, transcription factors, or enzymes, for example, have a central role in biological processes and functions and provide valuable information for describing physiological and pathogenesis mechanisms. Event extraction from biomedical literature has a broad range of applications, including support for information retrieval, knowledge summarization, and information extraction and discovery. However, automatic event extraction is a challenging task due to the ambiguity and diversity of natural language and higher-level linguistic phenomena, such as speculations and negations, which occur in biological texts and can lead to misunderstanding or incorrect interpretation. Many strategies have been proposed in the last decade, originating from different research areas such as natural language processing, machine learning, and statistics. This review summarizes the most representative approaches in biomolecular event extraction and presents an analysis of the current state of the art and of commonly used methods, features, and tools. Finally, current research trends and future perspectives are also discussed.

  20. Application of Nanodiamonds in Biomolecular Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Ping Cheng

    2010-03-01

    Full Text Available The combination of nanodiamond (ND with biomolecular mass spectrometry (MS makes rapid, sensitive detection of biopolymers from complex biosamples feasible. Due to its chemical inertness, optical transparency and biocompatibility, the advantage of NDs in MS study is unique. Furthermore, functionalization on the surfaces of NDs expands their application in the fields of proteomics and genomics for specific requirements greatly. This review presents methods of MS analysis based on solid phase extraction and elution on NDs and different application examples including peptide, protein, DNA, glycan and others. Owing to the quick development of nanotechnology, surface chemistry, new MS methods and the intense interest in proteomics and genomics, a huge increase of their applications in biomolecular MS analysis in the near future can be predicted.

  1. Membrane-based biomolecular smart materials

    International Nuclear Information System (INIS)

    Sarles, Stephen A; Leo, Donald J

    2011-01-01

    Membrane-based biomolecular materials are a new class of smart material that feature networks of artificial lipid bilayers contained within durable synthetic substrates. Bilayers contained within this modular material platform provide an environment that can be tailored to host an enormous diversity of functional biomolecules, where the functionality of the global material system depends on the type(s) and organization(s) of the biomolecules that are chosen. In this paper, we review a series of biomolecular material platforms developed recently within the Leo Group at Virginia Tech and we discuss several novel coupling mechanisms provided by these hybrid material systems. The platforms developed demonstrate that the functions of biomolecules and the properties of synthetic materials can be combined to operate in concert, and the examples provided demonstrate how the formation and properties of a lipid bilayer can respond to a variety of stimuli including mechanical forces and electric fields

  2. Aligning Biomolecular Networks Using Modular Graph Kernels

    Science.gov (United States)

    Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

    Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

  3. Biomolecular electrostatics and solvation: a computational perspective.

    Science.gov (United States)

    Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A

    2012-11-01

    An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

  4. NMRbox: A Resource for Biomolecular NMR Computation.

    Science.gov (United States)

    Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

    2017-04-25

    Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

  5. A statistical nanomechanism of biomolecular patterning actuated by surface potential

    Science.gov (United States)

    Lin, Chih-Ting; Lin, Chih-Hao

    2011-02-01

    Biomolecular patterning on a nanoscale/microscale on chip surfaces is one of the most important techniques used in vitro biochip technologies. Here, we report upon a stochastic mechanics model we have developed for biomolecular patterning controlled by surface potential. The probabilistic biomolecular surface adsorption behavior can be modeled by considering the potential difference between the binding and nonbinding states. To verify our model, we experimentally implemented a method of electroactivated biomolecular patterning technology and the resulting fluorescence intensity matched the prediction of the developed model quite well. Based on this result, we also experimentally demonstrated the creation of a bovine serum albumin pattern with a width of 200 nm in 5 min operations. This submicron noncovalent-binding biomolecular pattern can be maintained for hours after removing the applied electrical voltage. These stochastic understandings and experimental results not only prove the feasibility of submicron biomolecular patterns on chips but also pave the way for nanoscale interfacial-bioelectrical engineering.

  6. Molecular recognition of chromophore molecules to amine terminated surfaces

    International Nuclear Information System (INIS)

    Flores-Perez, Rosangelly; Ivanisevic, Albena

    2007-01-01

    We report the design and characterization of quartz surfaces that can bind to three retinal based chromophores. The amine terminated surfaces were engineered in order to mimic the environment of the opsin protein that accommodates binding of chromophore molecules in the human eye. Each surface coupling step was characterized by water contact angle measurements, ellipsometry, atomic force microscopy, X-ray photoelectron spectroscopy, and transmission infrared spectroscopy. The spectroscopic techniques confirmed that the three chromophore molecules can bind to the surface using a Schiff base mode. Our data suggests that the availability of the amine groups on the surface is critical in the accommodation of the binding of different chromophores

  7. Chiral interaction and biomolecular evolution

    International Nuclear Information System (INIS)

    Gilat, G.

    1992-01-01

    Recent developments in the concept of chiral interaction open now new options and dynamical possibilities for biomolecules which have so far been overlooked. A few of these possibilities are mentioned, such as the control mechanism of enzymatic activity and the role played by non-ergodicity in evolutionary processes. It is shown that chiral interaction, being a surface phenomenon, does not obey Barron's symmetry constraints, which are suitable for force fields present in bulk interactions. In particular, the situation at the ocean-air surface in the prebiotic era is described, as well as the possible role played by chiral interaction in conjunction with the terrestrial magnetic field normal to the ocean surface, which could have lead to a process of deracernization at the ocean-air interface. (author)

  8. Role of Many-Body Effects in Describing Low-Lying Excited States of pi-Conjugated Chromophores: High-Level Equation-of-Motion Coupled-Cluster Studies of Fused Porphyrin Systems

    Energy Technology Data Exchange (ETDEWEB)

    Kowalski, Karol; Olson, Ryan M.; Krishnamoorthy, Sriram; Tipparaju, Vinod; Apra, Edoardo

    2011-07-12

    The unusual photophysical properties of the pi-conjugated chrompohores makes them potential building blocks of various molecular devices. In particular, significant narrowing of the HOMO-LUMO gaps can be observed as an effect of functionalization chromophores with polycyclic aromatic hydrocabrons (PAHs). In this paper we present equation-of-motion coupled cluster calculations for vertical excitation energies of several functionalized forms of porphyrins. The results of free-base porphyrin (FBP) clearly demonstrate significant differences between functionalization of FBP with one- (anthracene) and two-dimensional (coronene) structures. We also compare the EOMCC results with the experimentally available results for the anthracene fused zinc porphyrin. The impact of various-type correlation effects is illustrated on several benchmark models where the comparison with the experiment is possible. In particular, we demonstrate that for all excited states considered in this paper, all of them being dominated by single excitations, the inclusion of triply excited configurations is crucial for attaining qualitative agreement with the experiment. We also demonstrate the parallel performance of the most computationally intensive part of the completely renormalized EOMCCSD(T) approach (CR-EOMCCSD(T)) across 120,000 cores.

  9. Computational Methods for Biomolecular Electrostatics

    Science.gov (United States)

    Dong, Feng; Olsen, Brett; Baker, Nathan A.

    2008-01-01

    An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der Waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems with a particular focus on how computational tools can be used to investigate these types of interactions. PMID:17964951

  10. Design rules for biomolecular adhesion: lessons from force measurements.

    Science.gov (United States)

    Leckband, Deborah

    2010-01-01

    Cell adhesion to matrix, other cells, or pathogens plays a pivotal role in many processes in biomolecular engineering. Early macroscopic methods of quantifying adhesion led to the development of quantitative models of cell adhesion and migration. The more recent use of sensitive probes to quantify the forces that alter or manipulate adhesion proteins has revealed much greater functional diversity than was apparent from population average measurements of cell adhesion. This review highlights theoretical and experimental methods that identified force-dependent molecular properties that are central to the biological activity of adhesion proteins. Experimental and theoretical methods emphasized in this review include the surface force apparatus, atomic force microscopy, and vesicle-based probes. Specific examples given illustrate how these tools have revealed unique properties of adhesion proteins and their structural origins.

  11. Single oligomer spectra probe chromophore nanoenvironments of tetrameric fluorescent proteins

    NARCIS (Netherlands)

    Blum, Christian; Meixner, Alfred J; Subramaniam, Vinod

    2006-01-01

    When analyzing the emission of a large number of individual chromophores embedded in a matrix, the spread of the observed parameters is a characteristic property for the particular chromophore-matrix system. To quantitatively assess the influence of the matrix on the single molecule emission

  12. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  13. Micro and Nanotechnologies Enhanced Biomolecular Sensing

    Directory of Open Access Journals (Sweden)

    Tza-Huei Wang

    2013-07-01

    Full Text Available This editorial summarizes some of the recent advances of micro and nanotechnology-based tools and devices for biomolecular detection. These include the incorporation of nanomaterials into a sensor surface or directly interfacing with molecular probes to enhance target detection via more rapid and sensitive responses, and the use of self-assembled organic/inorganic nanocomposites that inhibit exceptional spectroscopic properties to enable facile homogenous assays with efficient binding kinetics. Discussions also include some insight into microfluidic principles behind the development of an integrated sample preparation and biosensor platform toward a miniaturized and fully functional system for point of care applications.

  14. Benzimidazole acrylonitriles as multifunctional push-pull chromophores: Spectral characterisation, protonation equilibria and nanoaggregation in aqueous solutions

    Science.gov (United States)

    Horak, Ema; Vianello, Robert; Hranjec, Marijana; Krištafor, Svjetlana; Zamola, Grace Karminski; Steinberg, Ivana Murković

    2017-05-01

    Heterocyclic donor-π-acceptor molecular systems based on an N,N-dimethylamino phenylacrylonitrile benzimidazole skeleton have been characterised and are proposed for potential use in sensing applications. The benzimidazole moiety introduces a broad spectrum of useful multifunctional properties to the system including electron accepting ability, pH sensitivity and compatibility with biomolecules. The photophysical characterisation of the prototropic forms of these chromophores has been carried out in both solution and on immobilisation in polymer films. The experimental results are further supported by computational determination of pKa values. It is noticed that compound 3 forms nanoaggregates in aqueous solutions with aggregation-induced emission (AIE) at 600 nm. All the systems demonstrate spectral pH sensitivity in acidic media which shifts towards near-neutral values upon immobilisation in polymer films or upon aggregation in an aqueous environment (compound 3). The structure-property relationships of these functional chromophores, involving their spectral characteristics, acid-base equilibria, pKa values and aggregation effects have been determined. Potential applications of the molecules as pH and biomolecular sensors are proposed based on their pH sensitivity and AIE properties.

  15. NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers.

    Science.gov (United States)

    Sekhar, Ashok; Kay, Lewis E

    2013-08-06

    The importance of dynamics to biomolecular function is becoming increasingly clear. A description of the structure-function relationship must, therefore, include the role of motion, requiring a shift in paradigm from focus on a single static 3D picture to one where a given biomolecule is considered in terms of an ensemble of interconverting conformers, each with potentially diverse activities. In this Perspective, we describe how recent developments in solution NMR spectroscopy facilitate atomic resolution studies of sparsely populated, transiently formed biomolecular conformations that exchange with the native state. Examples of how this methodology is applied to protein folding and misfolding, ligand binding, and molecular recognition are provided as a means of illustrating both the power of the new techniques and the significant roles that conformationally excited protein states play in biology.

  16. An optics-based variable-temperature assay system for characterizing thermodynamics of biomolecular reactions on solid support

    Energy Technology Data Exchange (ETDEWEB)

    Fei, Yiyan; Landry, James P.; Zhu, X. D., E-mail: xdzhu@physics.ucdavis.edu [Department of Physics, University of California, One Shields Avenue, Davis, California 95616 (United States); Li, Yanhong; Yu, Hai; Lau, Kam; Huang, Shengshu; Chokhawala, Harshal A.; Chen, Xi [Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616 (United States)

    2013-11-15

    A biological state is equilibrium of multiple concurrent biomolecular reactions. The relative importance of these reactions depends on physiological temperature typically between 10 °C and 50 °C. Experimentally the temperature dependence of binding reaction constants reveals thermodynamics and thus details of these biomolecular processes. We developed a variable-temperature opto-fluidic system for real-time measurement of multiple (400–10 000) biomolecular binding reactions on solid supports from 10 °C to 60 °C within ±0.1 °C. We illustrate the performance of this system with investigation of binding reactions of plant lectins (carbohydrate-binding proteins) with 24 synthetic glycans (i.e., carbohydrates). We found that the lectin-glycan reactions in general can be enthalpy-driven, entropy-driven, or both, and water molecules play critical roles in the thermodynamics of these reactions.

  17. The global distribution and dynamics of chromophoric dissolved organic matter.

    Science.gov (United States)

    Nelson, Norman B; Siegel, David A

    2013-01-01

    Chromophoric dissolved organic matter (CDOM) is a ubiquitous component of the open ocean dissolved matter pool, and is important owing to its influence on the optical properties of the water column, its role in photochemistry and photobiology, and its utility as a tracer of deep ocean biogeochemical processes and circulation. In this review, we discuss the global distribution and dynamics of CDOM in the ocean, concentrating on developments in the past 10 years and restricting our discussion to open ocean and deep ocean (below the main thermocline) environments. CDOM has been demonstrated to exert primary control on ocean color by its absorption of light energy, which matches or exceeds that of phytoplankton pigments in most cases. This has important implications for assessing the ocean biosphere via ocean color-based remote sensing and the evaluation of ocean photochemical and photobiological processes. The general distribution of CDOM in the global ocean is controlled by a balance between production (primarily microbial remineralization of organic matter) and photolysis, with vertical ventilation circulation playing an important role in transporting CDOM to and from intermediate water masses. Significant decadal-scale fluctuations in the abundance of global surface ocean CDOM have been observed using remote sensing, indicating a potentially important role for CDOM in ocean-climate connections through its impact on photochemistry and photobiology.

  18. Converting Biomolecular Modelling Data Based on an XML Representation

    Directory of Open Access Journals (Sweden)

    Sun Yudong

    2008-06-01

    Full Text Available Biomolecular modelling has provided computational simulation based methods for investigating biological processes from quantum chemical to cellular levels. Modelling such microscopic processes requires atomic description of a biological system and conducts in fine timesteps. Consequently the simulations are extremely computationally demanding. To tackle this limitation, different biomolecular models have to be integrated in order to achieve high-performance simulations. The integration of diverse biomolecular models needs to convert molecular data between different data representations of different models. This data conversion is often non-trivial, requires extensive human input and is inevitably error prone. In this paper we present an automated data conversion method for biomolecular simulations between molecular dynamics and quantum mechanics/molecular mechanics models. Our approach is developed around an XML data representation called BioSimML (Biomolecular Simulation Markup Language. BioSimML provides a domain specific data representation for biomolecular modelling which can effciently support data interoperability between different biomolecular simulation models and data formats.

  19. Biomolecular Markers in Cancer of the Tongue

    Directory of Open Access Journals (Sweden)

    Daris Ferrari

    2009-01-01

    Full Text Available The incidence of tongue cancer is increasing worldwide, and its aggressiveness remains high regardless of treatment. Genetic changes and the expression of abnormal proteins have been frequently reported in the case of head and neck cancers, but the little information that has been published concerning tongue tumours is often contradictory. This review will concentrate on the immunohistochemical expression of biomolecular markers and their relationships with clinical behaviour and prognosis. Most of these proteins are associated with nodal stage, tumour progression and metastases, but there is still controversy concerning their impact on disease-free and overall survival, and treatment response. More extensive clinical studies are needed to identify the patterns of molecular alterations and the most reliable predictors in order to develop tailored anti-tumour strategies based on the targeting of hypoxia markers, vascular and lymphangiogenic factors, epidermal growth factor receptors, intracytoplasmatic signalling and apoptosis.

  20. Biomolecular simulations on petascale: promises and challenges

    International Nuclear Information System (INIS)

    Agarwal, Pratul K; Alam, Sadaf R

    2006-01-01

    Proteins work as highly efficient machines at the molecular level and are responsible for a variety of processes in all living cells. There is wide interest in understanding these machines for implications in biochemical/biotechnology industries as well as in health related fields. Over the last century, investigations of proteins based on a variety of experimental techniques have provided a wealth of information. More recently, theoretical and computational modeling using large scale simulations is providing novel insights into the functioning of these machines. The next generation supercomputers with petascale computing power, hold great promises as well as challenges for the biomolecular simulation scientists. We briefly discuss the progress being made in this area

  1. Micro- and nanodevices integrated with biomolecular probes.

    Science.gov (United States)

    Alapan, Yunus; Icoz, Kutay; Gurkan, Umut A

    2015-12-01

    Understanding how biomolecules, proteins and cells interact with their surroundings and other biological entities has become the fundamental design criterion for most biomedical micro- and nanodevices. Advances in biology, medicine, and nanofabrication technologies complement each other and allow us to engineer new tools based on biomolecules utilized as probes. Engineered micro/nanosystems and biomolecules in nature have remarkably robust compatibility in terms of function, size, and physical properties. This article presents the state of the art in micro- and nanoscale devices designed and fabricated with biomolecular probes as their vital constituents. General design and fabrication concepts are presented and three major platform technologies are highlighted: microcantilevers, micro/nanopillars, and microfluidics. Overview of each technology, typical fabrication details, and application areas are presented by emphasizing significant achievements, current challenges, and future opportunities. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

    Science.gov (United States)

    Tanaka, Shigenori; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Fukuzawa, Kaori

    2014-06-14

    Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

  3. Highly fluorescent benzofuran derivatives of the GFP chromophore

    DEFF Research Database (Denmark)

    Christensen, Mikkel Andreas; Jennum, Karsten Stein; Abrahamsen, Peter Bæch

    2012-01-01

    Intramolecular cyclization reactions of Green Fluorescent Protein chromophores (GFPc) containing an arylethynyl ortho-substituent at the phenol ring provide new aryl-substituted benzofuran derivatives of the GFPc. Some of these heteroaromatic compounds exhibit significantly enhanced fluorescence...

  4. Dual Mechanism Nonlinear Response of Selected Metal Organic Chromophores

    National Research Council Canada - National Science Library

    Peak, John D

    2007-01-01

    13 The goal for the research described herein is the development of a series of transition metal based metal organic chromophores that display both two-photon and excited state absorption (TPA/ESA) character...

  5. DNA algorithms of implementing biomolecular databases on a biological computer.

    Science.gov (United States)

    Chang, Weng-Long; Vasilakos, Athanasios V

    2015-01-01

    In this paper, DNA algorithms are proposed to perform eight operations of relational algebra (calculus), which include Cartesian product, union, set difference, selection, projection, intersection, join, and division, on biomolecular relational databases.

  6. Modeling, Analysis, Simulation, and Synthesis of Biomolecular Networks

    National Research Council Canada - National Science Library

    Ruben, Harvey; Kumar, Vijay; Sokolsky, Oleg

    2006-01-01

    ...) a first example of reachability analysis applied to a biomolecular system (lactose induction), 4) a model of tetracycline resistance that discriminates between two possible mechanisms for tetracycline diffusion through the cell membrane, and 5...

  7. Biomolecular surface construction by PDE transform.

    Science.gov (United States)

    Zheng, Qiong; Yang, Siyang; Wei, Guo-Wei

    2012-03-01

    This work proposes a new framework for the surface generation based on the partial differential equation (PDE) transform. The PDE transform has recently been introduced as a general approach for the mode decomposition of images, signals, and data. It relies on the use of arbitrarily high-order PDEs to achieve the time-frequency localization, control the spectral distribution, and regulate the spatial resolution. The present work provides a new variational derivation of high-order PDE transforms. The fast Fourier transform is utilized to accomplish the PDE transform so as to avoid stringent stability constraints in solving high-order PDEs. As a consequence, the time integration of high-order PDEs can be done efficiently with the fast Fourier transform. The present approach is validated with a variety of test examples in two-dimensional and three-dimensional settings. We explore the impact of the PDE transform parameters, such as the PDE order and propagation time, on the quality of resulting surfaces. Additionally, we utilize a set of 10 proteins to compare the computational efficiency of the present surface generation method and a standard approach in Cartesian meshes. Moreover, we analyze the present method by examining some benchmark indicators of biomolecular surface, that is, surface area, surface-enclosed volume, solvation free energy, and surface electrostatic potential. A test set of 13 protein molecules is used in the present investigation. The electrostatic analysis is carried out via the Poisson-Boltzmann equation model. To further demonstrate the utility of the present PDE transform-based surface method, we solve the Poisson-Nernst-Planck equations with a PDE transform surface of a protein. Second-order convergence is observed for the electrostatic potential and concentrations. Finally, to test the capability and efficiency of the present PDE transform-based surface generation method, we apply it to the construction of an excessively large biomolecule, a

  8. Multiscale Persistent Functions for Biomolecular Structure Characterization

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Kelin [Nanyang Technological University (Singapore). Division of Mathematical Sciences, School of Physical, Mathematical Sciences and School of Biological Sciences; Li, Zhiming [Central China Normal University, Wuhan (China). Key Laboratory of Quark and Lepton Physics (MOE) and Institute of Particle Physics; Mu, Lin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division

    2017-11-02

    Here in this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions (MRFs) with persistent homology analysis, so as to construct a series of multiscale persistent functions, particularly multiscale persistent entropies, for structure characterization. To clarify the fundamental idea of our method, the multiscale persistent entropy (MPE) model is discussed in great detail. Mathematically, unlike the previous persistent entropy (Chintakunta et al. in Pattern Recognit 48(2):391–401, 2015; Merelli et al. in Entropy 17(10):6872–6892, 2015; Rucco et al. in: Proceedings of ECCS 2014, Springer, pp 117–128, 2016), a special resolution parameter is incorporated into our model. Various scales can be achieved by tuning its value. Physically, our MPE can be used in conformational entropy evaluation. More specifically, it is found that our method incorporates in it a natural classification scheme. This is achieved through a density filtration of an MRF built from angular distributions. To further validate our model, a systematical comparison with the traditional entropy evaluation model is done. Additionally, it is found that our model is able to preserve the intrinsic topological features of biomolecular data much better than traditional approaches, particularly for resolutions in the intermediate range. Moreover, by comparing with traditional entropies from various grid sizes, bond angle-based methods and a persistent homology-based support vector machine method (Cang et al. in Mol Based Math Biol 3:140–162, 2015), we find that our MPE method gives the best results in terms of average true positive rate in a classic protein structure classification test. More interestingly, all-alpha and all-beta protein classes can be clearly separated from each other with zero error only in our model. Finally, a special protein structure index (PSI) is proposed, for the first

  9. Chromophoric dissolved organic matter export from U.S. rivers

    Science.gov (United States)

    Spencer, Robert G. M.; Aiken, George R.; Dornblaser, Mark M.; Butler, Kenna D.; Holmes, R. Max; Fiske, Greg; Mann, Paul J.; Stubbins, Aron

    2013-04-01

    Chromophoric dissolved organic matter (CDOM) fluxes and yields from 15 major U.S. rivers draining an assortment of terrestrial biomes are presented. A robust relationship between CDOM and dissolved organic carbon (DOC) loads is established (e.g., a350 versus DOC; r2 = 0.96, p CDOM yields are also correlated to watershed percent wetland (e.g. a350; r2 = 0.81, p CDOM export from ungauged watersheds. A large variation in CDOM yields was found across the rivers. The two rivers in the north-eastern U.S. (Androscoggin and Penobscot), the Edisto draining into the South Atlantic Bight, and some rivers draining into the Gulf of Mexico (Atchafalaya and Mobile) exhibit the highest CDOM yields, linked to extensive wetlands in these watersheds. If the Edisto CDOM yield is representative of other rivers draining into the South Atlantic Bight, this would result in a CDOM load equivalent to that of the Mississippi from a region of approximately 10% of the Mississippi watershed, indicating the importance of certain regions with respect to the role of terrigenous CDOM in ocean color budgets.

  10. Chromophoric dissolved organic matter export from U.S. rivers

    Science.gov (United States)

    Spencer, Robert G. M.; Aiken, George R.; Dornblaser, Mark M.; Butler, Kenna D.; Holmes, R. Max; Fiske, Greg; Mann, Paul J.; Stubbins, Aron

    2013-01-01

    Chromophoric dissolved organic matter (CDOM) fluxes and yields from 15 major U.S. rivers draining an assortment of terrestrial biomes are presented. A robust relationship between CDOM and dissolved organic carbon (DOC) loads is established (e.g., a350 versus DOC; r2 = 0.96, p CDOM yields are also correlated to watershed percent wetland (e.g. a350; r2 = 0.81, p CDOM export from ungauged watersheds. A large variation in CDOM yields was found across the rivers. The two rivers in the north-eastern U.S. (Androscoggin and Penobscot), the Edisto draining into the South Atlantic Bight, and some rivers draining into the Gulf of Mexico (Atchafalaya and Mobile) exhibit the highest CDOM yields, linked to extensive wetlands in these watersheds. If the Edisto CDOM yield is representative of other rivers draining into the South Atlantic Bight, this would result in a CDOM load equivalent to that of the Mississippi from a region of approximately 10% of the Mississippi watershed, indicating the importance of certain regions with respect to the role of terrigenous CDOM in ocean color budgets.

  11. Development of zwitterionic chromophores for electro-optic applications

    Science.gov (United States)

    Xiong, Ying

    In order to unlock the full potential of the zwitterionic NLO chromophores for electro-optic (EO) applications, a new series of PeQDM chromophores with large first hyperpolarizabilities (beta0 ˜ 600 x 10-30 esu) have been designed and synthesized. A large EO coefficient (r33) of 110 pm/V at 1550 nm has been realized with a 5 wt% (corresponding to 3.8 wt% core content) chromophore doped polymer. The EO study of guest-host polymers reveals that dipolar dye aggregation in a less polar medium is responsible for a low chromophore loading and low EO activity. Modification of NLO chromophore by attaching large dendrons can effectively increase the chromophore loading in a host and improve the poling efficiency. Crosslinkable NLO polymers have also been prepared to improve the temporal stability of the poled noncentrosymmetric order. The following are some important highlights from this thesis work. (1) A series of thermally stable zwitterionic chromophores (PeQDM) with large first hyperpolarizabilities (beta up to -1797 x 10-30 esu) are synthesized in good yields (˜ 50%). The charge-separated ground state is evident by a negative solvatochromism. X-ray crystallographic data further confirms the zwitterionic nature and demonstrates a face-to-face anti-parallel H-aggregation of two monomers due to strong electrostatic interactions between the dipoles. (2) PeQDM chromophores are also NIR fluorescent (lambdaPL ˜ 840-870 nm in solution) and labile to acid, making them potential candidates for NIR pH sensor applications. (3) The hydroxyl-containing PeQDM chromophores are modified with ES-dendron, which exhibit good solubility in solvents and polymers. Self-forming films can be prepared by direct casting or spin-coating of two dendrons modified chromophores (ES-PeQDM-2 and ES-PeQDM-3), in which the chromophore core contents reach 14.9 and 16.9 wt%, respectively. Compared to ES-PeQDM-2 with two dendrons only at the donor part (r33 = 0 pm/V), ES-PeQDM-3 with the bulky ES

  12. Integrated Spintronic Platforms for Biomolecular Recognition Detection

    Science.gov (United States)

    Martins, V. C.; Cardoso, F. A.; Loureiro, J.; Mercier, M.; Germano, J.; Cardoso, S.; Ferreira, R.; Fonseca, L. P.; Sousa, L.; Piedade, M. S.; Freitas, P. P.

    2008-06-01

    This paper covers recent developments in magnetoresistive based biochip platforms fabricated at INESC-MN, and their application to the detection and quantification of pathogenic waterborn microorganisms in water samples for human consumption. Such platforms are intended to give response to the increasing concern related to microbial contaminated water sources. The presented results concern the development of biological active DNA chips and protein chips and the demonstration of the detection capability of the present platforms. Two platforms are described, one including spintronic sensors only (spin-valve based or magnetic tunnel junction based), and the other, a fully scalable platform where each probe site consists of a MTJ in series with a thin film diode (TFD). Two microfluidic systems are described, for cell separation and concentration, and finally, the read out and control integrated electronics are described, allowing the realization of bioassays with a portable point of care unit. The present platforms already allow the detection of complementary biomolecular target recognition with 1 pM concentration.

  13. A multiscale modeling approach for biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Bowling, Alan, E-mail: bowling@uta.edu; Haghshenas-Jaryani, Mahdi, E-mail: mahdi.haghshenasjaryani@mavs.uta.edu [The University of Texas at Arlington, Department of Mechanical and Aerospace Engineering (United States)

    2015-04-15

    This paper presents a new multiscale molecular dynamic model for investigating the effects of external interactions, such as contact and impact, during stepping and docking of motor proteins and other biomolecular systems. The model retains the mass properties ensuring that the result satisfies Newton’s second law. This idea is presented using a simple particle model to facilitate discussion of the rigid body model; however, the particle model does provide insights into particle dynamics at the nanoscale. The resulting three-dimensional model predicts a significant decrease in the effect of the random forces associated with Brownian motion. This conclusion runs contrary to the widely accepted notion that the motor protein’s movements are primarily the result of thermal effects. This work focuses on the mechanical aspects of protein locomotion; the effect ATP hydrolysis is estimated as internal forces acting on the mechanical model. In addition, the proposed model can be numerically integrated in a reasonable amount of time. Herein, the differences between the motion predicted by the old and new modeling approaches are compared using a simplified model of myosin V.

  14. Microfluidic Devices for Studying Biomolecular Interactions

    Science.gov (United States)

    Wilson, Wilbur W.; Garcia, Carlos d.; Henry, Charles S.

    2006-01-01

    Microfluidic devices for monitoring biomolecular interactions have been invented. These devices are basically highly miniaturized liquid-chromatography columns. They are intended to be prototypes of miniature analytical devices of the laboratory on a chip type that could be fabricated rapidly and inexpensively and that, because of their small sizes, would yield analytical results from very small amounts of expensive analytes (typically, proteins). Other advantages to be gained by this scaling down of liquid-chromatography columns may include increases in resolution and speed, decreases in the consumption of reagents, and the possibility of performing multiple simultaneous and highly integrated analyses by use of multiple devices of this type, each possibly containing multiple parallel analytical microchannels. The principle of operation is the same as that of a macroscopic liquid-chromatography column: The column is a channel packed with particles, upon which are immobilized molecules of the protein of interest (or one of the proteins of interest if there are more than one). Starting at a known time, a solution or suspension containing molecules of the protein or other substance of interest is pumped into the channel at its inlet. The liquid emerging from the outlet of the channel is monitored to detect the molecules of the dissolved or suspended substance(s). The time that it takes these molecules to flow from the inlet to the outlet is a measure of the degree of interaction between the immobilized and the dissolved or suspended molecules. Depending on the precise natures of the molecules, this measure can be used for diverse purposes: examples include screening for solution conditions that favor crystallization of proteins, screening for interactions between drugs and proteins, and determining the functions of biomolecules.

  15. Direct Measurement of the Isomerization Barrier of the Isolated Retinal Chromophore

    DEFF Research Database (Denmark)

    Dilger, Jonathan; Musbat, Lihi; Sheves, Mordechai

    2015-01-01

    Isomerizations of the retinal chromophore were investigated using the IMS-IMS technique. Four different structural features of the chromophore were observed, isolated, excited collisionally, and the resulting isomer and fragment distributions were measured. By establishing the threshold activatio...

  16. Laser photodissociation and spectroscopy of mass-separated biomolecular ions

    CERN Document Server

    Polfer, Nicolas C

    2014-01-01

    This lecture notes book presents how enhanced structural information of biomolecular ions can be obtained from interaction with photons of specific frequency - laser light. The methods described in the book ""Laser photodissociation and spectroscopy of mass-separated biomolecular ions"" make use of the fact that the discrete energy and fast time scale of photoexcitation can provide more control in ion activation. This activation is the crucial process producing structure-informative product ions that cannot be generated with more conventional heating methods, such as collisional activation. Th

  17. Facile attachment of nonlinear optical chromophores to polycarbonates

    NARCIS (Netherlands)

    Faccini, M.; Balakrishnan, M.; Torosantucci, Riccardo; Driessen, A.; Reinhoudt, David; Verboom, Willem

    2008-01-01

    A versatile, generally applicable synthetic methodology for side-chain NLO polycarbonates was developed. This represents the first example of covalent incorporation of NLO chromophores to a prepolymerized polycarbonate backbone. This methodology allows to adjust the polymer backbone structure and to

  18. Single Oligomer Spectra Probe Chromophore Nanoenvironments of Tetrameric Fluorescent Proteins

    NARCIS (Netherlands)

    Blum, Christian; Meixner, Alfred J.; Subramaniam, Vinod

    2006-01-01

    When analyzing the emission of a large number of individual chromophores embedded in a matrix, the spread of the observed parameters is a characteristic property for the particular chromophore−matrix system. To quantitatively assess the influence of the matrix on the single molecule emission

  19. Modeling photoabsorption of the asFP595 chromophore.

    Science.gov (United States)

    Bravaya, Ksenia B; Bochenkova, Anastasia V; Granovsky, Alexander A; Savitsky, Alexander P; Nemukhin, Alexander V

    2008-09-18

    The fluorescent protein asFP595 is a promising photoswitchable biomarker for studying processes in living cells. We present the results of a high level theoretical study of photoabsorption properties of the model asFP595 chromophore molecule in biologically relevant protonation states: anionic, zwitterionic, and neutral. Ground state equilibrium geometry parameters are optimized in the PBE0/(aug)-cc-pVDZ density functional theory approximation. An augmented version of multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2) following the state-averaged CASSCF/(aug)-cc-pVDZ calculations is used to estimate the vertical S0-S1 excitation energies for all chromophore species. An accuracy of this approach is validated by comparing the computed estimates of the S0-S1 absorption maximum of the closely related chromophore from the DsRed protein to the known experimental value in the gas phase. An influence of the CASSCF active space on the aug-MCQDPT2 excitation energies is analyzed. The zwitterionic form of the asFP595 chromophore is found to be the most sensitive to a particular choice and amount of active orbitals. This observation is explained by the charge-transfer type of the S0-S1 transition involving the entire conjugated pi-electron system for the zwitterionic protonation state. According to the calculation results, the anionic form in the trans conformation is found to possess the most red-shifted absorption band with the maximum located at 543 nm. The bands of the zwitterionic and neutral forms are considerably blue-shifted compared to those of the anionic form. These conclusions are at variance with the results obtained in the TDDFT approximation for the asFP595 chromophore. The absorption wavelengths computed in the aug-MCQDPT2/CASSCF theory are as follows: 543 (535), 470 (476), and 415 (417) nm for the anionic, zwitterionic, and neutral forms of the trans and cis (in parentheses) isomers of the asFP595 chromophore. These data can be used as a

  20. The gecko visual pigment: the chromophore dark exchange reaction.

    Science.gov (United States)

    Crescitelli, F

    1988-02-01

    This study confirms the occurrence of a dark-exchange reaction in the extracted 521-pigment of the Tokay gecko (G. gekko). The present study involved the exchange, in the dark, of the natural 11-cis-chromophore by the 9-cis-10-F-retinal analog. This analog is able to combine with the 521-opsin to regenerate a photopigment at 492 nm. In addition to this shift in absorbance from 521 to 492 nm, the analog photopigment has a photosensitivity some 2.4% that of the native 521-system in the chloride-sufficient state. These two properties of the regenerated analog pigment have simplified the demonstration of a dark exchange of chromophores. At 15 degrees C the 9-cis-10-F-analog replaces the 11-cis-chromophore by at least 30% (density-wise) in about 15 hr. This exchange occurs with the system in the chloride-deficient state. The presence of chloride during the period in the dark significantly reduces the magnitude of the exchange. Apparently, the protein has a more open structure at the chromophoric binding site, allowing this interchange of chromophores. The addition of chloride induces a conformational change at this site, 'burying' the Schiff base and reducing the exchange reaction. The biological implication of this mobile property of the gecko opsin is that it is similar to the behavior of the cone pigment iodopsin but is unlike that of rhodopsins. This supports the idea that the gecko visual cells, despite their appearance as rods, are phylogenetically related to ancestral photopic receptors.

  1. GROMOS++Software for the Analysis of Biomolecular Simulation Trajectories

    NARCIS (Netherlands)

    Eichenberger, A.P.; Allison, J.R.; Dolenc, J.; Geerke, D.P.; Horta, B.A.C.; Meier, K; Oostenbrink, B.C.; Schmid, N.; Steiner, D; Wang, D.; van Gunsteren, W.F.

    2011-01-01

    GROMOS++ is a set of C++ programs for pre- and postprocessing of molecular dynamics simulation trajectories and as such is part of the GROningen MOlecular Simulation software for (bio)molecular simulation. It contains more than 70 programs that can be used to prepare data for the production of

  2. The HADDOCK web server for data-driven biomolecular docking

    NARCIS (Netherlands)

    de Vries, S.J.|info:eu-repo/dai/nl/304837717; van Dijk, M.|info:eu-repo/dai/nl/325811113; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238

    2010-01-01

    Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOC K is a popular docking program that takes a datadriven approach to docking, with support for

  3. Improvements to the APBS biomolecular solvation software suite.

    Science.gov (United States)

    Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

    2018-01-01

    The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

  4. From dynamics to structure and function of model biomolecular systems

    NARCIS (Netherlands)

    Fontaine-Vive-Curtaz, F.

    2007-01-01

    The purpose of this thesis was to extend recent works on structure and dynamics of hydrogen bonded crystals to model biomolecular systems and biological processes. The tools that we have used are neutron scattering (NS) and density functional theory (DFT) and force field (FF) based simulation

  5. Biomolecular strategies for cell surface engineering

    Science.gov (United States)

    Wilson, John Tanner

    Islet transplantation has emerged as a promising cell-based therapy for the treatment of diabetes, but its clinical efficacy remains limited by deleterious host responses that underlie islet destruction. In this dissertation, we describe the assembly of ultrathin conformal coatings that confer molecular-level control over the composition and biophysicochemical properties of the islet surface with implications for improving islet engraftment. Significantly, this work provides novel biomolecular strategies for cell surface engineering with broad biomedical and biotechnological applications in cell-based therapeutics and beyond. Encapsulation of cells and tissue offers a rational approach for attenuating deleterious host responses towards transplanted cells, but a need exists to develop cell encapsulation strategies that minimize transplant volume. Towards this end, we endeavored to generate nanothin films of diverse architecture with tunable properties on the extracellular surface of individual pancreatic islets through a process of layer-by-layer (LbL) self assembly. We first describe the formation of poly(ethylene glycol) (PEG)-rich conformal coatings on islets via LbL self assembly of poly(L-lysine)-g-PEG(biotin) and streptavidin. Multilayer thin films conformed to the geometrically and chemically heterogeneous islet surface, and could be assembled without loss of islet viability or function. Significantly, coated islets performed comparably to untreated controls in a murine model of allogenic intraportal islet transplantation, and, to our knowledge, this is the first study to report in vivo survival and function of nanoencapsulated cells or cell aggregates. Based on these findings, we next postulated that structurally similar PLL-g-PEG copolymers comprised of shorter PEG grafts might be used to initiate and propagate the assembly of polyelectrolyte multilayer (PEM) films on pancreatic islets, while simultaneously preserving islet viability. Through control of PLL

  6. Chromophore photophysics and dynamics in fluorescent proteins of the GFP family

    International Nuclear Information System (INIS)

    Nienhaus, Karin; Nienhaus, G Ulrich

    2016-01-01

    Proteins of the green fluorescent protein (GFP) family are indispensable for fluorescence imaging experiments in the life sciences, particularly of living specimens. Their essential role as genetically encoded fluorescence markers has motivated many researchers over the last 20 years to further advance and optimize these proteins by using protein engineering. Amino acids can be exchanged by site-specific mutagenesis, starting with naturally occurring proteins as templates. Optical properties of the fluorescent chromophore are strongly tuned by the surrounding protein environment, and a targeted modification of chromophore-protein interactions requires a profound knowledge of the underlying photophysics and photochemistry, which has by now been well established from a large number of structural and spectroscopic experiments and molecular-mechanical and quantum-mechanical computations on many variants of fluorescent proteins. Nevertheless, such rational engineering often does not meet with success and thus is complemented by random mutagenesis and selection based on the optical properties. In this topical review, we present an overview of the key structural and spectroscopic properties of fluorescent proteins. We address protein-chromophore interactions that govern ground state optical properties as well as processes occurring in the electronically excited state. Special emphasis is placed on photoactivation of fluorescent proteins. These light-induced reactions result in large structural changes that drastically alter the fluorescence properties of the protein, which enables some of the most exciting applications, including single particle tracking, pulse chase imaging and super-resolution imaging. We also present a few examples of fluorescent protein application in live-cell imaging experiments. (topical review)

  7. Chromophore photophysics and dynamics in fluorescent proteins of the GFP family

    Science.gov (United States)

    Nienhaus, Karin; Nienhaus, G. Ulrich

    2016-11-01

    Proteins of the green fluorescent protein (GFP) family are indispensable for fluorescence imaging experiments in the life sciences, particularly of living specimens. Their essential role as genetically encoded fluorescence markers has motivated many researchers over the last 20 years to further advance and optimize these proteins by using protein engineering. Amino acids can be exchanged by site-specific mutagenesis, starting with naturally occurring proteins as templates. Optical properties of the fluorescent chromophore are strongly tuned by the surrounding protein environment, and a targeted modification of chromophore-protein interactions requires a profound knowledge of the underlying photophysics and photochemistry, which has by now been well established from a large number of structural and spectroscopic experiments and molecular-mechanical and quantum-mechanical computations on many variants of fluorescent proteins. Nevertheless, such rational engineering often does not meet with success and thus is complemented by random mutagenesis and selection based on the optical properties. In this topical review, we present an overview of the key structural and spectroscopic properties of fluorescent proteins. We address protein-chromophore interactions that govern ground state optical properties as well as processes occurring in the electronically excited state. Special emphasis is placed on photoactivation of fluorescent proteins. These light-induced reactions result in large structural changes that drastically alter the fluorescence properties of the protein, which enables some of the most exciting applications, including single particle tracking, pulse chase imaging and super-resolution imaging. We also present a few examples of fluorescent protein application in live-cell imaging experiments.

  8. The Role of Chromophore Coupling in Singlet Fission

    Czech Academy of Sciences Publication Activity Database

    Johnson, J. C.; Nozik, A. J.; Michl, Josef

    2013-01-01

    Roč. 46, č. 6 (2013), s. 1290-1299 ISSN 0001-4842 Institutional support: RVO:61388963 Keywords : exciton fission * energy transfer * solar-cells * 1,3-diphenylisobenzofuran Subject RIV: CC - Organic Chemistry Impact factor: 24.348, year: 2013

  9. The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition.

    Directory of Open Access Journals (Sweden)

    Xiliang Zheng

    2015-04-01

    Full Text Available We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity, the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics.

  10. The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Giulio Caravagna

    Full Text Available After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii a model of enzymatic futile cycle and (iii a genetic toggle switch. In (ii and (iii we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

  11. The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

    Science.gov (United States)

    Caravagna, Giulio; Mauri, Giancarlo; d'Onofrio, Alberto

    2013-01-01

    After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i) the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii) a model of enzymatic futile cycle and (iii) a genetic toggle switch. In (ii) and (iii) we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

  12. Structural communication between the chromophore-binding pocket and the N-terminal extension in plant phytochrome phyB.

    Science.gov (United States)

    Velázquez Escobar, Francisco; Buhrke, David; Fernandez Lopez, Maria; Shenkutie, Sintayehu Manaye; von Horsten, Silke; Essen, Lars-Oliver; Hughes, Jon; Hildebrandt, Peter

    2017-05-01

    The N-terminal extension (NTE) of plant phytochromes has been suggested to play a functional role in signaling photoinduced structural changes. Here, we use resonance Raman spectroscopy to study the effect of the NTE on the chromophore structure of B-type phytochromes from two evolutionarily distant plants. NTE deletion seems to have no effect on the chromophore in the inactive Pr state, but alters the torsion of the C-D ring methine bridge and the surrounding hydrogen bonding network in the physiologically active Pfr state. These changes are accompanied by a shift of the conformational equilibrium between two Pfr substates, which might affect the thermal isomerization rate of the C-D double bond and, thus, account for the effect of the NTE on the dark reversion kinetics. © 2017 Federation of European Biochemical Societies.

  13. Gas phase absorption studies of photoactive yellow protein chromophore derivatives.

    Science.gov (United States)

    Rocha-Rinza, Toms; Christiansen, Ove; Rajput, Jyoti; Gopalan, Aravind; Rahbek, Dennis B; Andersen, Lars H; Bochenkova, Anastasia V; Granovsky, Alexander A; Bravaya, Ksenia B; Nemukhin, Alexander V; Christiansen, Kasper Lincke; Nielsen, Mogens Brøndsted

    2009-08-27

    Photoabsorption spectra of deprotonated trans p-coumaric acid and two of its methyl substituted derivatives have been studied in gas phase both experimentally and theoretically. We have focused on the spectroscopic effect of the location of the two possible deprotonation sites on the trans p-coumaric acid which originate to either a phenoxide or a carboxylate. Surprisingly, the three chromophores were found to have the same absorption maximum at 430 nm, in spite of having different deprotonation positions. However, the absorption of the chromophore in polar solution is substantially different for the distinct deprotonation locations. We also report on the time scales and pathways of relaxation after photoexcitation for the three photoactive yellow protein chromophore derivatives. As a result of these experiments, we could detect the phenoxide isomer within the deprotonated trans p-coumaric acid in gas phase; however, the occurrence of the carboxylate is uncertain. Several computational methods were used simultaneously to provide insights and assistance in the interpretation of our experimental results. The calculated excitation energies S(0)-S(1) are in good agreement with experiment for those systems having a negative charge on a phenoxide moiety. Although our augmented multiconfigurational quasidegenerate perturbation theory calculations agree with experiment in the description of the absorption spectrum of anions with a carboxylate functional group, there are some puzzling disagreements between experiment and some calculational methods in the description of these systems.

  14. Structural control of side-chain chromophores to achieve highly efficient electro-optic activity.

    Science.gov (United States)

    Yang, Yuhui; Chen, Zhuo; Liu, Jialei; Xiao, Hongyan; Zhen, Zhen; Liu, Xinhou; Jiang, Guohua

    2017-05-10

    A series of chromophores J1-J4 have been synthesized based on julolidine donors modified with different rigid steric hindrance groups. Compared with the chromophore (J1) without the isolation group, chromophores J2, J3 and J4 show better stability. Structural analysis and photophysical property measurements were carried out to compare the molecular mobility and steric hindrance effect of the different donor-modified chromophores. All of these chromophores with isolation groups showed superb thermal stabilities with high thermal decomposition temperatures above 250 °C. Furthermore, with rigid steric hindrance, chromophores J3 and J4 showed more enhanced thermal stabilities with thermal decomposition temperatures of 269 °C and 275 °C, respectively. Density functional theory was used to calculate the hyperpolarizability (β), and the high molecular hyperpolarizability of these chromophores can be effectively translated into large electro-optic coefficients. The electro-optic coefficients of poled films containing 20 wt% of these new chromophores doped in amorphous polycarbonate were 127, 266 and 209 pm V -1 at 1310 nm for chromophores J1-J3, respectively, while the film containing chromophore J4 showed the largest r 33 value of only 97 pm V -1 at 25 wt%. These results indicated that the introduced isolation group can reduce intermolecular electrostatic interactions, thus enhancing the macroscopic electro-optic activity, while the size of the isolation group should be suitable.

  15. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

    Directory of Open Access Journals (Sweden)

    Clarisse Gravina Ricci

    2018-02-01

    Full Text Available Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes.

  16. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

    Science.gov (United States)

    Ricci, Clarisse Gravina; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J. Andrew

    2018-01-01

    Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes. PMID:29484300

  17. Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy

    Science.gov (United States)

    Xu, Yao; Havenith, Martina

    2015-11-01

    Terahertz (THz) spectroscopy has turned out to be a powerful tool which is able to shed new light on the role of water in biomolecular processes. The low frequency spectrum of the solvated biomolecule in combination with MD simulations provides deep insights into the collective hydrogen bond dynamics on the sub-ps time scale. The absorption spectrum between 1 THz and 10 THz of solvated biomolecules is sensitive to changes in the fast fluctuations of the water network. Systematic studies on mutants of antifreeze proteins indicate a direct correlation between biological activity and a retardation of the (sub)-ps hydration dynamics at the protein binding site, i.e., a "hydration funnel." Kinetic THz absorption studies probe the temporal changes of THz absorption during a biological process, and give access to the kinetics of the coupled protein-hydration dynamics. When combined with simulations, the observed results can be explained in terms of a two-tier model involving a local binding and a long range influence on the hydration bond dynamics of the water around the binding site that highlights the significance of the changes in the hydration dynamics at recognition site for biomolecular recognition. Water is shown to assist molecular recognition processes.

  18. Herbal medicine: biomolecular and clinical aspects

    National Research Council Canada - National Science Library

    Benzie, Iris F. F; Wachtel-Galor, Sissi

    2011-01-01

    .... With over 3,550 current references, the book highlights the role of herbal medicine in national health care while providing case studies of widely used herbal remedies and their effects on human...

  19. Theoretical study of chromophores for biological sensing: Understanding the mechanism of rhodol based multi-chromophoric systems

    Science.gov (United States)

    Rivera-Jacquez, Hector J.; Masunov, Artëm E.

    2018-06-01

    Development of two-photon fluorescent probes can aid in visualizing the cellular environment. Multi-chromophore systems display complex manifolds of electronic transitions, enabling their use for optical sensing applications. Time-Dependent Density Functional Theory (TDDFT) methods allow for accurate predictions of the optical properties. These properties are related to the electronic transitions in the molecules, which include two-photon absorption cross-sections. Here we use TDDFT to understand the mechanism of aza-crown based fluorescent probes for metals sensing applications. Our findings suggest changes in local excitation in the rhodol chromophore between unbound form and when bound to the metal analyte. These changes are caused by a charge transfer from the aza-crown group and pyrazol units toward the rhodol unit. Understanding this mechanism leads to an optimized design with higher two-photon excited fluorescence to be used in medical applications.

  20. Biomolecular structure refinement using the GROMOS simulation software

    International Nuclear Information System (INIS)

    Schmid, Nathan; Allison, Jane R.; Dolenc, Jožica; Eichenberger, Andreas P.; Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van

    2011-01-01

    For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, 3 J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

  1. Biomolecular structure refinement using the GROMOS simulation software

    Energy Technology Data Exchange (ETDEWEB)

    Schmid, Nathan; Allison, Jane R.; Dolenc, Jozica; Eichenberger, Andreas P.; Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Swiss Federal Institute of Technology ETH, Laboratory of Physical Chemistry (Switzerland)

    2011-11-15

    For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, {sup 3}J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

  2. Probing microhydration effect on the electronic structure of the GFP chromophore anion: Photoelectron spectroscopy and theoretical investigations

    Energy Technology Data Exchange (ETDEWEB)

    Bhaskaran-Nair, Kiran; Shelton, William A. [Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Valiev, Marat; Kowalski, Karol, E-mail: karol.kowalski@pnnl.gov [William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352 (United States); Deng, S. H. M.; Wang, Xue-Bin, E-mail: xuebin.wang@pnnl.gov [Physical Sciences Division, Pacific Northwest National Laboratory, K8-88, P.O. Box 999, Richland, Washington 99352 (United States)

    2015-12-14

    The photophysics of the Green Fluorescent Protein (GFP) chromophore is critically dependent on its local structure and on its environment. Despite extensive experimental and computational studies, there remain many open questions regarding the key fundamental variables that govern this process. One outstanding problem is the role of autoionization as a possible relaxation pathway of the excited state under different environmental conditions. This issue is considered in our work through combined experimental and theoretical studies of microsolvated clusters of the deprotonated p-hydroxybenzylidene-2,3-dimethylimidazolinone anion (HBDI{sup −}), an analog of the GFP chromophore. Through selective generation of microsolvated structures of predetermined size and subsequent analysis of experimental photoelectron spectra by high level ab initio methods, we are able to precisely identify the structure of the system, establish the accuracy of theoretical data, and provide reliable description of auto-ionization process as a function of hydrogen-bonding environment. Our study clearly illustrates the first few water molecules progressively stabilize the excited state of the chromophore anion against the autodetached neutral state, which should be an important trait for crystallographic water molecules in GFPs that has not been fully explored to date.

  3. Application of biomolecular recognition via magnetic nanoparticle in nanobiotechnology

    Science.gov (United States)

    Shen, Wei-Zheng; Cetinel, Sibel; Montemagno, Carlo

    2018-05-01

    The marriage of biomolecular recognition and magnetic nanoparticle creates tremendous opportunities in the development of advanced technology both in academic research and in industrial sectors. In this paper, we review current progress on the magnetic nanoparticle-biomolecule hybrid systems, particularly employing the recognition pairs of DNA-DNA, DNA-protein, protein-protein, and protein-inorganics in several nanobiotechnology application areas, including molecular biology, diagnostics, medical treatment, industrial biocatalysts, and environmental separations.

  4. LDRD final report : energy conversion using chromophore-functionalized carbon nanotubes.

    Energy Technology Data Exchange (ETDEWEB)

    Vance, Andrew L.; Zifer, Thomas; Zhou, Xinjian; Leonard, Francois Leonard; Wong, Bryan Matthew; Kane, Alexander; Katzenmeyer, Aaron Michael; Krafcik, Karen Lee

    2010-09-01

    With the goal of studying the conversion of optical energy to electrical energy at the nanoscale, we developed and tested devices based on single-walled carbon nanotubes functionalized with azobenzene chromophores, where the chromophores serve as photoabsorbers and the nanotube as the electronic read-out. By synthesizing chromophores with specific absorption windows in the visible spectrum and anchoring them to the nanotube surface, we demonstrated the controlled detection of visible light of low intensity in narrow ranges of wavelengths. Our measurements suggested that upon photoabsorption, the chromophores isomerize to give a large change in dipole moment, changing the electrostatic environment of the nanotube. All-electron ab initio calculations were used to study the chromophore-nanotube hybrids, and show that the chromophores bind strongly to the nanotubes without disturbing the electronic structure of either species. Calculated values of the dipole moments supported the notion of dipole changes as the optical detection mechanism.

  5. Photoresponsive Block Copolymers Containing Azobenzenes and Other Chromophores

    Directory of Open Access Journals (Sweden)

    Takaomi Kobayashi

    2010-01-01

    Full Text Available Photoresponsive block copolymers (PRBCs containing azobenzenes and other chromophores can be easily prepared by controlled polymerization. Their photoresponsive behaviors are generally based on photoisomerization, photocrosslinking, photoalignment and photoinduced cooperative motions. When the photoactive block forms mesogenic phases upon microphase separation of PRBCs, supramolecular cooperative motion in liquid-crystalline PRBCs enables them to self-organize into hierarchical structures with photoresponsive features. This offers novel opportunities to photocontrol microphase-separated nanostructures of well-defined PRBCs and extends their diverse applications in holograms, nanotemplates, photodeformed devices and microporous films.

  6. DNA-Conjugated Organic Chromophores in DNA Stacking Interactions

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V.; Pedersen, Erik Bjerregaard

    2009-01-01

    Since the discovery of the intercalation of acridine derivatives into DNA (1961), chemists have synthesized many intercalators tethered to DNA. Advances in the chemical synthesis of modified nucleosides along with progress in oligonucleotide synthesis have made it possible to introduce organic ch...... review presents those efforts in the design of intercalators/organic chromophores as oligonucleotide conjugates that form a foundation for the generation of novel nucleic acid architectures......Since the discovery of the intercalation of acridine derivatives into DNA (1961), chemists have synthesized many intercalators tethered to DNA. Advances in the chemical synthesis of modified nucleosides along with progress in oligonucleotide synthesis have made it possible to introduce organic...

  7. Scanning probe and optical tweezer investigations of biomolecular interactions

    International Nuclear Information System (INIS)

    Rigby-Singleton, Shellie

    2002-01-01

    A complex array of intermolecular forces controls the interactions between and within biological molecules. The desire to empirically explore the fundamental forces has led to the development of several biophysical techniques. Of these, the atomic force microscope (AFM) and the optical tweezers have been employed throughout this thesis to monitor the intermolecular forces involved in biomolecular interactions. The AFM is a well-established force sensing technique capable of measuring biomolecular interactions at a single molecule level. However, its versatility has not been extrapolated to the investigation of a drug-enzyme complex. The energy landscape for the force induced dissociation of the DHFR-methotrexate complex was studied. Revealing an energy barrier to dissociation located ∼0.3 nm from the bound state. Unfortunately, the AFM has a limited range of accessible loading rates and in order to profile the complete energy landscape alternative force sensing instrumentation should be considered, for example the BFP and optical tweezers. Thus, this thesis outlines the development and construction an optical trap capable of measuring intermolecular forces between biomolecules at the single molecule level. To demonstrate the force sensing abilities of the optical set up, proof of principle measurements were performed which investigate the interactions between proteins and polymer surfaces subjected to varying degrees of argon plasma treatment. Complementary data was gained from measurements performed independently by the AFM. Changes in polymer resistance to proteins as a response to changes in polymer surface chemistry were detected utilising both AFM and optical tweezers measurements. Finally, the AFM and optical tweezers were employed as ultrasensitive biosensors. Single molecule investigations of the antibody-antigen interaction between the cardiac troponin I marker and its complementary antibody, reveals the impact therapeutic concentrations of heparin have

  8. Skin image illumination modeling and chromophore identification for melanoma diagnosis

    Science.gov (United States)

    Liu, Zhao; Zerubia, Josiane

    2015-05-01

    The presence of illumination variation in dermatological images has a negative impact on the automatic detection and analysis of cutaneous lesions. This paper proposes a new illumination modeling and chromophore identification method to correct lighting variation in skin lesion images, as well as to extract melanin and hemoglobin concentrations of human skin, based on an adaptive bilateral decomposition and a weighted polynomial curve fitting, with the knowledge of a multi-layered skin model. Different from state-of-the-art approaches based on the Lambert law, the proposed method, considering both specular reflection and diffuse reflection of the skin, enables us to address highlight and strong shading effects usually existing in skin color images captured in an uncontrolled environment. The derived melanin and hemoglobin indices, directly relating to the pathological tissue conditions, tend to be less influenced by external imaging factors and are more efficient in describing pigmentation distributions. Experiments show that the proposed method gave better visual results and superior lesion segmentation, when compared to two other illumination correction algorithms, both designed specifically for dermatological images. For computer-aided diagnosis of melanoma, sensitivity achieves 85.52% when using our chromophore descriptors, which is 8~20% higher than those derived from other color descriptors. This demonstrates the benefit of the proposed method for automatic skin disease analysis.

  9. Depth distributions of light action spectra for skin chromophores

    Science.gov (United States)

    Barun, V. V.; Ivanov, A. P.

    2010-03-01

    Light action spectra over wavelengths of 300-1000 nm are calculated for components of the human cutaneous covering: melanin, basal (bloodless) tissue, and blood oxy- and deoxyhemoglobin. The transformation of the spectra with depth in biological tissue results from two factors. The first is the wavelength dependence of the absorption coefficient corresponding to a particular skin chromophore and the second is the spectral selectivity of the radiation flux in biological tissue. This factor is related to the optical properties of all chromophores. A significant change is found to take place in the spectral distribution of absorbed radiant power with increasing depth. The action spectrum of light for the molecular oxygen contained in all components of biological tissue is also studied in the 625-645 nm range. The spectra are found to change with both the volume fraction of blood vessels and the degree of oxygenation of the blood. These results are useful for analyzing processes associated with optical absorption that are possible mechanisms for the interaction of light with biological tissues: photodissociation of oxyhemoglobin and the light-oxygen effect.

  10. New closed-form approximation for skin chromophore mapping.

    Science.gov (United States)

    Välisuo, Petri; Kaartinen, Ilkka; Tuchin, Valery; Alander, Jarmo

    2011-04-01

    The concentrations of blood and melanin in skin can be estimated based on the reflectance of light. Many models for this estimation have been built, such as Monte Carlo simulation, diffusion models, and the differential modified Beer-Lambert law. The optimization-based methods are too slow for chromophore mapping of high-resolution spectral images, and the differential modified Beer-Lambert is not often accurate enough. Optimal coefficients for the differential Beer-Lambert model are calculated by differentiating the diffusion model, optimized to the normal skin spectrum. The derivatives are then used in predicting the difference in chromophore concentrations from the difference in absorption spectra. The accuracy of the method is tested both computationally and experimentally using a Monte Carlo multilayer simulation model, and the data are measured from the palm of a hand during an Allen's test, which modulates the blood content of skin. The correlations of the given and predicted blood, melanin, and oxygen saturation levels are correspondingly r = 0.94, r = 0.99, and r = 0.73. The prediction of the concentrations for all pixels in a 1-megapixel image would take ∼ 20 min, which is orders of magnitude faster than the methods based on optimization during the prediction.

  11. Synergy of Two Highly Specific Biomolecular Recognition Events

    DEFF Research Database (Denmark)

    Ejlersen, Maria; Christensen, Niels Johan; Sørensen, Kasper K

    2018-01-01

    Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino......-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA...

  12. Instrumental biosensors: new perspectives for the analysis of biomolecular interactions.

    Science.gov (United States)

    Nice, E C; Catimel, B

    1999-04-01

    The use of instrumental biosensors in basic research to measure biomolecular interactions in real time is increasing exponentially. Applications include protein-protein, protein-peptide, DNA-protein, DNA-DNA, and lipid-protein interactions. Such techniques have been applied to, for example, antibody-antigen, receptor-ligand, signal transduction, and nuclear receptor studies. This review outlines the principles of two of the most commonly used instruments and highlights specific operating parameters that will assist in optimising experimental design, data generation, and analysis.

  13. Application of Hidden Markov Models in Biomolecular Simulations.

    Science.gov (United States)

    Shukla, Saurabh; Shamsi, Zahra; Moffett, Alexander S; Selvam, Balaji; Shukla, Diwakar

    2017-01-01

    Hidden Markov models (HMMs) provide a framework to analyze large trajectories of biomolecular simulation datasets. HMMs decompose the conformational space of a biological molecule into finite number of states that interconvert among each other with certain rates. HMMs simplify long timescale trajectories for human comprehension, and allow comparison of simulations with experimental data. In this chapter, we provide an overview of building HMMs for analyzing bimolecular simulation datasets. We demonstrate the procedure for building a Hidden Markov model for Met-enkephalin peptide simulation dataset and compare the timescales of the process.

  14. Branched charge-transfer chromophores featuring a 4,5-dicyanoimidazole unit

    Czech Academy of Sciences Publication Activity Database

    Bureš, F.; Kulhánek, J.; Mikysek, T.; Ludvík, Jiří; Lokaj, J.

    2010-01-01

    Roč. 51, č. 15 (2010), s. 2055-2058 ISSN 0040-4039 Institutional research plan: CEZ:AV0Z40400503 Keywords : non-linear optical chromophores * 2-photon absorption * imidazole chromophores Subject RIV: CG - Electrochemistry Impact factor: 2.618, year: 2010

  15. Absorption tuning of the green fluorescent protein chromophore: synthesis and studies of model compounds

    DEFF Research Database (Denmark)

    Brøndsted Nielsen, Mogens; Andersen, Lars Henrik; Rinza, Tomás Rocha

    2011-01-01

    The green fluorescent protein (GFP) chromophore is a heterocyclic compound containing a p-hydroxybenzylidine attached to an imidazol-5(4H)-one ring. This review covers the synthesis of a variety of model systems for elucidating the intrinsic optical properties of the chromophore in the gas phase ...

  16. Ultraviolet-resonance femtosecond stimulated Raman study of the initial events in photoreceptor chromophore

    Directory of Open Access Journals (Sweden)

    Tahara T.

    2013-03-01

    Full Text Available Newly-developed ultraviolet-resonance femtosecond stimulated-Raman spectroscopy was utilized to study the initial structural evolution of photoactive yellow protein chromophore in solution. The obtained spectra changed drastically within 1 ps, demonstrating rapid in-plane deformations of the chromophore.

  17. Contrasting the excited-state dynamics of the photoactive yellow protein chromophore: Protein versus solvent environments

    NARCIS (Netherlands)

    Vengris, M.; Horst, M.A.; Zgrablic, G.; van Stokkum, I.H.M.; Haacke, S.; Chergui, M.; Hellingwerf, K.J.; van Grondelle, R.; Larsen, D.S.

    2004-01-01

    Wavelength- and time-resolved fluorescence experiments have been performed on the photoactive yellow protein, the E46Q mutant, the hybrids of these proteins containing a nonisomerizing "locked" chromophore, and the native and locked chromophores in aqueous solution. The ultrafast dynamics of these

  18. Chromophore Structure of Photochromic Fluorescent Protein Dronpa: Acid-Base Equilibrium of Two Cis Configurations.

    Science.gov (United States)

    Higashino, Asuka; Mizuno, Misao; Mizutani, Yasuhisa

    2016-04-07

    Dronpa is a novel photochromic fluorescent protein that exhibits fast response to light. The present article is the first report of the resonance and preresonance Raman spectra of Dronpa. We used the intensity and frequency of Raman bands to determine the structure of the Dronpa chromophore in two thermally stable photochromic states. The acid-base equilibrium in one photochromic state was observed by spectroscopic pH titration. The Raman spectra revealed that the chromophore in this state shows a protonation/deprotonation transition with a pKa of 5.2 ± 0.3 and maintains the cis configuration. The observed resonance Raman bands showed that the other photochromic state of the chromophore is in a trans configuration. The results demonstrate that Raman bands selectively enhanced for the chromophore yield valuable information on the molecular structure of the chromophore in photochromic fluorescent proteins after careful elimination of the fluorescence background.

  19. Ultrafast dual photoresponse of isolated biological chromophores: link to the photoinduced mode-specific non-adiabatic dynamics in proteins

    DEFF Research Database (Denmark)

    Bochenkova, Anastasia; Andersen, Lars Henrik

    2013-01-01

    The anionic wild-type Green Fluorescent Protein (GFP) chromophore defines the entire class of naturally occurring chromophores, which are based on the oxydized tyrosine side chain. The GFP chromophore exhibits an enriched photoinduced non-adiabatic dynamics in the multiple excited-state decay cha...

  20. Synthetic Approach to biomolecular science by cyborg supramolecular chemistry.

    Science.gov (United States)

    Kurihara, Kensuke; Matsuo, Muneyuki; Yamaguchi, Takumi; Sato, Sota

    2018-02-01

    To imitate the essence of living systems via synthetic chemistry approaches has been attempted. With the progress in supramolecular chemistry, it has become possible to synthesize molecules of a size and complexity close to those of biomacromolecules. Recently, the combination of precisely designed supramolecules with biomolecules has generated structural platforms for designing and creating unique molecular systems. Bridging between synthetic chemistry and biomolecular science is also developing methodologies for the creation of artificial cellular systems. This paper provides an overview of the recently expanding interdisciplinary research to fuse artificial molecules with biomolecules, that can deepen our understanding of the dynamical ordering of biomolecules. Using bottom-up approaches based on the precise chemical design, synthesis and hybridization of artificial molecules with biological materials have been realizing the construction of sophisticated platforms having the fundamental functions of living systems. The effective hybrid, molecular cyborg, approaches enable not only the establishment of dynamic systems mimicking nature and thus well-defined models for biophysical understanding, but also the creation of those with highly advanced, integrated functions. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Photochirogenesis: Photochemical Models on the Origin of Biomolecular Homochirality

    Directory of Open Access Journals (Sweden)

    Cornelia Meinert

    2010-05-01

    Full Text Available Current research focuses on a better understanding of the origin of biomolecular asymmetry by the identification and detection of the possibly first chiral molecules that were involved in the appearance and evolution of life on Earth. We have reasons to assume that these molecules were specific chiral amino acids. Chiral amino acids have been identified in both chondritic meteorites and simulated interstellar ices. Present research reasons that circularly polarized electromagnetic radiation was identified in interstellar environments and an asymmetric interstellar photon-molecule interaction might have triggered biomolecular symmetry breaking. We review on the possible prebiotic interaction of ‘chiral photons’ in the form of circularly polarized light, with early chiral organic molecules. We will highlight recent studies on enantioselective photolysis of racemic amino acids by circularly polarized light and experiments on the asymmetric photochemical synthesis of amino acids from only one C and one N containing molecules by simulating interstellar environments. Both approaches are based on circular dichroic transitions of amino acids that will be presented as well.

  2. Biomolecular logic systems: applications to biosensors and bioactuators

    Science.gov (United States)

    Katz, Evgeny

    2014-05-01

    The paper presents an overview of recent advances in biosensors and bioactuators based on the biocomputing concept. Novel biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce output in the form of YES/NO response. Compared to traditional single-analyte sensing devices, biocomputing approach enables a high-fidelity multi-analyte biosensing, particularly beneficial for biomedical applications. Multi-signal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert to medical emergencies, along with an immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly exemplified for liver injury. Wide-ranging applications of multi-analyte digital biosensors in medicine, environmental monitoring and homeland security are anticipated. "Smart" bioactuators, for example for signal-triggered drug release, were designed by interfacing switchable electrodes and biocomputing systems. Integration of novel biosensing and bioactuating systems with the biomolecular information processing systems keeps promise for further scientific advances and numerous practical applications.

  3. Ion induced fragmentation of biomolecular systems at low collision energies

    International Nuclear Information System (INIS)

    Bernigaud, V; Adoui, L; Chesnel, J Y; Rangama, J; Huber, B A; Manil, B; Alvarado, F; Bari, S; Hoekstra, R; Postma, J; Schlathoelter, T

    2009-01-01

    In this paper, we present results of different collision experiments between multiply charged ions at low collision energies (in the keV-region) and biomolecular systems. This kind of interaction allows to remove electrons form the biomolecule without transferring a large amount of vibrational excitation energy. Nevertheless, following the ionization of the target, fragmentation of biomolecular species may occur. It is the main objective of this work to study the physical processes involved in the dissociation of highly electronically excited systems. In order to elucidate the intrinsic properties of certain biomolecules (porphyrins and amino acids) we have performed experiments in the gas phase with isolated systems. The obtained results demonstrate the high stability of porphyrins after electron removal. Furthermore, a dependence of the fragmentation pattern produced by multiply charged ions on the isomeric structure of the alanine molecule has been shown. By considering the presence of other surrounding biomolecules (clusters of nucleobases), a strong influence of the environment of the biomolecule on the fragmentation channels and their modification, has been clearly proven. This result is explained, in the thymine and uracil case, by the formation of hydrogen bonds between O and H atoms, which is known to favor planar cluster geometries.

  4. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations.

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules.

  5. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson-Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post-analysis of structural and electrical properties of biomolecules.

  6. Sea cucumbers reduce chromophoric dissolved organic matter in aquaculture tanks.

    Science.gov (United States)

    Sadeghi-Nassaj, Seyed Mohammad; Catalá, Teresa S; Álvarez, Pedro A; Reche, Isabel

    2018-01-01

    Mono-specific aquaculture effluents contain high concentrations of nutrients and organic matter, which affect negatively the water quality of the recipient ecosystems. A fundamental feature of water quality is its transparency. The fraction of dissolved organic matter that absorbs light is named chromophoric dissolved organic matter (CDOM). A sustainable alternative to mono-specific aquaculture is the multitrophic aquaculture that includes species trophically complementary named "extractive" species that uptake the waste byproducts. Sea cucumbers are recognized as efficient extractive species due to the consumption of particulate organic matter (POM). However, the effects of sea cucumbers on CDOM are still unknown. During more than one year, we monitored CDOM in two big-volume tanks with different trophic structure. One of the tanks (-holothurian) only contained around 810 individuals of Anemonia sulcata , whereas the other tank (+holothurian) also included 90 individuals of Holothuria tubulosa and Holothuria forskali . We routinely analyzed CDOM absorption spectra and determined quantitative (absorption coefficients at 325 nm) and qualitative (spectral slopes) optical parameters in the inlet waters, within the tanks, and in their corresponding effluents. To confirm the time-series results, we also performed three experiments. Each experiment consisted of two treatments: +holothurians (+H) and -holothurians (-H). We set up three +H tanks with 80 individuals of A. sulcata and 10 individuals of H. tubulosa in each tank and four -H tanks that contained only 80 individuals of A. sulcata . In the time-series, absorption coefficients at 325 nm ( a 325 ) and spectral slopes from 275 to 295 nm ( S 275-295 ) were significantly lower in the effluent of the +holothurian tank (average: 0.33 m -1 and 16 µm -1 , respectively) than in the effluent of the -holothurian tank (average: 0.69 m -1 and 34 µm -1 , respectively), the former being similar to those found in the inlet

  7. PREFACE: Radiation Damage in Biomolecular Systems (RADAM07)

    Science.gov (United States)

    McGuigan, Kevin G.

    2008-03-01

    The annual meeting of the COST P9 Action `Radiation damage in biomolecular systems' took place from 19-22 June 2007 in the Royal College of Surgeons in Ireland, in Dublin. The conference was structured into 5 Working Group sessions: Electrons and biomolecular interactions Ions and biomolecular interactions Radiation in physiological environments Theoretical developments for radiation damage Track structure in cells Each of the five working groups presented two sessions of invited talks. Professor Ron Chesser of Texas Tech University, USA gave a riveting plenary talk on `Mechanisms of Adaptive Radiation Responses in Mammals at Chernobyl' and the implications his work has on the Linear-No Threshold model of radiation damage. In addition, this was the first RADAM meeting to take place after the Alexander Litvenenko affair and we were fortunate to have one of the leading scientists involved in the European response Professor Herwig Paretzke of GSF-Institut für Strahlenschutz, Neuherberg, Germany, available to speak. The remaining contributions were presented in the poster session. A total of 72 scientific contributions (32 oral, 40 poster), presented by 97 participants from 22 different countries, gave an overview on the current progress in the 5 different subfields. A 1-day pre-conference `Early Researcher Tutorial Workshop' on the same topic kicked off on 19 June attended by more than 40 postgrads, postdocs and senior researchers. Twenty papers, based on these reports, are included in this volume of Journal of Physics: Conference Series. All the contributions in this volume were fully refereed, and they represent a sample of the courses, invited talks and contributed talks presented during RADAM07. The interdisciplinary RADAM07 conference brought together researchers from a variety of different fields with a common interest in biomolecular radiation damage. This is reflected by the disparate backgrounds of the authors of the papers presented in these proceedings

  8. Synthesis and properties of the para-trimethylammonium analogues of green fluorescence protein (GFP) chromophore: The mimic of protonated GFP chromophore.

    Science.gov (United States)

    Fanjiang, Ming-Wei; Li, Ming-Ju; Sung, Robert; Sung, Kuangsen

    2018-04-01

    At low pH, protons from the external, bulk solution can protonate the phenoxide group of the p-HBDI chromophore in wild-type green fluorescent protein (wtGFP) and its mutants, and likely continue to tentatively protonate the phenol hydroxyl group of the same chromophores. Because the protonated GFP chromophore is a transient, we prepare the stable p-trimethylammonium analogues (2a and 2b) of the GFP chromophore to mimic it and explore their properties. What we found is that the p-trimethylammonium analogues of the GFP chromophore have the highly electrophilic amidine carbon, blue-shifted electronic absorption, smaller molar absorptivity, smaller fluorescent quantum yield, and faster E-Z thermoisomerization rate. The amidine carbon of the p-trimethylammonium analogue (2b) of the GFP chromophore is the only site that is attacked by very weak nucleophile of water, resulting in ring-opening of the imidazolinone moiety. The half-life of its decay rate in D 2 O is around 33 days. Actually, acid-catalyzed hydrolysis of p-HBDI also results in ring-opening of the imidazolinone moiety. The ratio of the acid-catalyzed hydrolysis rate constants [k obs (p-HBDI)/k obs (1b)] between p-HBDI and 1b (p-dimethylammonium analogue of the GFP chromophore) is dramatically increased from 0.30 at pH = 2 to 0.63 at pH = 0. This is the evidence that more and more phenol hydroxyl groups of p-HBDI are tentatively protonated in a low-pH aqueous solution and that accelerates hydrolysis of p-HBDI in the way similar to the quaternary ammonium derivatives 2a and 2b in water. With this view point, 2a and 2b still can partially mimic the cationic p-HBDI with the protonated phenol hydroxyl group. Implication of the experiment is that the amidine carbon of the chromophore in wtGFP and its mutants at very low pH should be highly electrophilic. Whether ring-opening of the imidazolinone moiety of the GFP chromophore would occur or not depends on if water molecules can reach the amidine carbon of

  9. Gamma ray induced chromophore modification of softwood thermomechanical pulp

    International Nuclear Information System (INIS)

    Robert, S.; Daneault, C.; Viel, C.; Lepine, F.

    1992-01-01

    This study focuses on bleaching a softwood (black spruce, balsam fur) thermomechanical pulp with gamma rays. Gamma rays are known for their enormous penetrating power, along with their ionizing properties. They can generate highly energetic radicals capable of oxidizing lignin chromophores. The authors studied the influence of isopropyl alcohol, sodium borohydride, oxygen, hydrogen peroxide, nitrogen dioxide and water along with gamma ray irradiation of the pulps. The authors measured the optimal dose and dose rate, along with the influence of the radical scavengers like oxygen on the bleaching effect of gamma irradiated pulps. They observe various degrees of bleaching of these pulps. Evidence relates this bleaching to the generation of perhydroxyl anions upon irradiation of water. Also, they were able to pinpoint the influence of the dose rate on the rate of formation and disappearance of these perhydroxyl anions and their influence on bleaching kinetics. Stability toward photoyellowing, and photoyellowing's kinetic of papers from these pulps was also studied

  10. Perspective: Markov models for long-timescale biomolecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schwantes, C. R.; McGibbon, R. T. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); Pande, V. S., E-mail: pande@stanford.edu [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); Department of Computer Science, Stanford University, Stanford, California 94305 (United States); Department of Structural Biology, Stanford University, Stanford, California 94305 (United States); Biophysics Program, Stanford University, Stanford, California 94305 (United States)

    2014-09-07

    Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics.

  11. ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

    Science.gov (United States)

    Parvatikar, Akash; Vacaliuc, Gabriel S; Ramanathan, Arvind; Chennubhotla, S Chakra

    2018-05-08

    Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. Orientation of biomolecular assemblies in a microfluidic jet

    International Nuclear Information System (INIS)

    Priebe, M; Kalbfleisch, S; Tolkiehn, M; Salditt, T; Koester, S; Abel, B; Davies, R J

    2010-01-01

    We have investigated multilamellar lipid assemblies in a microfluidic jet, operating at high shear rates of the order of 10 7 s -1 . Compared to classical Couette cells or rheometers, the shear rate was increased by at least 2-3 orders of magnitude, and the sample volume was scaled down correspondingly. At the same time, the jet is characterized by high extensional stress due to elongational flow. A focused synchrotron x-ray beam was used to measure the structure and orientation of the lipid assemblies in the jet. The diffraction patterns indicate conventional multilamellar phases, aligned with the membrane normals oriented along the velocity gradient of the jet. The results indicate that the setup may be well suited for coherent diffractive imaging of oriented biomolecular assemblies and macromolecules at the future x-ray free electron laser (XFEL) sources.

  13. DNA-assisted swarm control in a biomolecular motor system.

    Science.gov (United States)

    Keya, Jakia Jannat; Suzuki, Ryuhei; Kabir, Arif Md Rashedul; Inoue, Daisuke; Asanuma, Hiroyuki; Sada, Kazuki; Hess, Henry; Kuzuya, Akinori; Kakugo, Akira

    2018-01-31

    In nature, swarming behavior has evolved repeatedly among motile organisms because it confers a variety of beneficial emergent properties. These include improved information gathering, protection from predators, and resource utilization. Some organisms, e.g., locusts, switch between solitary and swarm behavior in response to external stimuli. Aspects of swarming behavior have been demonstrated for motile supramolecular systems composed of biomolecular motors and cytoskeletal filaments, where cross-linkers induce large scale organization. The capabilities of such supramolecular systems may be further extended if the swarming behavior can be programmed and controlled. Here, we demonstrate that the swarming of DNA-functionalized microtubules (MTs) propelled by surface-adhered kinesin motors can be programmed and reversibly regulated by DNA signals. Emergent swarm behavior, such as translational and circular motion, can be selected by tuning the MT stiffness. Photoresponsive DNA containing azobenzene groups enables switching between solitary and swarm behavior in response to stimulation with visible or ultraviolet light.

  14. Review of MEMS differential scanning calorimetry for biomolecular study

    Science.gov (United States)

    Yu, Shifeng; Wang, Shuyu; Lu, Ming; Zuo, Lei

    2017-12-01

    Differential scanning calorimetry (DSC) is one of the few techniques that allow direct determination of enthalpy values for binding reactions and conformational transitions in biomolecules. It provides the thermodynamics information of the biomolecules which consists of Gibbs free energy, enthalpy and entropy in a straightforward manner that enables deep understanding of the structure function relationship in biomolecules such as the folding/unfolding of protein and DNA, and ligand bindings. This review provides an up to date overview of the applications of DSC in biomolecular study such as the bovine serum albumin denaturation study, the relationship between the melting point of lysozyme and the scanning rate. We also introduce the recent advances of the development of micro-electro-mechanic-system (MEMS) based DSCs.

  15. Techniques of biomolecular quantification through AMS detection of radiocarbon

    International Nuclear Information System (INIS)

    Vogel, S.J.; Turteltaub, K.W.; Frantz, C.; Felton, J.S.; Gledhill, B.L.

    1992-01-01

    Accelerator mass spectrometry offers a large gain over scintillation counting in sensitivity for detecting radiocarbon in biomolecular tracing. Application of this sensitivity requires new considerations of procedures to extract or isolate the carbon fraction to be quantified, to inventory all carbon in the sample, to prepare graphite from the sample for use in the spectrometer, and to derive a meaningful quantification from the measured isotope ratio. These procedures need to be accomplished without contaminating the sample with radiocarbon, which may be ubiquitous in laboratories and on equipment previously used for higher dose, scintillation experiments. Disposable equipment, materials and surfaces are used to control these contaminations. Quantification of attomole amounts of labeled substances are possible through these techniques

  16. Perspective: Markov models for long-timescale biomolecular dynamics

    International Nuclear Information System (INIS)

    Schwantes, C. R.; McGibbon, R. T.; Pande, V. S.

    2014-01-01

    Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics

  17. Hybrid organic semiconductor lasers for bio-molecular sensing.

    Science.gov (United States)

    Haughey, Anne-Marie; Foucher, Caroline; Guilhabert, Benoit; Kanibolotsky, Alexander L; Skabara, Peter J; Burley, Glenn; Dawson, Martin D; Laurand, Nicolas

    2014-01-01

    Bio-functionalised luminescent organic semiconductors are attractive for biophotonics because they can act as efficient laser materials while simultaneously interacting with molecules. In this paper, we present and discuss a laser biosensor platform that utilises a gain layer made of such an organic semiconductor material. The simple structure of the sensor and its operation principle are described. Nanolayer detection is shown experimentally and analysed theoretically in order to assess the potential and the limits of the biosensor. The advantage conferred by the organic semiconductor is explained, and comparisons to laser sensors using alternative dye-doped materials are made. Specific biomolecular sensing is demonstrated, and routes to functionalisation with nucleic acid probes, and future developments opened up by this achievement, are highlighted. Finally, attractive formats for sensing applications are mentioned, as well as colloidal quantum dots, which in the future could be used in conjunction with organic semiconductors.

  18. THz time domain spectroscopy of biomolecular conformational modes

    International Nuclear Information System (INIS)

    Markelz, Andrea; Whitmire, Scott; Hillebrecht, Jay; Birge, Robert

    2002-01-01

    We discuss the use of terahertz time domain spectroscopy for studies of conformational flexibility and conformational change in biomolecules. Protein structural dynamics are vital to biological function with protein flexibility affecting enzymatic reaction rates and sensory transduction cycling times. Conformational mode dynamics occur on the picosecond timescale and with the collective vibrational modes associated with these large scale structural motions in the 1-100 cm -1 range. We have performed THz time domain spectroscopy (TTDS) of several biomolecular systems to explore the sensitivity of TTDS to distinguish different molecular species, different mutations within a single species and different conformations of a given biomolecule. We compare the measured absorbances to normal mode calculations and find that the TTDS absorbance reflects the density of normal modes determined by molecular mechanics calculations, and is sensitive to both conformation and mutation. These early studies demonstrate some of the advantages and limitations of using TTDS for the study of biomolecules

  19. High-speed AFM for Studying Dynamic Biomolecular Processes

    Science.gov (United States)

    Ando, Toshio

    2008-03-01

    Biological molecules show their vital activities only in aqueous solutions. It had been one of dreams in biological sciences to directly observe biological macromolecules (protein, DNA) at work under a physiological condition because such observation is straightforward to understanding their dynamic behaviors and functional mechanisms. Optical microscopy has no sufficient spatial resolution and electron microscopy is not applicable to in-liquid samples. Atomic force microscopy (AFM) can visualize molecules in liquids at high resolution but its imaging rate was too low to capture dynamic biological processes. This slow imaging rate is because AFM employs mechanical probes (cantilevers) and mechanical scanners to detect the sample height at each pixel. It is quite difficult to quickly move a mechanical device of macroscopic size with sub-nanometer accuracy without producing unwanted vibrations. It is also difficult to maintain the delicate contact between a probe tip and fragile samples. Two key techniques are required to realize high-speed AFM for biological research; fast feedback control to maintain a weak tip-sample interaction force and a technique to suppress mechanical vibrations of the scanner. Various efforts have been carried out in the past decade to materialize high-speed AFM. The current high-speed AFM can capture images on video at 30-60 frames/s for a scan range of 250nm and 100 scan lines, without significantly disturbing week biomolecular interaction. Our recent studies demonstrated that this new microscope can reveal biomolecular processes such as myosin V walking along actin tracks and association/dissociation dynamics of chaperonin GroEL-GroES that occurs in a negatively cooperative manner. The capacity of nanometer-scale visualization of dynamic processes in liquids will innovate on biological research. In addition, it will open a new way to study dynamic chemical/physical processes of various phenomena that occur at the liquid-solid interfaces.

  20. Integration of biomolecular logic gates with field-effect transducers

    Energy Technology Data Exchange (ETDEWEB)

    Poghossian, A., E-mail: a.poghossian@fz-juelich.de [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany); Malzahn, K. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Abouzar, M.H. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany); Mehndiratta, P. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Katz, E. [Department of Chemistry and Biomolecular Science, NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, NY 13699-5810 (United States); Schoening, M.J. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany)

    2011-11-01

    Highlights: > Enzyme-based AND/OR logic gates are integrated with a capacitive field-effect sensor. > The AND/OR logic gates compose of multi-enzyme system immobilised on sensor surface. > Logic gates were activated by different combinations of chemical inputs (analytes). > The logic output (pH change) produced by the enzymes was read out by the sensor. - Abstract: The integration of biomolecular logic gates with field-effect devices - the basic element of conventional electronic logic gates and computing - is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO{sub 2}-Ta{sub 2}O{sub 5} structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta{sub 2}O{sub 5}) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

  1. Integration of biomolecular logic gates with field-effect transducers

    International Nuclear Information System (INIS)

    Poghossian, A.; Malzahn, K.; Abouzar, M.H.; Mehndiratta, P.; Katz, E.; Schoening, M.J.

    2011-01-01

    Highlights: → Enzyme-based AND/OR logic gates are integrated with a capacitive field-effect sensor. → The AND/OR logic gates compose of multi-enzyme system immobilised on sensor surface. → Logic gates were activated by different combinations of chemical inputs (analytes). → The logic output (pH change) produced by the enzymes was read out by the sensor. - Abstract: The integration of biomolecular logic gates with field-effect devices - the basic element of conventional electronic logic gates and computing - is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO 2 -Ta 2 O 5 structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta 2 O 5 ) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

  2. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    International Nuclear Information System (INIS)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database

  3. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J. [eds.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database.

  4. Sea cucumbers reduce chromophoric dissolved organic matter in aquaculture tanks

    Directory of Open Access Journals (Sweden)

    Seyed Mohammad Sadeghi-Nassaj

    2018-02-01

    Full Text Available Background Mono-specific aquaculture effluents contain high concentrations of nutrients and organic matter, which affect negatively the water quality of the recipient ecosystems. A fundamental feature of water quality is its transparency. The fraction of dissolved organic matter that absorbs light is named chromophoric dissolved organic matter (CDOM. A sustainable alternative to mono-specific aquaculture is the multitrophic aquaculture that includes species trophically complementary named “extractive” species that uptake the waste byproducts. Sea cucumbers are recognized as efficient extractive species due to the consumption of particulate organic matter (POM. However, the effects of sea cucumbers on CDOM are still unknown. Methods During more than one year, we monitored CDOM in two big-volume tanks with different trophic structure. One of the tanks (−holothurian only contained around 810 individuals of Anemonia sulcata, whereas the other tank (+holothurian also included 90 individuals of Holothuria tubulosa and Holothuria forskali. We routinely analyzed CDOM absorption spectra and determined quantitative (absorption coefficients at 325 nm and qualitative (spectral slopes optical parameters in the inlet waters, within the tanks, and in their corresponding effluents. To confirm the time-series results, we also performed three experiments. Each experiment consisted of two treatments: +holothurians (+H and –holothurians (−H. We set up three +H tanks with 80 individuals of A. sulcata and 10 individuals of H. tubulosa in each tank and four –H tanks that contained only 80 individuals of A. sulcata. Results In the time-series, absorption coefficients at 325 nm (a325 and spectral slopes from 275 to 295 nm (S275−295 were significantly lower in the effluent of the +holothurian tank (average: 0.33 m−1 and 16 µm−1, respectively than in the effluent of the −holothurian tank (average: 0.69 m−1 and 34 µm−1, respectively, the former

  5. Proceedings of the international advisory committee on 'biomolecular dynamics instrument DNA' and the workshop on 'biomolecular dynamics backscattering spectrometers'

    International Nuclear Information System (INIS)

    Arai, Masatoshi; Aizawa, Kazuya; Nakajima, Kenji; Shibata, Kaoru; Takahashi, Nobuaki

    2008-08-01

    A workshop entitled 'Biomolecular Dynamics Backscattering Spectrometers' was held on February 27th - 29th, 2008 at J-PARC Center, Japan Atomic Energy Agency. This workshop was planned to be held for aiming to realize an innovative neutron backscattering instrument, namely DNA, in the MLF and thus four leading scientists in the field of neutron backscattering instruments were invited as the International Advisory Committee (IAC member: Dr. Dan Neumann (Chair); Prof. Ferenc Mezei; Dr. Hannu Mutka; Dr. Philip Tregenna-Piggott) for DNA from institutes in the United States, France and Switzerland, where backscattering instruments are in-service. It was therefore held in the form of lecture anterior and then in the form of the committee posterior. This report includes the executive summary of the IAC and materials of the presentations in the IAC and the workshop. (author)

  6. Chromophoric Dissolved Organic Material, Aqua MODIS, NPP, 0.125 degrees, East US

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — MODIS data is used to develop an index of the amount of chromophoric dissolved organic material (CDOM) in the surface waters. CDOM absorbs heavily in the blue...

  7. Chromophoric Dissolved Organic Material, Aqua MODIS, NPP, 0.125 degrees, West US

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — MODIS data is used to develop an index of the amount of chromophoric dissolved organic material (CDOM) in the surface waters. CDOM absorbs heavily in the blue...

  8. Preparation and optical characteristics of layered perovskite-type lead-bromide-incorporated azobenzene chromophores

    Science.gov (United States)

    Sasai, Ryo; Shinomura, Hisashi

    2013-02-01

    Lead bromide-based layered perovskite powders with azobenzene derivatives were prepared by a homogeneous precipitation method. From the diffuse reflectance (DR) and photoluminescence (PL) spectra of the hybrid powder materials, the present hybrids exhibited sharp absorption and PL peaks originating from excitons produced in the PbBr42- layer. When the present hybrid powder was irradiated with UV light at 350 nm, the absorption band from the trans-azobenzene chromophore, observed around 350 nm, decreased, while the absorption band from the cis-azobenzene chromophore, observed around 450 nm, increased. These results indicate that azobenzene chromophores in the present hybrid materials exhibit reversible photoisomerization. Moreover, it was found that the PL intensity from the exciton also varied due to photoisomerization of the azobenzene chromophores in the present hybrid. Thus, for the first time we succeeded in preparing the azobenzene derivative lead-bromide-based layered perovskite with photochromism before and after UV light irradiation.

  9. CHROMOPHORIC DISSOLVED ORGANIC MATTER (CDOM) SOURCE CHARACTERIZATION IN THE LOUISIANA BIGHT

    Science.gov (United States)

    Chromophoric dissolved organic matter (CDOM) in the Mississippi plume region may have several distinct sources: riverine (terrestrial soils), wetland (terrestrial plants), biological production (phytoplankton, zooplankton, microbial), and sediments. Complex mixing, photodegradati...

  10. CHROMOPHORIC DISSOLVED ORGANIC MATTER (CDOM) DERIVED FROM DECOMPOSITION OF VARIOUS VASCULAR PLANT AND ALGAL SOURCES

    Science.gov (United States)

    Chromophoric dissolved organic (CDOM) in aquatic environments is derived from the microbial decomposition of terrestrial and microbial organic matter. Here we present results of studies of the spectral properties and photoreactivity of the CDOM derived from several organic matter...

  11. Photobleaching Kinetics of Chromophoric Dissolved Organic Matter Derived from Mangrove Leaf Litter and Floating Sargassum Colonies

    Science.gov (United States)

    We examined the photoreactivity of chromophoric dissolved organic matter (CDOM) derived from Rhizophora mangle (red mangrove) leaf litter and floating Sargassum colonies as these marine plants can be important contributors to coastal and open ocean CDOM pools, respectively. Mangr...

  12. Chromophoric Dissolved Organic Material, Aqua MODIS, NPP, 0.125 degrees, Gulf of Mexico

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — MODIS data is used to develop an index of the amount of chromophoric dissolved organic material (CDOM) in the surface waters. CDOM absorbs heavily in the blue...

  13. Chromophoric Dissolved Organic Material, Aqua MODIS, NPP, 0.05 degrees, Global, Science Quality

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — MODIS data is used to develop an index of the amount of chromophoric dissolved organic material (CDOM) in the surface waters. CDOM absorbs heavily in the blue...

  14. Organic small molecule semiconducting chromophores for use in organic electronic devices

    Energy Technology Data Exchange (ETDEWEB)

    Welch, Gregory C.; Hoven, Corey V.; Nguyen, Thuc-Quyen

    2018-02-13

    Small organic molecule semi-conducting chromophores containing a pyridalthiadiazole, pyridaloxadiazole, or pyridaltriazole core structure are disclosed. Such compounds can be used in organic heterojunction devices, such as organic small molecule solar cells and transistors.

  15. Photo-fragmentation and electron-detachment studies of gas-phase chromophore ions

    DEFF Research Database (Denmark)

    Rahbek, Dennis Bo

    . Depending on the function of the protein, this may result in human vision, emission of light at a higher wavelength, fluorescence, or harvesting of energy used as an energy source by bacteria, algae or plants. The interaction between these chromophores and the surrounding protein is crucial for fine...... in terms of oscillator strength and excitation energies. Interestingly, the effects are similar for both of the chromophore families....

  16. The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores

    Science.gov (United States)

    Law, Y. K.; Hassanali, A. A.

    2018-03-01

    In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.

  17. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics

    KAUST Repository

    Sobhy, M. A.; Elshenawy, M. M.; Takahashi, Masateru; Whitman, B. H.; Walter, N. G.; Hamdan, S. M.

    2011-01-01

    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation

  18. Sulfates as chromophores for multiwavelength photoacoustic imaging phantoms

    Science.gov (United States)

    Fonseca, Martina; An, Lu; Beard, Paul; Cox, Ben

    2017-12-01

    As multiwavelength photoacoustic imaging becomes increasingly widely used to obtain quantitative estimates, the need for validation studies conducted on well-characterized experimental phantoms becomes ever more pressing. One challenge that such studies face is the design of stable, well-characterized phantoms and absorbers with properties in a physiologically realistic range. This paper performs a full experimental characterization of aqueous solutions of copper and nickel sulfate, whose properties make them close to ideal as chromophores in multiwavelength photoacoustic imaging phantoms. Their absorption varies linearly with concentration, and they mix linearly. The concentrations needed to yield absorption values within the physiological range are below the saturation limit. The shape of their absorption spectra makes them useful analogs for oxy- and deoxyhemoglobin. They display long-term photostability (no indication of bleaching) as well as resistance to transient effects (no saturable absorption phenomena), and are therefore suitable for exposure to typical pulsed photoacoustic light sources, even when exposed to the high number of pulses required in scanning photoacoustic imaging systems. In addition, solutions with tissue-realistic, predictable, and stable scattering can be prepared by mixing sulfates and Intralipid, as long as an appropriate emulsifier is used. Finally, the Grüneisen parameter of the sulfates was found to be larger than that of water and increased linearly with concentration.

  19. hPDB – Haskell library for processing atomic biomolecular structures in protein data bank format

    OpenAIRE

    Gajda, Michał Jan

    2013-01-01

    Background Protein DataBank file format is used for the majority of biomolecular data available today. Haskell is a lazy functional language that enjoys a high-level class-based type system, a growing collection of useful libraries and a reputation for efficiency. Findings I present a fast library for processing biomolecular data in the Protein Data Bank format. I present benchmarks indicating that this library is faster than other frequently used Protein Data Bank parsing programs. The propo...

  20. A compact hard X-ray source for medical imaging and biomolecular studies

    International Nuclear Information System (INIS)

    Cline, D.B.; Green, M.A.; Kolonko, J.

    1995-01-01

    There are a large number of synchrotron light sources in the world. However, these sources are designed for physics, chemistry, and engineering studies. To our knowledge, none have been optimized for either medical imaging or biomolecular studies. There are special needs for these applications. We present here a preliminary design of a very compact source, small enough for a hospital or a biomolecular laboratory, that is suitable for these applications. (orig.)

  1. Fluorescent sensors for selective detection of thiols: expanding the intramolecular displacement based mechanism to new chromophores.

    Science.gov (United States)

    Niu, Li-Ya; Zheng, Hai-Rong; Chen, Yu-Zhe; Wu, Li-Zhu; Tung, Chen-Ho; Yang, Qing-Zheng

    2014-03-21

    Biological thiols, including cysteine (Cys), homocystein (Hcy) and glutathione (GSH), play crucial roles in maintaining the appropriate redox status of biological systems. An abnormal level of biothiols is associated with different diseases, therefore, the discrimination between them is of great importance. Herein, we present two fluorescent sensors for selective detection of biothiols based on our recently reported intramolecular displacement mechanism. We expanded this mechanism to commercially available chromophores, 4-chloro-7-nitro-2,1,3-benzoxadiazole (NBD-Cl) and heptamethine cyanine dye IR-780. The sensors operate by undergoing displacement of chloride by thiolate. The amino groups of Cys/Hcy further replace the thiolate to form amino-substituted products, which exhibit dramatically different photophysical properties compared to sulfur-substituted products from the reaction with GSH. NBD-Cl is highly selective towards Cys/Hcy and exhibits significant fluorescence enhancement. IR-780 showed a variation in its fluorescence ratio towards Cys over other thiols. Both of the sensors can be used for live-cell imaging of Cys. The wide applicability of the mechanism may provide a powerful tool for developing novel fluorescent sensors for selective detection of biothiols.

  2. Absorption and fluorescence characteristics of chromophoric dissolved organic matter in the Yangtze Estuary.

    Science.gov (United States)

    Sun, Qiyuan; Wang, Chao; Wang, Peifang; Hou, Jun; Ao, Yanhui

    2014-03-01

    The Yangtze Estuary is heavily influenced by coast-continent geochemical processes and anthropogenic activity; thus, the source and distribution of chromophoric dissolved organic matter (CDOM) in the estuary are strongly impacted by these processes. Here, a series of samples were collected from across the Yangtze Estuary to investigate the source and spatial dynamics of CDOM and its components throughout the system. Three indices (a(355), spectral slope, and fluorescence) were then calculated and interpreted. The results indicated that the distribution of CDOM was dominated by allochthonous input, conservative mixing, and phase transfer. The contribution of biogenic CDOM to total CDOM increased with salinity, and three individual CDOM components were identified upon fluorescence excitation emission matrix spectroscopy and parallel factor analysis of the water samples: C1, corresponding to humic substance-like CDOM, C2, corresponding to tryptophan-like CDOM, and C3, corresponding to tyrosine-like CDOM. C1 primarily originated from a terrestrial source, C2 had widespread origins, none of which played a dominant role, and C3 mainly originated from allochthonous input in the medium salinity area. Unexpectedly, no marine humic-like component was found in the surface water of the Yangtze Estuary, possibly because turbidity decreased the depth of sunlight penetration, limiting production of this component.

  3. [Spectral characteristics variations of chromophoric dissolved organic matter during growth of filamentous green macroalgae].

    Science.gov (United States)

    Jiang, De-gang; Huang, Qing-hui; Li, Jian-hua

    2010-07-01

    As an important component of dissolved organic matter (DOM), chromophoric dissolved organic matter (CDOM) plays a central role in the global biogeochemical carbon cycle. Macroalgae are essential producers in aquatic ecosystems. They can release a considerable part of photosynthetic products as CDOM. So changes in optical properties of CDOM are studied on filamentous green macroalgae-Chadophorasle found in tidal flats of a brackish Lake Beihu in natural field condition by using spectrometry. Humic-like fluorescence peaks and protein-like fluorescence peaks detected by fluorescence excitation-emission matrix spectrum (EEMS) change little in control experiment but increase dramatically in incubation experiment. Applying parallel factor analysis (PARAFAC) together with fluorescence excitation-emission matrix can get four components of CDOM (C1, C2, C3 and C4) which are relative to humic-like fluorescence peak A(C), M and protein-like fluorescence peak B, T respectively. In incubation experiment four components increase by 211.5%, 255.8%, 75.3% and 129.3% respectively while in control experiment components have little changes except C1 decreasing by 34.3%. Absorption coefficient alpha (355) increases by 92.9% and has positive significant correlation (P CDOM molecular weight and composition, M and S values in incubation experiment are smaller than in control experiment, which illustrate that aromatic and macromolecular CDOM is produced in growth of Chadophorasle. All results indicate that growth of Chadophorasle can change the content and composition of CDOM.

  4. Phase sensitive spectral domain interferometry for label free biomolecular interaction analysis and biosensing applications

    Science.gov (United States)

    Chirvi, Sajal

    Biomolecular interaction analysis (BIA) plays vital role in wide variety of fields, which include biomedical research, pharmaceutical industry, medical diagnostics, and biotechnology industry. Study and quantification of interactions between natural biomolecules (proteins, enzymes, DNA) and artificially synthesized molecules (drugs) is routinely done using various labeled and label-free BIA techniques. Labeled BIA (Chemiluminescence, Fluorescence, Radioactive) techniques suffer from steric hindrance of labels on interaction site, difficulty of attaching labels to molecules, higher cost and time of assay development. Label free techniques with real time detection capabilities have demonstrated advantages over traditional labeled techniques. The gold standard for label free BIA is surface Plasmon resonance (SPR) that detects and quantifies the changes in refractive index of the ligand-analyte complex molecule with high sensitivity. Although SPR is a highly sensitive BIA technique, it requires custom-made sensor chips and is not well suited for highly multiplexed BIA required in high throughput applications. Moreover implementation of SPR on various biosensing platforms is limited. In this research work spectral domain phase sensitive interferometry (SD-PSI) has been developed for label-free BIA and biosensing applications to address limitations of SPR and other label free techniques. One distinct advantage of SD-PSI compared to other label-free techniques is that it does not require use of custom fabricated biosensor substrates. Laboratory grade, off-the-shelf glass or plastic substrates of suitable thickness with proper surface functionalization are used as biosensor chips. SD-PSI is tested on four separate BIA and biosensing platforms, which include multi-well plate, flow cell, fiber probe with integrated optics and fiber tip biosensor. Sensitivity of 33 ng/ml for anti-IgG is achieved using multi-well platform. Principle of coherence multiplexing for multi

  5. Dose controlled low energy electron irradiator for biomolecular films.

    Science.gov (United States)

    Kumar, S V K; Tare, Satej T; Upalekar, Yogesh V; Tsering, Thupten

    2016-03-01

    We have developed a multi target, Low Energy Electron (LEE), precise dose controlled irradiator for biomolecular films. Up to seven samples can be irradiated one after another at any preset electron energy and dose under UHV conditions without venting the chamber. In addition, one more sample goes through all the steps except irradiation, which can be used as control for comparison with the irradiated samples. All the samples are protected against stray electron irradiation by biasing them at -20 V during the entire period, except during irradiation. Ethernet based communication electronics hardware, LEE beam control electronics and computer interface were developed in house. The user Graphical User Interface to control the irradiation and dose measurement was developed using National Instruments Lab Windows CVI. The working and reliability of the dose controlled irradiator has been fully tested over the electron energy range of 0.5 to 500 eV by studying LEE induced single strand breaks to ΦX174 RF1 dsDNA.

  6. A fast mollified impulse method for biomolecular atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fath, L., E-mail: lukas.fath@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Hochbruck, M., E-mail: marlis.hochbruck@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Singh, C.V., E-mail: chandraveer.singh@utoronto.ca [Department of Materials Science & Engineering, University of Toronto (Canada)

    2017-03-15

    Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice–ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.

  7. Spin valve sensor for biomolecular identification: Design, fabrication, and characterization

    Science.gov (United States)

    Li, Guanxiong

    Biomolecular identification, e.g., DNA recognition, has broad applications in biology and medicine such as gene expression analysis, disease diagnosis, and DNA fingerprinting. Therefore, we have been developing a magnetic biodetection technology based on giant magnetoresistive spin valve sensors and magnetic nanoparticle (developed for the magnetic nanoparticle detection, assuming the equivalent average field of magnetic nanoparticles and the coherent rotation of spin valve free layer magnetization. Micromagnetic simulations have also been performed for the spin valve sensors. The analytical model and micromagnetic simulations are found consistent with each other and are in good agreement with experiments. The prototype spin valve sensors have been fabricated at both micron and submicron scales. We demonstrated the detection of a single 2.8-mum magnetic microbead by micron-sized spin valve sensors. Based on polymer-mediated self-assembly and fine lithography, a bilayer lift-off process was developed to deposit magnetic nanoparticles onto the sensor surface in a controlled manner. With the lift-off deposition method, we have successfully demonstrated the room temperature detection of monodisperse 16-nm Fe3O 4 nanoparticles in a quantity from a few tens to several hundreds by submicron spin valve sensors, proving the feasibility of the nanoparticle detection. As desired for quantitative biodetection, a fairly linear dependence of sensor signal on the number of nanoparticles has been confirmed. The initial detection of DNA hybridization events labeled by magnetic nanoparticles further proved the magnetic biodetection concept.

  8. Dose controlled low energy electron irradiator for biomolecular films

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, S. V. K., E-mail: svkk@tifr.res.in; Tare, Satej T.; Upalekar, Yogesh V.; Tsering, Thupten [Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005 (India)

    2016-03-15

    We have developed a multi target, Low Energy Electron (LEE), precise dose controlled irradiator for biomolecular films. Up to seven samples can be irradiated one after another at any preset electron energy and dose under UHV conditions without venting the chamber. In addition, one more sample goes through all the steps except irradiation, which can be used as control for comparison with the irradiated samples. All the samples are protected against stray electron irradiation by biasing them at −20 V during the entire period, except during irradiation. Ethernet based communication electronics hardware, LEE beam control electronics and computer interface were developed in house. The user Graphical User Interface to control the irradiation and dose measurement was developed using National Instruments Lab Windows CVI. The working and reliability of the dose controlled irradiator has been fully tested over the electron energy range of 0.5 to 500 eV by studying LEE induced single strand breaks to ΦX174 RF1 dsDNA.

  9. A biomolecular proportional integral controller based on feedback regulations of protein level and activity.

    Science.gov (United States)

    Mairet, Francis

    2018-02-01

    Homeostasis is the capacity of living organisms to keep internal conditions regulated at a constant level, despite environmental fluctuations. Integral feedback control is known to play a key role in this behaviour. Here, I show that a feedback system involving transcriptional and post-translational regulations of the same executor protein acts as a proportional integral (PI) controller, leading to enhanced transient performances in comparison with a classical integral loop. Such a biomolecular controller-which I call a level and activity-PI controller (LA-PI)-is involved in the regulation of ammonium uptake by Escherichia coli through the transporter AmtB. The P II molecules, which reflect the nitrogen status of the cell, inhibit both the production of AmtB and its activity (via the NtrB-NtrC system and the formation of a complex with GlnK, respectively). Other examples of LA-PI controller include copper and zinc transporters, and the redox regulation in photosynthesis. This scheme has thus emerged through evolution in many biological systems, surely because of the benefits it offers in terms of performances (rapid and perfect adaptation) and economy (protein production according to needs).

  10. Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

    Science.gov (United States)

    Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha

    2018-02-05

    Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Cancer genetics meets biomolecular mechanism-bridging an age-old gulf.

    Science.gov (United States)

    González-Sánchez, Juan Carlos; Raimondi, Francesco; Russell, Robert B

    2018-02-01

    Increasingly available genomic sequencing data are exploited to identify genes and variants contributing to diseases, particularly cancer. Traditionally, methods to find such variants have relied heavily on allele frequency and/or familial history, often neglecting to consider any mechanistic understanding of their functional consequences. Thus, while the set of known cancer-related genes has increased, for many, their mechanistic role in the disease is not completely understood. This issue highlights a wide gap between the disciplines of genetics, which largely aims to correlate genetic events with phenotype, and molecular biology, which ultimately aims at a mechanistic understanding of biological processes. Fortunately, new methods and several systematic studies have proved illuminating for many disease genes and variants by integrating sequencing with mechanistic data, including biomolecular structures and interactions. These have provided new interpretations for known mutations and suggested new disease-relevant variants and genes. Here, we review these approaches and discuss particular examples where these have had a profound impact on the understanding of human cancers. © 2018 Federation of European Biochemical Societies.

  12. Dielectric Properties of Azo Polymers: Effect of the Push-Pull Azo Chromophores

    Directory of Open Access Journals (Sweden)

    Xuan Zhang

    2018-01-01

    Full Text Available The relationship between the structure and the dielectric properties of the azo polymers was studied. Four azo polymers were synthesized through the azo-coupling reaction between the same precursor (PAZ and diazonium salts of 4-aminobenzoic acid ethyl ester, 4-aminobenzonitrile, 4-nitroaniline, and 2-amino-5-nitrothiazole, respectively. The precursor and azo polymers were characterized by 1H NMR, FT-IR, UV-vis, GPC, and DSC. The dielectric constant and dielectric loss of the samples were measured in the frequency range of 100 Hz–200 kHz. Due to the existence of the azo chromophores, the dielectric constant of the azo polymers increases compared with that of the precursor. In addition, the dielectric constant of the azo polymers increases with the increase of the polarity of the azo chromophores. A random copolymer (PAZ-NT-PAZ composed of the azo polymer PAZ-NT and the precursor PAZ was also prepared to investigate the content of the azo chromophores on the dielectric properties of the azo polymers. It showed that the dielectric constant increases with the increase of the azo chromophores. The results show that the dielectric constant of this kind of azo polymers can be controlled by changing the structures and contents of azo chromophores during the preparation process.

  13. Photophysics of organometallic platinum(II) derivatives of the diketopyrrolopyrrole chromophore

    KAUST Repository

    Goswami, Subhadip

    2014-12-18

    A pair of diketopyrrolopyrrole (DPP) chromophores that are end-functionalized with platinum containing "auxochromes" were subjected to electrochemical and photophysical study. The chromophores contain either platinum acetylide or ortho-metalated 2-thienylpyridinyl(platinum) end-groups (DPP-Pt(CC) and DPP-Pt(acac), respectively). The ground state redox potentials of the chromophores were determined by solution electrochemistry, and the HOMO and LUMO levels were estimated. The chromophores\\' photophysical properties were characterized by absorption, photoluminescence, and time-resolved absorption spectroscopy on time scales from sub-picoseconds to microseconds. Density functional theory (DFT) computations were performed to understand the molecular orbitals involved in both the singlet and triplet excited state photophysics. The results reveal that in both platinum DPP derivatives the organometallic auxochromes have a significant effect on the chromophores\\' photophysics. The most profound effect is a reduction in the fluorescence yields accompanied by enhanced triplet yields due to spin-orbit coupling induced by the metal centers. The effects are most pronounced in DPP-Pt(acac), indicating that the orthometalated platinum auxochrome is able to induce spin-orbital coupling to a greater extent compared to the platinum acetylide units. (Figure Presented).

  14. Tautomeric forms of PPI dendrimers functionalized with 4-(4′-ethoxybenzoyloxy)salicylaldehyde chromophores

    International Nuclear Information System (INIS)

    Franckevičius, M.; Vaišnoras, R.; Marcos, M.; Serrano, J.L.; Gruodis, A.; Galikova, N.; Gulbinas, V.

    2012-01-01

    Highlights: ► SA chromophore groups are formed by bonding terminal groups to PPI dendrimers. ► SA chromophore groups reveal four most stable tautomeric forms. ► Tautomeric properties of SA groups depend on the dendrimer generation and solvent. ► Aggregation of SA chromophores facilitates formation of the trans-keto tautomers. ► Fluorescence of PPI SA dendrimers is attributed to nπ ∗ states of keto tautomers. -- Abstract: Bonding of the promesogenic unit derived from 4-(4′-ethoxybenzoyloxy)salicylaldehyde to the amino terminated PPI dendrimer chains results in formation of the salicylidenimine chromophore groups. Absorption and fluorescence investigations of the dendrimer solutions supported by the quantum chemistry calculations revealed that the chromophore groups may exist in enol and keto tautomeric forms with relative concentrations depending on the dendrimer generation and solvent. The dendrimer fluorescence is attributed to nπ ∗ states of keto tautomers which may also be formed from excited enol tautomers.

  15. Photophysics of organometallic platinum(II) derivatives of the diketopyrrolopyrrole chromophore

    KAUST Repository

    Goswami, Subhadip; Winkel, Russell W.; Alarousu, Erkki; Ghiviriga, Ion; Mohammed, Omar F.; Schanze, Kirk S.

    2014-01-01

    A pair of diketopyrrolopyrrole (DPP) chromophores that are end-functionalized with platinum containing "auxochromes" were subjected to electrochemical and photophysical study. The chromophores contain either platinum acetylide or ortho-metalated 2-thienylpyridinyl(platinum) end-groups (DPP-Pt(CC) and DPP-Pt(acac), respectively). The ground state redox potentials of the chromophores were determined by solution electrochemistry, and the HOMO and LUMO levels were estimated. The chromophores' photophysical properties were characterized by absorption, photoluminescence, and time-resolved absorption spectroscopy on time scales from sub-picoseconds to microseconds. Density functional theory (DFT) computations were performed to understand the molecular orbitals involved in both the singlet and triplet excited state photophysics. The results reveal that in both platinum DPP derivatives the organometallic auxochromes have a significant effect on the chromophores' photophysics. The most profound effect is a reduction in the fluorescence yields accompanied by enhanced triplet yields due to spin-orbit coupling induced by the metal centers. The effects are most pronounced in DPP-Pt(acac), indicating that the orthometalated platinum auxochrome is able to induce spin-orbital coupling to a greater extent compared to the platinum acetylide units. (Figure Presented).

  16. Biomolecular detection using a metal semiconductor field effect transistor

    Science.gov (United States)

    Estephan, Elias; Saab, Marie-Belle; Buzatu, Petre; Aulombard, Roger; Cuisinier, Frédéric J. G.; Gergely, Csilla; Cloitre, Thierry

    2010-04-01

    In this work, our attention was drawn towards developing affinity-based electrical biosensors, using a MESFET (Metal Semiconductor Field Effect Transistor). Semiconductor (SC) surfaces must be prepared before the incubations with biomolecules. The peptides route was adapted to exceed and bypass the limits revealed by other types of surface modification due to the unwanted unspecific interactions. As these peptides reveal specific recognition of materials, then controlled functionalization can be achieved. Peptides were produced by phage display technology using a library of M13 bacteriophage. After several rounds of bio-panning, the phages presenting affinities for GaAs SC were isolated; the DNA of these specific phages were sequenced, and the peptide with the highest affinity was synthesized and biotinylated. To explore the possibility of electrical detection, the MESFET fabricated with the GaAs SC were used to detect the streptavidin via the biotinylated peptide in the presence of the bovine Serum Albumin. After each surface modification step, the IDS (current between the drain and the source) of the transistor was measured and a decrease in the intensity was detected. Furthermore, fluorescent microscopy was used in order to prove the specificity of this peptide and the specific localisation of biomolecules. In conclusion, the feasibility of producing an electrical biosensor using a MESFET has been demonstrated. Controlled placement, specific localization and detection of biomolecules on a MESFET transistor were achieved without covering the drain and the source. This method of functionalization and detection can be of great utility for biosensing application opening a new way for developing bioFETs (Biomolecular Field-Effect Transistor).

  17. Evolution of biomolecular loadings along a major river system

    Science.gov (United States)

    Freymond, Chantal V.; Kündig, Nicole; Stark, Courcelle; Peterse, Francien; Buggle, Björn; Lupker, Maarten; Plötze, Michael; Blattmann, Thomas M.; Filip, Florin; Giosan, Liviu; Eglinton, Timothy I.

    2018-02-01

    Understanding the transport history and fate of organic carbon (OC) within river systems is crucial in order to constrain the dynamics and significance of land-ocean interactions as a component of the global carbon cycle. Fluvial export and burial of terrestrial OC in marine sediments influences atmospheric CO2 over a range of timescales, while river-dominated sedimentary sequences can provide valuable archives of paleoenvironmental information. While there is abundant evidence that the association of organic matter (OM) with minerals exerts an important influence on its stability as well as hydrodynamic behavior in aquatic systems, there is a paucity of information on where such associations form and how they evolve during fluvial transport. Here, we track total organic carbon (TOC) and terrestrial biomarker concentrations (plant wax-derived long-chain fatty acids (FA), branched glycerol dialkyl glycerol tetraethers (brGDGTs) and lignin-derived phenols) in sediments collected along the entire course of the Danube River system in the context of sedimentological parameters. Mineral-specific surface area-normalized biomarker and TOC concentrations show a systematic decrease from the upper to the lower Danube basin. Changes in OM loading of the available mineral phase correspond to a net decrease of 70-80% of different biomolecular components. Ranges for biomarker loadings on Danube River sediments, corresponding to 0.4-1.5 μgFA/m2 for long-chain (n-C24-32) fatty acids and 17-71 ngbrGDGT/m2 for brGDGTs, are proposed as a benchmark for comparison with other systems. We propose that normalizing TOC as well as biomarker concentrations to mineral surface area provides valuable quantitative constraints on OM dynamics and organo-mineral interactions during fluvial transport from terrigenous source to oceanic sink.

  18. Soft Supercharging of Biomolecular Ions in Electrospray Ionization Mass Spectrometry

    Science.gov (United States)

    Chingin, Konstantin; Xu, Ning; Chen, Huanwen

    2014-06-01

    The charge states of biomolecular ions in ESI-MS can be significantly increased by the addition of low-vapor supercharging (SC) reagents into the spraying solution. Despite the considerable interest from the community, the mechanistic aspects of SC are not well understood and are hotly debated. Arguments that denaturation accounts for the increased charging observed in proteins sprayed from aqueous solutions containing SC reagent have been published widely, but often with incomplete or ambiguous supporting data. In this work, we explored ESI MS charging and SC behavior of several biopolymers including proteins and DNA oligonucleotides. Analytes were ionized from 100 mM ammonium acetate (NH4Ac) aqueous buffer in both positive (ESI+) and negative (ESI-) ion modes. SC was induced either with m-NBA or by the elevated temperature of ESI capillary. For all the analytes studied we, found striking differences in the ESI MS response to these two modes of activation. The data suggest that activation with m-NBA results in more extensive analyte charging with lower degree of denaturation. When working solution with m-NBA was analyzed at elevated temperatures, the SC effect from m-NBA was neutralized. Instead, the net SC effect was similar to the SC effect achieved by thermal activation only. Overall, our observations indicate that SC reagents enhance ESI charging of biomolecules via distinctly different mechanism compared with the traditional approaches based on analyte denaturation. Instead, the data support the hypothesis that the SC phenomenon involves a direct interaction between a biopolymer and SC reagent occurring in evaporating ESI droplets.

  19. Studies of the charge instabilities in the complex nano-objects: clusters and bio-molecular systems

    International Nuclear Information System (INIS)

    Manil, B.

    2007-11-01

    For the last 6 years, my main research works focused on i) the Coulomb instabilities and the fragmentation processes of fullerenes and clusters of fullerenes ii) the stability and the reactivity of complex bio-molecular systems. Concerning the clusters of fullerenes, which are van der Waals type clusters, we have shown that the multiply charged species, obtained in collisions with slow highly charged ions, keep their structural properties but become very good electric conductor. In another hand, with the aim to understand the role of the biologic environment at the molecular scale in the irradiation damage of complex biomolecules, we have studied the charge stabilities of clusters of small biomolecules and the dissociation processes of larger nano-hydrated biomolecules. Theses studies have shown that first, specific molecular recognition mechanisms continue to exist in gas phase and secondly, a small and very simple biochemical environment is enough to change the dynamics of instabilities. (author)

  20. Computational methods to study the structure and dynamics of biomolecules and biomolecular processes from bioinformatics to molecular quantum mechanics

    CERN Document Server

    2014-01-01

    Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over t...

  1. Synthesis of Dendrimer Containing Carbazole Unit as a Core Chromophore

    International Nuclear Information System (INIS)

    Han, Seung Choul; Lee, Jae Wook; Jin, Sungho

    2012-01-01

    Dendrimers, which are prepared by repetition of a given set of reactions using either divergent or convergent strategies, are highly branched and regular macromolecules with well-defined structures and have served as functional objects in nanotechnology and nano-materials science. Following conventional organic small molecules and polymers, dendrimers are now regarded as the third class of materials for use in organic light-emitting diodes (OLEDs) and have attracted much attention due to their distinguished properties. Dendrimers contain three distinct structural parts that are the core, end-groups, and branched units connecting core and periphery. For light-emitting dendrimers, the core is usually selected as the luminescent chromophore, and the dendrons and their periphery are charge transporting units and can also tune the solubility. In contrast to linear polymers, dendrimers are sphere-like with dimensions of the order of nanometers depending on the generation number. By careful structural design, dendrimers combine the potential advantages of both small molecules and polymers. Therefore, the innovative strategy different from conventional convergent and divergent routes has been required to simplify dendrimer synthesis. Recent solid chemistry is the click chemistry which is the copper-catalyzed 1,3-dipolar cycloaddition reaction between alkyne and azide developed by Sharpless and Tornφe. This reaction has many advantages: very high yields, mild and simple reaction conditions, oxygen and water tolerance, and easy isolation of product. This reaction is clearly a breakthrough in the synthesis of dendrimers and dendritic and polymer materials. We have developed the fusion and stitching methods for the synthesis of various dendrimers using click chemistry between an alkyne and an azide. Overall, this method was found to be a straightforward strategy for the synthesis of triazole-based dendrimers. Taking advantage of this fact, herein we report a feasible route

  2. Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.

    Science.gov (United States)

    Thibault, J C; Roe, D R; Eilbeck, K; Cheatham, T E; Facelli, J C

    2015-01-01

    Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that are biologically significant. Molecular simulations have become a standard tool for toxicology and pharmacology research, but organizing and sharing data - both within the same organization and among different ones - remains a substantial challenge. In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data. Our efforts include the design of data models and dictionary tools that allow the standardization of the metadata used to describe the biomedical simulations, the development of a thesaurus and ontology for computational reasoning when searching for biomolecular simulations in distributed environments, and the development of systems based on these models to manage and share the data at a large scale (iBIOMES), and within smaller groups of researchers at laboratory scale (iBIOMES Lite), that take advantage of the standardization of the meta data used to describe biomolecular simulations.

  3. Chemical modification of glass surface with a monolayer of nonchromophoric and chromophoric methacrylate terpolymer

    Energy Technology Data Exchange (ETDEWEB)

    Janik, Ryszard [Department of Polymer Engineering and Technology, Wroclaw University of Technology, 50-370 Wroclaw (Poland); Kucharski, Stanislaw, E-mail: stanislaw.kucharski@pwr.wroc.pl [Department of Polymer Engineering and Technology, Wroclaw University of Technology, 50-370 Wroclaw (Poland); Sobolewska, Anna [Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, 50-370 Wroclaw (Poland); Barille, Regis [Institut des Sciences et Techniques Moleculaires d' Angers ' Moltech Anjou' , CNRS UMR 6200, 49045 Angers (France)

    2010-11-15

    The methacrylate terpolymers, a nonchromophoric and chromophoric one, containing 2-hydroxyethyl groups were reacted with 3-isocyanatopropyltriethoxysilane to obtain reactive polymers able to form covalent bonding with -SiOH groups of the glass surface via triethoxysilane group condensation. Chemical modification of the Corning 2949 glass plates treated in this way resulted in increase of wetting angle from 11{sup o} to ca. 70-73{sup o}. Determination of ellipsometric parameters revealed low value of the substrate refractive index as compared with that of bulk Corning 2949 glass suggesting roughness of the surface. The AFM image of the bare glass surface and that modified with terpolymer monolayer confirmed this phenomenon. Modification of the glass with the terpolymer monolayer made it possible to create the substrate surface well suited for deposition of familiar chromophore film by spin-coating. The chromophore polymer film deposited onto the modified glass surface was found to be resistant to come unstuck in aqueous solution.

  4. Stabilization of structure in near-infrared fluorescent proteins by binding of biliverdin chromophore

    Science.gov (United States)

    Stepanenko, Olesya V.; Stepanenko, Olga V.; Bublikov, G. S.; Kuznetsova, I. M.; Verkhusha, V. V.; Turoverov, K. K.

    2017-07-01

    Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes and their mutants with different location of Cys residues, which able to bind a biliverdin chromophore, or without these Cys residues were studied using intrinsic tryptophan fluorescence, NIR fluorescence and circular dichroism. It was shown that a covalent binding of the biliverdin chromophore to a Cys residue via thioether group substantially stabilizes the spatial structure of NIR FPs. The stability of the protein structure and the chromophore association strength strongly depends on the location of Cys residues and decreases in the following order: a protein with Cys residues in both domains, a protein with Cys in PAS domains, and a protein with Cys in GAF domains. NIR FPs without Cys residues capable to covalently attach biliverdin have the lowest stability, comparable to NIR FP apoforms.

  5. Quantitative analysis of valence photoemission spectra and quasiparticle excitations at chromophore-semiconductor interfaces.

    Science.gov (United States)

    Patrick, Christopher E; Giustino, Feliciano

    2012-09-14

    Investigating quasiparticle excitations of molecules on surfaces through photoemission spectroscopy forms a major part of nanotechnology research. Resolving spectral features at these interfaces requires a comprehensive theory of electron removal and addition processes in molecules and solids which captures the complex interplay of image charges, thermal effects, and configurational disorder. Here, we develop such a theory and calculate the quasiparticle energy-level alignment and the valence photoemission spectrum for the prototype biomimetic solar cell interface between anatase TiO(2) and the N3 chromophore. By directly matching our calculated photoemission spectrum to experimental data, we clarify the atomistic origin of the chromophore peak at low binding energy. This case study sets a new standard in the interpretation of photoemission spectroscopy at complex chromophore-semiconductor interfaces.

  6. Optomechanical Control of Quantum Yield in Trans-Cis Ultrafast Photoisomerization of a Retinal Chromophore Model.

    Science.gov (United States)

    Valentini, Alessio; Rivero, Daniel; Zapata, Felipe; García-Iriepa, Cristina; Marazzi, Marco; Palmeiro, Raúl; Fdez Galván, Ignacio; Sampedro, Diego; Olivucci, Massimo; Frutos, Luis Manuel

    2017-03-27

    The quantum yield of a photochemical reaction is one of the most fundamental quantities in photochemistry, as it measures the efficiency of the transduction of light energy into chemical energy. Nature has evolved photoreceptors in which the reactivity of a chromophore is enhanced by its molecular environment to achieve high quantum yields. The retinal chromophore sterically constrained inside rhodopsin proteins represents an outstanding example of such a control. In a more general framework, mechanical forces acting on a molecular system can strongly modify its reactivity. Herein, we show that the exertion of tensile forces on a simplified retinal chromophore model provokes a substantial and regular increase in the trans-to-cis photoisomerization quantum yield in a counterintuitive way, as these extension forces facilitate the formation of the more compressed cis photoisomer. A rationale for the mechanochemical effect on this photoisomerization mechanism is also proposed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Effect of some colloid surfactants on spectrophotometric characteristics of metal chelates with chromophore organic reagents

    International Nuclear Information System (INIS)

    Chernova, R.K.

    1977-01-01

    Theoretical regularities and prospects of using surface active substances (SAS) in spectrophotometric determination of metal ions (including ions of rare-earth elements, transition metals, Be(3)) with chromophore chelating reagents were investigated. The chromophore reagents investigated were pyrocatechol violet, phenolcarboxylic acids of the triarylmethane series, fluorones, phthalexones and azo-compounds. As SAS certain long-chain quaternary ammonium and pyridinium salts (LQAS) were employed. From the results reported it follows that the introduction of LQAS in the system of Mesup(n+)-chromophore reagent is a rather effective method of enhancing the contrast rendition and, in some cases, the sensitivity and selectivity of the reagents. Explanations are suggested as to the factors which cause the changes observed in the contrast of the reactions in the presence of SAS; the underlying phenomena are the ligand-ligand interactions between the organic reagents and SAS and solubilization processes of the reaction products by the micelles of SAS

  8. Solid state supramolecular structure of diketopyrrolopyrrole chromophores: correlating stacking geometry with visible light absorption

    OpenAIRE

    Pop, Flavia; Lewis, William; Amabilino, David B.

    2016-01-01

    Mono- and di-alkylated 1,4-diketo-3,6-dithiophenylpyrrolo[3-4-c]pyrrole derivatives (TDPPs) have been synthesised and their solid state packing and absorption properties have been correlated. In this library of compounds the bulkier substituents distort the geometry of the chromophores and shift the lowest energy absorption band as a consequence of reduced π–π stacking and inter-chromophore overlap. Longitudinal displacement of the conjugated core is affected by donor–acceptor intermolecular ...

  9. Performance of Popular XC-Functionals for the Description of Excitation Energies in GFP-Like Chromophore Models

    DEFF Research Database (Denmark)

    List, Nanna Holmgaard; Olsen, Jógvan Magnus Haugaard; Rocha-Rinza, Tomás

    2012-01-01

    this task. We present an evaluation of the performance of commonly used XC-functionals for the prediction of excitation energies of GFP-like chromophores. In particular, we have considered the TD-DFT vertical excitation energies of chromophores displaying different charge states. We compare the quality...

  10. Removal of Chromophore-proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor

    Directory of Open Access Journals (Sweden)

    Heli eLehtivuori

    2015-11-01

    Full Text Available Genetically encoded fluorescent markers have revolutionized cell and molecular biology due to their biological compatibility, controllable spatiotemporal expression, and photostability. To achieve in vivo imaging in whole animals, longer excitation wavelength probes are needed due to the superior ability of near infrared light to penetrate tissues unimpeded by absorbance from biomolecules or autofluorescence of water. Derived from near infrared-absorbing bacteriophytochromes, phytofluors are engineered to fluoresce in this region of the electromagnetic spectrum, although high quantum yield remains an elusive goal. An invariant aspartate residue is of utmost importance for photoconversion in native phytochromes, presumably due to the proximity of its backbone carbonyl to the pyrrole ring nitrogens of the biliverdin (BV chromophore as well as the size and charge of the side chain. We hypothesized that the polar interaction network formed by the charged side chain may contribute to the decay of the excited state via proton transfer. Thus, we chose to further probe the role of this amino acid by removing all possibility for polar interactions with its carboxylate side chain by incorporating leucine instead. The resultant fluorescent protein, WiPhy2, maintains BV binding, monomeric status, and long maximum excitation wavelength while minimizing undesirable protoporphyrin IXα binding in cells. A crystal structure and time-resolved fluorescence spectroscopy reveal that water near the BV chromophore is excluded and thus validate our hypothesis that removal of polar interactions leads to enhanced fluorescence by increasing the lifetime of the excited state. This new phytofluor maintains its fluorescent properties over a broad pH range and does not suffer from photobleaching. WiPhy2 achieves the best compromise to date between high fluorescence quantum yield and long illumination wavelength in this class of fluorescent proteins.

  11. Engineering intracellular active transport systems as in vivo biomolecular tools.

    Energy Technology Data Exchange (ETDEWEB)

    Bachand, George David; Carroll-Portillo, Amanda

    2006-11-01

    Active transport systems provide essential functions in terms of cell physiology and metastasis. These systems, however, are also co-opted by invading viruses, enabling directed transport of the virus to and from the cell's nucleus (i.e., the site of virus replication). Based on this concept, fundamentally new approaches for interrogating and manipulating the inner workings of living cells may be achievable by co-opting Nature's active transport systems as an in vivo biomolecular tool. The overall goal of this project was to investigate the ability to engineer kinesin-based transport systems for in vivo applications, specifically the collection of effector proteins (e.g., transcriptional regulators) within single cells. In the first part of this project, a chimeric fusion protein consisting of kinesin and a single chain variable fragment (scFv) of an antibody was successfully produced through a recombinant expression system. The kinesin-scFv retained both catalytic and antigenic functionality, enabling selective capture and transport of target antigens. The incorporation of a rabbit IgG-specific scFv into the kinesin established a generalized system for functionalizing kinesin with a wide range of target-selective antibodies raised in rabbits. The second objective was to develop methods of isolating the intact microtubule network from live cells as a platform for evaluating kinesin-based transport within the cytoskeletal architecture of a cell. Successful isolation of intact microtubule networks from two distinct cell types was demonstrated using glutaraldehyde and methanol fixation methods. This work provides a platform for inferring the ability of kinesin-scFv to function in vivo, and may also serve as a three-dimensional scaffold for evaluating and exploiting kinesin-based transport for nanotechnological applications. Overall, the technology developed in this project represents a first-step in engineering active transport system for in vivo

  12. Sources and transformations of dissolved lignin phenols and chromophoric dissolved organic matter in Otsuchi Bay, Japan

    Directory of Open Access Journals (Sweden)

    Chia-Jung eLu

    2016-06-01

    Full Text Available Dissolved lignin phenols and optical properties of dissolved organic matter (DOM were measured to investigate the sources and transformations of terrigenous DOM (tDOM in Otsuchi Bay, Japan. Three rivers discharge into the bay, and relatively high values of syringyl:vanillyl phenols (0.73 ± 0.07 and cinnamyl:vanillyl phenols (0.33 ± 0.10 indicated large contributions of non-woody angiosperm tissues to lignin and tDOM. The physical mixing of river and seawater played an important role in controlling the concentrations and distributions of lignin phenols and chromophoric DOM (CDOM optical properties in the bay. Lignin phenol concentrations and the CDOM absorption coefficient at 350 nm, a(350, were strongly correlated in river and bay waters. Measurements of lignin phenols and CDOM in bay waters indicated a variety of photochemical and biological transformations of tDOM, including oxidation reactions, photobleaching and a decrease in molecular weight. Photodegradation and biodegradation of lignin and CDOM were investigated in decomposition experiments with river water and native microbial assemblages exposed to natural sunlight or kept in the dark. There was a rapid and substantial removal of lignin phenols and CDOM during the first few days in the light treatment, indicating transformations of tDOM and CDOM can occur soon after discharge of buoyant river water into the bay. The removal of lignin phenols was slightly greater in the dark (34% than in the light (30% during the remaining 59 days of the incubation. Comparison of the light and dark treatments indicated biodegradation was responsible for 67% of total lignin phenol removal during the 62-day incubation exposed to natural sunlight, indicating biodegradation is a dominant removal process in Otsuchi Bay.

  13. Formation of Chromophoric Dissolved Organic Matter by Bacterial Degradation of Phytoplankton-Derived Aggregates

    Directory of Open Access Journals (Sweden)

    Joanna D. Kinsey

    2018-01-01

    Full Text Available Organic matter produced and released by phytoplankton during growth is processed by heterotrophic bacterial communities that transform dissolved organic matter into biomass and recycle inorganic nutrients, fueling microbial food web interactions. Bacterial transformation of phytoplankton-derived organic matter also plays a poorly known role in the formation of chromophoric dissolved organic matter (CDOM which is ubiquitous in the ocean. Despite the importance of organic matter cycling, growth of phytoplankton and activities of heterotrophic bacterial communities are rarely measured in concert. To investigate CDOM formation mediated by microbial processing of phytoplankton-derived aggregates, we conducted growth experiments with non-axenic monocultures of three diatoms (Skeletonema grethae, Leptocylindrus hargravesii, Coscinodiscus sp. and one haptophyte (Phaeocystis globosa. Phytoplankton biomass, carbon concentrations, CDOM and base-extracted particulate organic matter (BEPOM fluorescence, along with bacterial abundance and hydrolytic enzyme activities (α-glucosidase, β-glucosidase, leucine-aminopeptidase were measured during exponential growth and stationary phase (~3–6 weeks and following 6 weeks of degradation. Incubations were performed in rotating glass bottles to keep cells suspended, promoting cell coagulation and, thus, formation of macroscopic aggregates (marine snow, more similar to surface ocean processes. Maximum carbon concentrations, enzyme activities, and BEPOM fluorescence occurred during stationary phase. Net DOC concentrations (0.19–0.46 mg C L−1 increased on the same order as open ocean concentrations. CDOM fluorescence was dominated by protein-like signals that increased throughout growth and degradation becoming increasingly humic-like, implying the production of more complex molecules from planktonic-precursors mediated by microbial processing. Our experimental results suggest that at least a portion of open

  14. Chromophoric Dissolved Organic Matter across a Marine Distributed Biological Observatory in the Pacific Arctic Region

    Science.gov (United States)

    Berman, S. L.; Frey, K. E.; Shake, K. L.; Cooper, L. W.; Grebmeier, J. M.

    2014-12-01

    Dissolved organic matter (DOM) plays an important role in marine ecosystems as both a carbon source for the microbial food web (and thus a source of CO2 to the atmosphere) and as a light inhibitor in marine environments. The presence of chromophoric dissolved organic matter (CDOM; the optically active portion of total DOM) can have significant controlling effects on transmittance of sunlight through the water column and therefore on primary production as well as the heat balance of the upper ocean. However, CDOM is also susceptible to photochemical degradation, which decreases the flux of solar radiation that is absorbed. Knowledge of the current spatial and temporal distribution of CDOM in marine environments is thus critical for understanding how ongoing and future changes in climate may impact these biological, biogeochemical, and physical processes. We describe the quantity and quality of CDOM along five key productive transects across a developing Distributed Biological Observatory (DBO) in the Pacific Arctic region. The samples were collected onboard the CCGS Sir Wilfred Laurier in July 2013 and 2014. Monitoring of the variability of CDOM along transects of high productivity can provide important insights into biological and biogeochemical cycling across the region. Our analyses include overall concentrations of CDOM, as well as proxy information such as molecular weight, lability, and source (i.e., autochthonous vs. allochthonous) of organic matter. We utilize these field observations to compare with satellite-derived CDOM concentrations determined from the Aqua MODIS satellite platform, which ultimately provides a spatially and temporally continuous synoptic view of CDOM concentrations throughout the region. Examining the current relationships among CDOM, sea ice variability, biological productivity, and biogeochemical cycling in the Pacific Arctic region will likely provide key insights for how ecosystems throughout the region will respond in future

  15. ATR-FTIR Spectroscopic Evidence for Biomolecular Phosphorus and Carboxyl Groups Facilitating Bacterial Adhesion to Iron Oxides

    Science.gov (United States)

    Parikh, Sanjai J.; Mukome, Fungai N.D.; Zhang, Xiaoming

    2014-01-01

    Attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy has been used to probe the binding of bacteria to hematite (α-Fe2O3) and goethite (α-FeOOH). In situ ATR-FTIR experiments with bacteria (Pseudomonas putida, P. aeruginosa, Escherichia coli), mixed amino acids, polypeptide extracts, deoxyribonucleic acid (DNA), and a suite of model compounds were conducted. These compounds represent carboxyl, catecholate, amide, and phosphate groups present in siderophores, amino acids, polysaccharides, phospholipids, and DNA. Due in part to the ubiquitous presence of carboxyl groups in biomolecules, numerous IR peaks corresponding to outer-sphere or unbound (1400 cm−1) and inner-sphere (1310-1320 cm−1) coordinated carboxyl groups are noted following reaction of bacteria and biomolecules with α-Fe2O3 and α-FeOOH. However, the data also reveal that the presence of low-level amounts (i.e., 0.45-0.79%) of biomolecular phosphorous groups result in strong IR bands at ~1043 cm−1, corresponding to inner-sphere Fe-O-P bonds, underscoring the importance of bacteria associated P-containing groups in biomolecule and cell adhesion. Spectral comparisons also reveal slightly greater P-O-Fe contributions for bacteria (Pseudomonad, E. coli) deposited on α-FeOOH, as compared to α-Fe2O3. This data demonstrates that slight differences in bacterial adhesion to Fe oxides can be attributed to bacterial species and Fe-oxide minerals. However, more importantly, the strong binding affinity of phosphate in all bacteria samples to both Fe-oxides results in the formation of inner-sphere Fe-O-P bonds, signifying the critical role of biomolecular P in the initiation of bacterial adhesion. PMID:24859052

  16. Chromophore-protein coupling beyond nonpolarizable models: understanding absorption in green fluorescent protein

    NARCIS (Netherlands)

    Daday, C.; Curutchet, C.; Sinicropi, A.; Mennucci, B.; Filippi, Claudia

    2015-01-01

    The nature of the coupling of the photoexcited chromophore with the environment in a prototypical system like green fluorescent protein (GFP) is to date not understood, and its description still defies state-of-the-art multiscale approaches. To identify which theoretical framework of the

  17. Engineering a genetically-encoded SHG chromophore by electrostatic targeting to the membrane

    Directory of Open Access Journals (Sweden)

    Yuka eJinno

    2014-11-01

    Full Text Available Although second harmonic generation (SHG microscopy provides unique imaging advantages for voltage imaging and other biological applications, genetically-encoded SHG chromophores remain relatively unexplored. SHG only arises from non-centrosymmetric media, so an anisotropic arrangement of chromophores is essential to provide strong SHG signals. Here, inspired by the mechanism by which K-Ras4B associates with plasma membranes, we sought to achieve asymmetric arrangements of chromophores at the membrane-cytoplasm interface using the fluorescent protein mVenus. After adding a farnesylation motif to the C-terminus of mVenus, nine amino acids composing its -barrel surface were replaced by lysine, forming an electrostatic patch. This protein (mVe9Knus-CVIM was efficiently targeted to the plasma membrane in a geometrically defined manner and exhibited SHG in HEK293 cells. In agreement with its design, mVe9Knus-CVIM hyperpolarizability was oriented at a small angle (~7.3º from the membrane normal. Genetically-encoded SHG chromophores could serve as a molecular platform for imaging membrane potential.

  18. Gas-phase infrared spectrum of the anionic GFP-chromophore

    NARCIS (Netherlands)

    Almasian, M.; Grzetic, J.; G. Berden,; Bakker, B.; Buma, W. J.; Oomens, J.

    2012-01-01

    The gas-phase IR spectrum of the anionic chromophore of the green fluorescent protein (p-hydroxy-benzylidene-2,3-dimethylimidazolidinone, HBDI) is recorded in the 800–1800 cm−1 frequency range using the free electron laser FELIX in combination with an electrospray ionization (ESI) Fourier

  19. Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant.

    Science.gov (United States)

    Bose, Samik; Chakrabarty, Suman; Ghosh, Debashree

    2016-05-19

    Hybrid quantum mechanics/molecular mechanics (QM/MM) is applied to the fluorinated green fluorescent protein (GFP) chromophore (DFHBDI) in its deprotonated form to understand the solvatochromic shifts in its vertical detachment energy (VDE) and vertical excitation energy (VEE). This variant of the GFP chromophore becomes fluorescent in an RNA environment and has a wide range of applications in biomedical and biochemical fields. From microsolvation studies, we benchmark (with respect to full QM) the accuracy of our QM/MM calculations with effective fragment potential (EFP) as the MM method of choice. We show that while the solvatochromic shift in the VEE is minimal (0.1 eV blue shift) and its polarization component is only 0.03 eV, the effect of the solvent on the VDE is quite large (3.85 eV). We also show by accurate calculations on the solvatochromic shift of the VDE that polarization accounts for ∼0.23 eV and therefore cannot be neglected. The effect of the counterions on the VDE of the deprotonated chromophore in solvation is studied in detail, and a charge-smearing scheme is suggested for charged chromophores.

  20. Preparation and optical characteristics of layered perovskite-type lead-bromide-incorporated azobenzene chromophores

    International Nuclear Information System (INIS)

    Sasai, Ryo; Shinomura, Hisashi

    2013-01-01

    Lead bromide-based layered perovskite powders with azobenzene derivatives were prepared by a homogeneous precipitation method. From the diffuse reflectance (DR) and photoluminescence (PL) spectra of the hybrid powder materials, the present hybrids exhibited sharp absorption and PL peaks originating from excitons produced in the PbBr 4 2− layer. When the present hybrid powder was irradiated with UV light at 350 nm, the absorption band from the trans-azobenzene chromophore, observed around 350 nm, decreased, while the absorption band from the cis-azobenzene chromophore, observed around 450 nm, increased. These results indicate that azobenzene chromophores in the present hybrid materials exhibit reversible photoisomerization. Moreover, it was found that the PL intensity from the exciton also varied due to photoisomerization of the azobenzene chromophores in the present hybrid. Thus, for the first time we succeeded in preparing the azobenzene derivative lead-bromide-based layered perovskite with photochromism before and after UV light irradiation. - Graphical abstract: For the first time, we succeeded in preparing the azobenzene derivative lead-bromide-based layered perovskite with photochromism before and after UV light irradiation. Highlights: ► PbBr-based layered perovskite with azobenezene derivatives could be synthesized by a homogeneous precipitation method. ► Azobenzene derivatives incorporated the present hybrid that exhibited reversible photoisomerization under UV and/or visible light irradiation. ► PL property of the present hybrid could also be varied by photoisomerization.

  1. 2,4,5-trihydroxy-3-methylacetophenone: A cellulosic chromophore as a case study of aromaticity

    Science.gov (United States)

    Nele Sophie Zwirchmayr; Thomas Elder; Markus Bacher; Andreas Hofinger-Horvath; Paul Kosma; Thomas. Rosenau

    2017-01-01

    The title compound (2,4,5-trihydroxy-3-methylacetophenone, 1) was isolated as chromophore from aged cellulosic pulps. The peculiar feature of the compound is its weak aromatic system that can be converted into nonaromatic (quinoid or cyclic aliphatic) tautomers, depending on the conditions and reaction partners. In alkaline media, the participation of quinoid canonic...

  2. Production of Chromophoric Dissolved Organic Matter from Mangrove Leaf Litter and Floating Sargassum Colonies

    Science.gov (United States)

    Chromophoric dissolved organic matter (CDOM) strongly absorbs solar radiation in the blue-green and serves as the primary attenuator of water column ultraviolet radiation (UV-R). CDOM interferes with remote sensing of ocean chlorophyll and can control UV-R-induced damage to light...

  3. Orientation phenomena in chromophore DR1-containing polymer films and their non-linear optical response

    International Nuclear Information System (INIS)

    Moencke, Doris; Mountrichas, Grigoris; Pispas, Stergios; Kamitsos, Efstratios I.

    2011-01-01

    The effectiveness of chromophore alignment in polymer films following corona poling can be assessed by the generated second harmonic signal. Optimization of the stability and strength of this nonlinear optical response may improve with a better understanding of the underlying principal order phenomena. Structural analysis by vibrational, optical, and 1 H NMR spectroscopy reveals side chain tacticity, aggregation effects, and changes in orientation as a function of temperature. Co-polymers with the functionalized chromophore Disperse Red 1 methacrylate (MDR1) were prepared for three different methacrylate types. High side chain polarity and short side chain length increase generally chromophore aggregation in films, whereas the very long poly-ether side chains in PMEO based co-polymers are wrapped separately around the DR1 entities. Side chain tacticity depends on space requirements, but also on the capacity of side groups to form OH-bridges. Side chain tacticity might present an additional parameter for the assessment of chromophore aggregation and poling induced alignments. Stepwise heating of co-polymer films causes an increase in the number of random over ordered side chain arrangements. Cross-linking by anhydride formation is observed after heating the methacrylic acid based co-polymer.

  4. Ultrafast dynamics of isolated model photoactive yellow protein chromophores: "Chemical perturbation theory" in the laboratory

    NARCIS (Netherlands)

    Vengris, M.; Larsen, D.S.; van der Horst, M.A.; Larsen, O.F.A.; Hellingwerf, K.J.; van Grondelle, R.

    2005-01-01

    Pump-probe and pump-dump probe experiments have been performed on several isolated model chromophores of the photoactive yellow protein (PYP). The observed transient absorption spectra are discussed in terms of the spectral signatures ascribed to solvation, excited-state twisting, and vibrational

  5. Ultrafast excited and ground-state dynamics of the green fluorescent protein chromophore in solution

    NARCIS (Netherlands)

    Vengris, M.; van Stokkum, I.H.M.; He, X.; Bell, A.F.; Tonge, P.J.; van Grondelle, R.; Larsen, D.S.

    2004-01-01

    Ultrafast dispersed pump-dump-probe spectroscopy was applied to HBDI (4′-hydroxybenzylidene-2,3-dimethylimidazolinone), a model green fluorescent protein (GFP) chromophore in solution with different protonation states. The measured three-dimensional data was analyzed using a global analysis method

  6. How far can a single hydrogen bond tune the spectral properties of the GFP chromophore?

    DEFF Research Database (Denmark)

    Kiefer, Hjalte; Lattouf, Elie; Persen, Natascha Wardinghus

    2015-01-01

    Photoabsorption of the hydrogen-bonded complex of a neutral and an anionic Green Fluorescent Protein chromophore has been studied using a new dual-detection approach to action-absorption spectroscopy. Following absorption of one photon, dissociation through a single channel ensures that the full ...

  7. [Effect of Charge-Transfer Complex on Ultraviolet-Visible (UV-Vis) Absorption Property of Chromophoric Dissolved Organic Matter (CDOM) in Waters of Typical Water-Level Fluctuation Zones of the Three Gorges Reservoir Areas].

    Science.gov (United States)

    Jiang, Tao; Liang, Jian; Zhang, Mu-xue; Wang, Ding-yong; Wei, Shi-qiang; Lu, Song

    2016-02-15

    As an important fraction of dissolved organic matter (DOM), chromophoric dissolved organic matter (CDOM) plays a key role in decision of the optical properties and photogeochemistry of DOM, and further affects pollutant fate and global carbon cycle. These optical properties are ascribed to two chromophoric systems including superposition of individual chromophores and charge-transfer (CT) complexation between electron donor (e.g., phenols and indoles) and acceptor (e.g., quinones and other oxidized aromatics) in DOM structures. Thus in this study, based on the "double-chromophoric system" model, DOM samples from four typical water-level fluctuation zones of Three Gorges Reservoir (TGR) areas were selected, to investigate the effect and contribution of charge-transfer complex to ultraviolet-visible (UV-Vis) absorption property of CDOM. Using NaBH, reduction method, original featureless absorption curve was classified into two independent curves caused by individual chromophoric group, which were derived from a simple superposition of independent chromophore and charge-transfer complex, respectively. Also, the changes in curve properties and specific parameters before and after NaBH4 reduction were compared. The results showed that in all DOM samples from the four sites of TGR, more than 35% of absorption was attributed from CT complex. Shibaozhai of Zhongxian and Zhenxi of Fuling showed the highest proportion ( > 50%). It suggested that the role of CT complex in CDOM property could not be neglected. After removal of CT complex, absorption curve showed blue-shift and CDOM concentration [a (355)] decreased significantly. Meanwhile, because of deforming of bonds by reduction, DOM structures became more dispersive and the molecular size was decreased, resulting in the lower spectral slope (S) observed, which evidentially supported that the supermolecular association structure of DOM was self-assembled through CT complex. Meanwhile, deceasing hydrophobic components led

  8. Simultaneous control of emission localization and two-photon absorption efficiency in dissymmetrical chromophores

    International Nuclear Information System (INIS)

    Tretiak, Sergei

    2009-01-01

    The aim of the present work is to demonstrate that combined spectral tuning of fluorescence and two-photon absorption (TPA) properties of multipolar chromophores can be achieved by introduction of slight electronic chemical dissymmetry. In that perspective, two novel series of structurally related chromophores have been designed and studied: a first series based on rod-like quadrupolar chromophores bearing different electron-donating (D) end groups and a second series based on three-branched octupolar chromophores built from a trigonal donating moiety and bearing various acceptor (A) peripheral groups. The influence of the electronic dissymmetry is investigated by combined experimental and theoretical studies of the linear and nonlinear optical properties of dissymmetric chromophores compared to their symmetrical counterparts. In both types of systems (i.e. quadrupoles and octupoles) experiments and theory reveal that excitation is essentially delocalized and that excitation involves synchronized charge redistribution between the different D and A moieties within the multipolar structure (i.e. concerted intramolecular charge transfer). In contrast, the emission stems only from a particular dipolar subunit bearing the strongest D or A moieties due to fast excitation localization after excitation prior to emission. Hence control of emission characteristics (polarization and emission spectrum) in addition to localization can be achieved by controlled introduction of electronic dissymmetry (i.e. replacement of one of the D or A end-groups by a slightly stronger D(prime) or A(prime) units). Interestingly dissymmetrical functionalization of both quadrupolar and octupolar compounds does not lead to significant loss in TPA responses and can even be beneficial due to the spectral broadening and peak position tuning that it allows. This study thus reveals an original molecular engineering route strategy allowing major TPA enhancement in multipolar structures due to concerted

  9. Triplet excited state properties in variable gap π-conjugated donor–acceptor–donor chromophores

    KAUST Repository

    Cekli, Seda; Winkel, Russell W.; Alarousu, Erkki; Mohammed, Omar F.; Schanze, Kirk S.

    2016-01-01

    A series of variable band-gap donor–acceptor–donor (DAD) chromophores capped with platinum(II) acetylide units has been synthesized and fully characterized by electrochemical and photophysical methods, with particular emphasis placed on probing triplet excited state properties. A counter-intuitive trend of increasing fluorescence quantum efficiency and lifetime with decreasing excited state energy (optical gap) is observed across the series of DAD chromophores. Careful study of the excited state dynamics, including triplet yields (as inferred from singlet oxygen sensitization), reveals that the underlying origin of the unusual trend in the fluorescence parameters is that the singlet–triplet intersystem crossing rate and yield decrease with decreasing optical gap. It is concluded that the rate of intersystem crossing decreases as the LUMO is increasingly localized on the acceptor unit in the DAD chromophore, and this result is interpreted as arising because the extent of spin–orbit coupling induced by the platinum heavy metal centers decreases as the LUMO is more localized on the acceptor. In addition to the trend in intersystem crossing, the results show that the triplet decay rates follow the Energy Gap Law correlation over a 1.8 eV range of triplet energy and 1000-fold range of triplet decay rates. Finally, femtosecond transient absorption studies for the DAD chromophores reveals a strong absorption in the near-infrared region which is attributed to the singlet excited state. This spectral band appears to be general for DAD chromophores, and may be a signature of the charge transfer (CT) singlet excited state.

  10. Triplet excited state properties in variable gap π-conjugated donor–acceptor–donor chromophores

    KAUST Repository

    Cekli, Seda

    2016-02-12

    A series of variable band-gap donor–acceptor–donor (DAD) chromophores capped with platinum(II) acetylide units has been synthesized and fully characterized by electrochemical and photophysical methods, with particular emphasis placed on probing triplet excited state properties. A counter-intuitive trend of increasing fluorescence quantum efficiency and lifetime with decreasing excited state energy (optical gap) is observed across the series of DAD chromophores. Careful study of the excited state dynamics, including triplet yields (as inferred from singlet oxygen sensitization), reveals that the underlying origin of the unusual trend in the fluorescence parameters is that the singlet–triplet intersystem crossing rate and yield decrease with decreasing optical gap. It is concluded that the rate of intersystem crossing decreases as the LUMO is increasingly localized on the acceptor unit in the DAD chromophore, and this result is interpreted as arising because the extent of spin–orbit coupling induced by the platinum heavy metal centers decreases as the LUMO is more localized on the acceptor. In addition to the trend in intersystem crossing, the results show that the triplet decay rates follow the Energy Gap Law correlation over a 1.8 eV range of triplet energy and 1000-fold range of triplet decay rates. Finally, femtosecond transient absorption studies for the DAD chromophores reveals a strong absorption in the near-infrared region which is attributed to the singlet excited state. This spectral band appears to be general for DAD chromophores, and may be a signature of the charge transfer (CT) singlet excited state.

  11. Synthesis and electro-optic properties of the chromophore-containing NLO polyarylate polymers

    Science.gov (United States)

    Ren, Haohui; Peng, Chengcheng; Bo, Shuhui; Fan, Guofang; Xu, Guangming; Zhao, Hui; Zhen, Zhen; Liu, Xinhou

    2014-03-01

    Base on the same two monomers, diphenolic acid (DPA) and isophthaloyl chloride (IPC), three chromophore-containing nonlinear optical (NLO) polyarylate polymers were prepared. A tricyanofuran (TCF)-acceptor type chromophore group was in main-chain (mPAR-chr1), side-chain (sPAR-chr1) and side-chain with a 1,1-bis(4-hydroxyphenyl)-1-phenyl-2,2,2-trifluoroethane (BPAPF) group (sPAR-F-chr1), respectively. The obtained polymers were characterized and evaluated by UV-Vis, 1H NMR, DSC and TGA. All the polymers exhibited good electro-optic (EO) activity. The relationship between EO coefficients (r33) and the chromophore concentration of the three polymers were also characterized and discussed. There were no obvious differences found in EO activity between mPAR-chr1 and sPAR-chr1 polyarylates with the same chromophore. The fluorinated block polyarylate sPAR-F-chr1 has the largest r33 value in these three polyarylates which is 52 pm/V at the wavelength of 1310 nm (which is almost twice the r33 value of normal polymers contained the same chormophore at the same content), when the concentration of chromophore 1 is 18wt.%. 85% of the r33 value was retained in the sPAR-F-chr1 after being heated at 85°C for 600 hours. The polymer sPAR-F-chr1, with good solubility, high Tg (above 200 °C) and side functional group at the same time, may probably be a practical NLO material. These properties make the new polyarylates have potential applications in EO devices such as EO modulators and switches.

  12. A possibly universal red chromophore for modeling color variations on Jupiter

    Science.gov (United States)

    Sromovsky, L. A.; Baines, K. H.; Fry, P. M.; Carlson, R. W.

    2017-07-01

    A new laboratory-generated chemical compound made from photodissociated ammonia (NH3) molecules reacting with acetylene (C2H2) was suggested as a possible coloring agent for Jupiter's Great Red Spot (GRS) by Carlson et al. (2016, Icarus 274, 106-115). Baines et al. (2016, Icarus, submitted) showed that the GRS spectrum measured by the visual channels of the Cassini VIMS instrument in 2000 could be accurately fit by a cloud model in which the chromophore appeared as a physically thin layer of small particles immediately above the main cloud layer of the GRS. Here we show that the same chromophore and same layer location can also provide close matches to the short wavelength spectra of many other cloud features on Jupiter, suggesting this material may be a nearly universal chromophore that could explain the various degrees of red coloration on Jupiter. This is a robust conclusion, even for 12% changes in VIMS calibration and large uncertainties in the refractive index of the main cloud layer due to uncertain fractions of NH4SH and NH3 in its cloud particles. The chromophore layer can account for color variations among north and south equatorial belts, equatorial zone, and the Great Red Spot, by varying particle size from 0.12 μm to 0.29 μm and 1-μm optical depth from 0.06 to 0.76. The total mass of the chromophore layer is much less variable, ranging from 18 to 30 μg/cm2, except in the equatorial zone, where it is only 10-13 μg/cm2. We also found a depression of the ammonia volume mixing ratio in the two belt regions, which averaged 0.4 - 0.5 ×10-4 immediately below the ammonia condensation level, while the other regions averaged twice that value.

  13. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics

    Science.gov (United States)

    Likic, Vladimir A.

    2006-01-01

    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  14. Electrostatics in biomolecular simulations : where are we now and where are we heading?

    NARCIS (Netherlands)

    Karttunen, M.E.J.; Rottler, J.; Vattulainen, I.; Sagui, C.

    2008-01-01

    Chapter 2. In this review, we discuss current methods and developments in the treatment of electrostatic interactions in biomolecular and soft matter simulations. We review the current ‘work horses’, namely, Ewald summation based methods such the Particle-Mesh Ewald, and others, and also newer

  15. Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

    Energy Technology Data Exchange (ETDEWEB)

    Jurrus, Elizabeth [Pacific Northwest National Laboratory, Richland Washington; Engel, Dave [Pacific Northwest National Laboratory, Richland Washington; Star, Keith [Pacific Northwest National Laboratory, Richland Washington; Monson, Kyle [Pacific Northwest National Laboratory, Richland Washington; Brandi, Juan [Pacific Northwest National Laboratory, Richland Washington; Felberg, Lisa E. [University of California, Berkeley California; Brookes, David H. [University of California, Berkeley California; Wilson, Leighton [University of Michigan, Ann Arbor Michigan; Chen, Jiahui [Southern Methodist University, Dallas Texas; Liles, Karina [Pacific Northwest National Laboratory, Richland Washington; Chun, Minju [Pacific Northwest National Laboratory, Richland Washington; Li, Peter [Pacific Northwest National Laboratory, Richland Washington; Gohara, David W. [St. Louis University, St. Louis Missouri; Dolinsky, Todd [FoodLogiQ, Durham North Carolina; Konecny, Robert [University of California San Diego, San Diego California; Koes, David R. [University of Pittsburgh, Pittsburgh Pennsylvania; Nielsen, Jens Erik [Protein Engineering, Novozymes A/S, Copenhagen Denmark; Head-Gordon, Teresa [University of California, Berkeley California; Geng, Weihua [Southern Methodist University, Dallas Texas; Krasny, Robert [University of Michigan, Ann Arbor Michigan; Wei, Guo-Wei [Michigan State University, East Lansing Michigan; Holst, Michael J. [University of California San Diego, San Diego California; McCammon, J. Andrew [University of California San Diego, San Diego California; Baker, Nathan A. [Pacific Northwest National Laboratory, Richland Washington; Brown University, Providence Rhode Island

    2017-10-24

    The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.

  16. Affinity Capillary Electrophoresis – A Powerful Tool to Investigate Biomolecular Interactions

    Czech Academy of Sciences Publication Activity Database

    Kašička, Václav

    2017-01-01

    Roč. 30, č. 5 (2017), s. 248 ISSN 1471-6577 Institutional support: RVO:61388963 Keywords : capillary affinity electrophoresis * biomolecular interactions * binding constants Subject RIV: CB - Analytical Chemistry, Separation OBOR OECD: Analytical chemistry Impact factor: 0.663, year: 2016

  17. ALTERNATIVAS BIOMOLECULARES EN EL TRATAMIENTO DE LA OBESIDAD

    Directory of Open Access Journals (Sweden)

    Fernando Lizcano

    2010-09-01

    Full Text Available

    Resumen

    La obesidad se ha convertido en un problema de salud pública que cobija tanto a países desarrollados como a aquellos en vía de desarrollo. En la mayoría de los casos las políticas de salud no han tenido el efecto deseado para reducir la prevalencia de esta patología y muchos de los fármacos útiles para contrarrestar la obesidad no han podido continuar en el mercado debido a serios efectos secundarios. Algunas alternativas terapéuticas más agresivas como la cirugías reductivas han demostrado una utilidad restringida. Incluso, recientes observaciones han puesto de manifiesto las consecuencias a largo plazo de este tipo de intervenciones.

    En la búsqueda de nuevas estrategias para el tratamiento de la obesidad se ha investigado, tanto en la propia célula grasa como en los genes que podrían ser modificados y cuya función está enfocada en regular el gasto calórico y la termogénesis adaptativa. Algunos de estos genes son modificados por factores de transcripción que pueden determinar la característica fenotípica de la célula grasa. Recientemente se ha observado que en la persona adulta es posible evidenciar vestigios de célula grasa parda que puede gastar energía en forma de calor y esta modificación podría ser una alternativa terapéutica en la obesidad. Nuestro grupo de investigación ha observado que mediante la modificación de la función de la proteína del retinoblastoma (pRb se pueden aumentar los genes que estimulan la pérdida calórica en el adipocito.

    Palabras clave: Grasa Parda, Obesidad, transcripción, EID1, transdiferenciación

    BIOMOLECULAR OPTIONS IN TREATING OBESITY

    Abstract

    Obesity is a public health issue for both developed and third world countries. Although many efforts have been made to reverse the trend of this prevalent pathology, no results have been obtained with public health policies in most cases. Furthermore, many medicines approved for

  18. Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

    Science.gov (United States)

    Chu, Xiakun; Gan, Linfeng; Wang, Erkang; Wang, Jin

    2013-01-01

    Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding–folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative “coupled binding–folding” and three-state noncooperative “folding prior to binding” scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding–folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding–folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found “U-shape” temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments. PMID:23754431

  19. PHOTOREACTIVITY OF CHROMOPHORIC DISSOLVED ORGANIC MATTER (CDOM) DERIVED FROM DECOMPOSITION OF VARIOUS VASCULAR PLANT AND ALGAL SOURCES

    Science.gov (United States)

    Chromophoric dissolved organic matter (CDOM) in aquatic environments is derived from the microbial decomposition of terrestrial and microbial organic matter. Here we present results of studies of the spectral properties and photoreactivity of the CDOM derived from several organi...

  20. Novel multi-chromophor light absorber concepts for DSSCs for efficient electron injection

    Energy Technology Data Exchange (ETDEWEB)

    Schuetz, Robert; Strothkaemper, Christian; Bartelt, Andreas; Hannappel, Thomas; Eichberger, Rainer [Helmholtz-Zentrum Berlin fuer Materialien und Energie, Hahn-Meitner-Platz 1, 14109 Berlin (Germany); Fasting, Carlo [Institut fuer Organische Chemie, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin (Germany); Thomas, Inara [Helmholtz-Zentrum Berlin fuer Materialien und Energie, Hahn-Meitner-Platz 1, 14109 Berlin (Germany); Institut fuer Organische Chemie, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin (Germany)

    2011-07-01

    Dye sensitized solar cells (DSSCs) operate by injecting electrons from the excited state of a light-harvesting dye into the continuum of conduction band states of a wide bandgap semiconductor. The light harvesting efficiency of pure organic dyes is limited by a narrow spectral electronic transition. A beneficial broad ground state absorption in the VIS region can be achieved by applying a single molecular dye system with multiple chromophors involving a Foerster resonance energy transfer (FRET) mechanism for an efficient electron injection. A model donor acceptor dye system capable for FRET chemically linked to colloidal TiO{sub 2} and ZnO nanorod surfaces was investigated in UHV environment. We used VIS/NIR femtosecond transient absorption spectroscopy and optical pump terahertz probe spectroscopy to study the charge injection dynamics of the antenna system. Different chromophors attached to a novel scaffold/anchor system connecting the organic absorber unit to the metal oxide semiconductor were probed.

  1. Photoabsorption of green and red fluorescent protein chromophore anions in vacuo.

    Science.gov (United States)

    Wan, Songbo; Liu, Shasha; Zhao, Guangjiu; Chen, Maodu; Han, Keli; Sun, Mengtao

    2007-09-01

    Photoabsorption properties of green and red fluorescent protein chromophore anions in vacuo were investigated theoretically, based on the experimental results in gas phase [Phys. Rev. Lett. 2001, 87, 228102; Phys. Rev. Lett. 2003, 90, 118103]. Their calculated transition energies in absorption with TD-DFT and ZINDO methods are directly compared to the experimental reports in gas phase, and the calculations with ZINDO method can correctly reproduce the absorption spectra. The orientation and strength of their transition dipole moments were revealed with transition density. We also showed the orientation and result of their intramolecular charge transfer with transition difference density. The calculated results show that with the increase of the extended conjugated system, the orientation of transition dipole moments and the orientation of charge transfer can be reversed. They are the linear responds with the external electric fields. These theoretical results reveal the insight understanding of the photoinduced dynamics of green and red fluorescent protein chromophore anions and cations in vacuo.

  2. Chromophoric dissolved organic matter in experimental mesocosms maintained under different pCO2 levels

    OpenAIRE

    Rochelle-Newall, E.; Delille, B.; Frankignoulle, M.; Gattuso, J.-P.; Jacquet, S.; Riebesell, Ulf; Terbrüggen, A.; Zondervan, I.

    2004-01-01

    Chromophoric dissolved organic matter (CDOM) represents the optically active fraction of the bulk dissolved organic matter (DOM) pool. Recent evidence pointed towards a microbial source of CDOM in the aquatic environment and led to the proposal that phytoplankton is not a direct source of CDOM, but that heterotrophic bacteria, through reprocessing of DOM of algal origin, are an important source of CDOM. In a recent experiment designed at looking at the effects of elevated pCO2 on blooms of th...

  3. Biogeneration of chromophoric dissolved organic matter by bacteria and krill in the southern ocean

    OpenAIRE

    Ortega-Retuerta, E.; Frazer, Thomas K.; Duarte, Carlos M.; Ruiz-Halpern, Sergio; Tovar-Sánchez, Antonio; Arrieta López de Uralde, Jesús M.; Reche, Isabel

    2009-01-01

    Chromophoric dissolved organic matter (CDOM), the optically active fraction of dissolved organic matter, is primarily generated by pelagic organisms in the open ocean. In this study, we experimentally determined the quantity and spectral quality of CDOM generated by bacterioplankton using two different substrates (with and without photoproducts) and by Antarctic krill Euphausia superba and evaluated their potential contributions to CDOM dynamics in the peninsular region of the Southern Ocean....

  4. Resolving Electronic Transitions in Synthetic Fluorescent Protein Chromophores by Magnetic Circular Dichroism

    Czech Academy of Sciences Publication Activity Database

    Štěpánek, P.; Cowie, T. Y.; Šafařík, Martin; Šebestík, Jaroslav; Pohl, Radek; Bouř, Petr

    2016-01-01

    Roč. 17, č. 15 (2016), s. 2348-2354 ISSN 1439-4235 R&D Projects: GA ČR GA13-03978S; GA ČR(CZ) GA16-05935S Institutional support: RVO:61388963 Keywords : density functional calculations * fluorescence protein chromophores * magnetic circular dichroism * organic synthesis * spectral simulations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.075, year: 2016

  5. Imidazole as a parent π-conjugated backbone in charge-transfer chromophores

    Directory of Open Access Journals (Sweden)

    Jiří Kulhánek

    2012-01-01

    Full Text Available Research activities in the field of imidazole-derived push–pull systems featuring intramolecular charge transfer (ICT are reviewed. Design, synthetic pathways, linear and nonlinear optical properties, electrochemistry, structure–property relationships, and the prospective application of such D-π-A organic materials are described. This review focuses on Y-shaped imidazoles, bi- and diimidazoles, benzimidazoles, bis(benzimidazoles, imidazole-4,5-dicarbonitriles, and imidazole-derived chromophores chemically bound to a polymer chain.

  6. Utilizing chromophoric dissolved organic matter measurements to derive export and reactivity of dissolved organic carbon exported to the Arctic Ocean: A case study of the Yukon River, Alaska

    Science.gov (United States)

    Spencer, R.G.M.; Aiken, G.R.; Butler, K.D.; Dornblaser, M.M.; Striegl, Robert G.; Hernes, P.J.

    2009-01-01

    The quality and quantity of dissolved organic matter (DOM) exported by Arctic rivers is known to vary with hydrology and this exported material plays a fundamental role in the biogeochemical cycling of carbon at high latitudes. We highlight the potential of optical measurements to examine DOM quality across the hydrograph in Arctic rivers. Furthermore, we establish chromophoric DOM (CDOM) relationships to dissolved organic carbon (DOC) and lignin phenols in the Yukon River and model DOC and lignin loads from CDOM measurements, the former in excellent agreement with long-term DOC monitoring data. Intensive sampling across the historically under-sampled spring flush period highlights the importance of this time for total export of DOC and particularly lignin. Calculated riverine DOC loads to the Arctic Ocean show an increase from previous estimates, especially when new higher discharge data are incorporated. Increased DOC loads indicate decreased residence times for terrigenous DOM in the Arctic Ocean with important implications for the reactivity and export of this material to the Atlantic Ocean. Citation: Spencer, R. G. M., G. R. Aiken, K. D. Butler, M. M. Dornblaser, R. G. Striegl, and P. J. Hernes (2009), Utilizing chromophoric dissolved organic matter measurements to derive export and reactivity of dissolved organic carbon exported to the Arctic Ocean: A case study of the Yukon River, Alaska, Geophys. Res. Lett., 36, L06401, doi:10.1029/ 2008GL036831. Copyright 2009 by the American Geophysical Union.

  7. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Jeffrey K Noel

    2016-01-01

    Full Text Available Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape.

  8. The laboratory technology of discrete molecular separation: the historical development of gel electrophoresis and the material epistemology of biomolecular science, 1945-1970.

    Science.gov (United States)

    Chiang, Howard Hsueh-hao

    2009-01-01

    Preparative and analytical methods developed by separation scientists have played an important role in the history of molecular biology. One such early method is gel electrophoresis, a technique that uses various types of gel as its supporting medium to separate charged molecules based on size and other properties. Historians of science, however, have only recently begun to pay closer attention to this material epistemological dimension of biomolecular science. This paper substantiates the historiographical thread that explores the relationship between modern laboratory practice and the production of scientific knowledge. It traces the historical development of gel electrophoresis from the mid-1940s to the mid-1960s, with careful attention to the interplay between technical developments and disciplinary shifts, especially the rise of molecular biology in this time-frame. Claiming that the early 1950s marked a decisive shift in the evolution of electrophoretic methods from moving boundary to zone electrophoresis, I reconstruct various trajectories in which scientists such as Oliver Smithies sought out the most desirable solid supporting medium for electrophoretic instrumentation. Biomolecular knowledge, I argue, emerged in part from this process of seeking the most appropriate supporting medium that allowed for discrete molecular separation and visualization. The early 1950s, therefore, marked not only an important turning point in the history of separation science, but also a transformative moment in the history of the life sciences as the growth of molecular biology depended in part on the epistemological access to the molecular realm available through these evolving technologies.

  9. An apolipoprotein-enriched biomolecular corona switches the cellular uptake mechanism and trafficking pathway of lipid nanoparticles.

    Science.gov (United States)

    Digiacomo, L; Cardarelli, F; Pozzi, D; Palchetti, S; Digman, M A; Gratton, E; Capriotti, A L; Mahmoudi, M; Caracciolo, G

    2017-11-16

    Following exposure to biological milieus (e.g. after systemic administration), nanoparticles (NPs) get covered by an outer biomolecular corona (BC) that defines many of their biological outcomes, such as the elicited immune response, biodistribution, and targeting abilities. In spite of this, the role of BC in regulating the cellular uptake and the subcellular trafficking properties of NPs has remained elusive. Here, we tackle this issue by employing multicomponent (MC) lipid NPs, human plasma (HP) and HeLa cells as models for nanoformulations, biological fluids, and target cells, respectively. By conducting confocal fluorescence microscopy experiments and image correlation analyses, we quantitatively demonstrate that the BC promotes a neat switch of the cell entry mechanism and subsequent intracellular trafficking, from macropinocytosis to clathrin-dependent endocytosis. Nano-liquid chromatography tandem mass spectrometry identifies apolipoproteins as the most abundant components of the BC tested here. Interestingly, this class of proteins target the LDL receptors, which are overexpressed in clathrin-enriched membrane domains. Our results highlight the crucial role of BC as an intrinsic trigger of specific NP-cell interactions and biological responses and set the basis for a rational exploitation of the BC for targeted delivery.

  10. Free volume modifications in chalcone chromophore doped PMMA films by electron irradiation: Positron annihilation study

    Science.gov (United States)

    Ismayil; Ravindrachary, V.; Praveena, S. D.; Mahesha, M. G.

    2018-03-01

    The free volume related fluorescence behaviour in electron beam irradiated chalcone chromophore doped Poly(methyl methacrylate) (PMMA) composite films have been studied using FTIR, UV-Visible, XRD and Positron Annihilation techniques. From the FTIR spectral study it is found that the formation of polarons and bipolaron takes place due to cross linking as well as chain scission processes at lower and higher doses respectively. It reveals that the formation of various polaronic defect levels upon irradiation is responsible for the creation of three optical energy band gaps within the polymer films as obtained from UV-Visible spectra. The crosslinking process at lower doses increases the distance between the pendant groups to reduce the interchain distance and chain scission process at higher doses decreases interchain separation to enhance the number of polarons in the polymer composites as suggested by XRD studies. The fluorescence studies show the enhancement of fluorescence emission at lower doses and reduction at higher doses under electron irradiation. The positron annihilation study suggests that the low radiation doses induce crosslinking which affect the free volume properties and in turn hinders the chalcone molecular rotation within the polymer composite. At higher doses chain scission process support polymer matrix relaxation and facilitates non-radiative transition of the chromophore upon excitation. This study shows that fluorescence enhancement and mobility of chromophore within the polymer matrix is directly related to the free volume around it.

  11. Chromophores from photolyzed ammonia reacting with acetylene: Application to Jupiters Great Red Spot

    Science.gov (United States)

    Carlson, Robert W.; Baines, Kevin H.; Anderson, M. S.; Filacchione, G.; Simon, A. A.

    2016-01-01

    The high altitude of Jupiter's Great Red Spot (GRS) may enhance the upward flux of gaseous ammonia (NH3 ) into the high troposphere, where NH3 molecules can be photodissociated and initiate a chain of chemical reactions with downwelling acetylene molecules (C2H2 ). These reactions, experimentally studied earlier by (Ferris and Ishikawa [1987] Nature 326, 777-778) and (Ferris and Ishikawa [1988] J. Amer. Chem. Soc. 110, 4306-4312), produce chromophores that absorb in the visible and ultraviolet regions. In this work we photolyzed mixtures of NH3 and C2H2 using ultraviolet radiation with a wavelength of 214 nm and measured the spectral transmission of the deposited films in the visible region (400-740 nm). From these transmission data we estimated the imaginary indices of refraction. Assuming that ammonia grains at the top of the GRS clouds are coated with this material, we performed layered sphere and radiative transfer calculations to predict GRS reflection spectra. Comparison of those results with observed and previously unreported Cassini visible spectra and with true-color images of the GRS show that the unknown GRS chromophore is spectrally consistent with the coupled NH3-C2H2 photochemical products produced in our laboratory experiments. Using high-resolution mass spectrometry and infrared spectroscopy we infer that the chromophore-containing residue is composed of aliphatic azine, azo, and diazo compounds.

  12. Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence

    Science.gov (United States)

    Rumyantsev, Konstantin A.; Shcherbakova, Daria M.; Zakharova, Natalia I.; Emelyanov, Alexander V.; Turoverov, Konstantin K.; Verkhusha, Vladislav V.

    2015-12-01

    Fluorescent proteins (FP) are used to study various biological processes. Recently, a series of near-infrared (NIR) FPs based on bacterial phytochromes was developed. Finding ways to improve NIR FPs is becoming progressively important. By applying rational design and molecular evolution we have engineered R. palustris bacterial phytochrome into a single-domain NIR FP of 19.6 kDa, termed GAF-FP, which is 2-fold and 1.4-fold smaller than bacterial phytochrome-based NIR FPs and GFP-like proteins, respectively. Engineering of GAF-FP involved a substitution of 15% of its amino acids and a deletion of the knot structure. GAF-FP covalently binds two tetrapyrrole chromophores, biliverdin (BV) and phycocyanobilin (PCB). With the BV chromophore GAF-FP absorbs at 635 nm and fluoresces at 670 nm. With the PCB chromophore GAF-FP becomes blue-shifted and absorbs at 625 nm and fluoresces at 657 nm. The GAF-FP structure has a high tolerance to small peptide insertions. The small size of GAF-FP and its additional absorbance band in the violet range has allowed for designing a chimeric protein with Renilla luciferase. The chimera exhibits efficient non-radiative energy transfer from luciferase to GAF-FP, resulting in NIR bioluminescence. This study opens the way for engineering of small NIR FPs and NIR luciferases from bacterial phytochromes.

  13. Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model.

    Science.gov (United States)

    Gozem, Samer; Huntress, Mark; Schapiro, Igor; Lindh, Roland; Granovsky, Alexander A; Angeli, Celestino; Olivucci, Massimo

    2012-11-13

    The ground state potential energy surface of the retinal chromophore of visual pigments (e.g., bovine rhodopsin) features a low-lying conical intersection surrounded by regions with variable charge-transfer and diradical electronic structures. This implies that dynamic electron correlation may have a large effect on the shape of the force fields driving its reactivity. To investigate this effect, we focus on mapping the potential energy for three paths located along the ground state CASSCF potential energy surface of the penta-2,4-dieniminium cation taken as a minimal model of the retinal chromophore. The first path spans the bond length alternation coordinate and intercepts a conical intersection point. The other two are minimum energy paths along two distinct but kinetically competitive thermal isomerization coordinates. We show that the effect of introducing the missing dynamic electron correlation variationally (with MRCISD) and perturbatively (with the CASPT2, NEVPT2, and XMCQDPT2 methods) leads, invariably, to a stabilization of the regions with charge transfer character and to a significant reshaping of the reference CASSCF potential energy surface and suggesting a change in the dominating isomerization mechanism. The possible impact of such a correction on the photoisomerization of the retinal chromophore is discussed.

  14. Smartphone snapshot mapping of skin chromophores under triple-wavelength laser illumination

    Science.gov (United States)

    Spigulis, Janis; Oshina, Ilze; Berzina, Anna; Bykov, Alexander

    2017-09-01

    Chromophore distribution maps are useful tools for skin malformation severity assessment and for monitoring of skin recovery after burns, surgeries, and other interactions. The chromophore maps can be obtained by processing several spectral images of skin, e.g., captured by hyperspectral or multispectral cameras during seconds or even minutes. To avoid motion artifacts and simplify the procedure, a single-snapshot technique for mapping melanin, oxyhemoglobin, and deoxyhemoglobin of in-vivo skin by a smartphone under simultaneous three-wavelength (448-532-659 nm) laser illumination is proposed and examined. Three monochromatic spectral images related to the illumination wavelengths were extracted from the smartphone camera RGB image data set with respect to crosstalk between the RGB detection bands. Spectral images were further processed accordingly to Beer's law in a three chromophore approximation. Photon absorption path lengths in skin at the exploited wavelengths were estimated by means of Monte Carlo simulations. The technique was validated clinically on three kinds of skin lesions: nevi, hemangiomas, and seborrheic keratosis. Design of the developed add-on laser illumination system, image-processing details, and the results of clinical measurements are presented and discussed.

  15. Red-light absorption and fluorescence of phytochrome chromophores: A comparative theoretical study

    Energy Technology Data Exchange (ETDEWEB)

    Falklöf, Olle; Durbeej, Bo, E-mail: bodur@ifm.liu.se

    2013-11-08

    Highlights: • Calculation of red-light absorption and emission of phytochrome chromophores. • Comparison of TD-DFT and ab initio methods. • Pure functionals show better accuracy than hybrid functionals. - Abstract: Currently, much experimental effort is being invested in the engineering of phytochromes, a large superfamily of photoreceptor proteins, into fluorescent proteins suitable for bioimaging in the near-infrared regime. In this work, we gain insight into the potential of computational methods to contribute to this development by investigating how well representative quantum chemical methods reproduce recently recorded red-light absorption and emission maxima of synthetic derivatives of the bilin chromophores of phytochromes. Focusing on the performance of time-dependent density functional theory but using also the ab initio CIS(D), CC2 and CASPT2 methods, we explore how various methodological considerations influence computed spectra and find, somewhat surprisingly, that density functionals lacking exact exchange reproduce the experimental measurements with smaller errors than functionals that include exact exchange. Thus, for the important class of chromophores that bilins constitute, the widely established trend that hybrid functionals give more accurate excitation energies than pure functionals does not apply.

  16. Mechanism of ascorbic acid interference in biochemical tests that use peroxide and peroxidase to generate chromophore.

    Science.gov (United States)

    Martinello, Flávia; Luiz da Silva, Edson

    2006-11-01

    Ascorbic acid interferes negatively in peroxidase-based tests (Trinder method). However, the precise mechanism remains unclear for tests that use peroxide, a phenolic compound and 4-aminophenazone (4-AP). We determined the chemical mechanism of this interference, by examining the effects of ascorbic acid in the reaction kinetics of the production and reduction of the oxidized chromophore in urate, cholesterol, triglyceride and glucose tests. Reaction of ascorbic acid with the Trinder method constituents was also verified. Ascorbic acid interfered stoichiometrically with all tests studied. However, it had two distinct effects on the reaction rate. In the urate test, ascorbic acid decreased the chromophore formation with no change in its production kinetics. In contrast, in cholesterol, triglyceride and glucose tests, an increase in the lag phase of color development occurred. Of all the Trinder constituents, only peroxide reverted the interference. In addition, ascorbic acid did not interfere with oxidase activity nor reduce significantly the chromophore formed. Peroxide depletion was the predominant chemical mechanism of ascorbic acid interference in the Trinder method with phenolics and 4-AP. Distinctive effects of ascorbic acid on the reaction kinetics of urate, cholesterol, glucose and triglyceride might be due to the rate of peroxide production by oxidases.

  17. Fiber optic-based fluorescence detection system for in vivo studies of exogenous chromophore pharmacokinetics

    Science.gov (United States)

    Doiron, Daniel R.; Dunn, J. B.; Mitchell, W. L.; Dalton, Brian K.; Garbo, Greta M.; Warner, Jon A.

    1995-05-01

    The detection and quantification of the concentration of exogenous chromophores in-vivo by their fluorescence is complicated by many physical and geometrical parameters. Measurement of such signals is advantageous in determining the pharmacokinetics of photosensitizers such as those used in photodynamic therapy (PDT) or to assist in the diagnosis of tissue histological state. To overcome these difficulties a ratio based fiber optic contact fluorometer has been developed. This fluorescence detection system (FDS) uses the ratio of the fluorescence emission peak of the exogenous chromophore to that of endogenous chromophores, i.e. autofluorescence, to correct for a variety of parameters affecting the magnitude of the measured signals. By doing so it also minimizes the range of baseline measurements prior to exogenous drug injection, for various tissue types. Design of the FDS and results of its testing in animals and patients using the second generation photosensitizer Tin ethyletiopurpurin (SnET2) are presented. These results support the feasibility and usefulness of the Ratio FDS system.

  18. HPDB-Haskell library for processing atomic biomolecular structures in Protein Data Bank format.

    Science.gov (United States)

    Gajda, Michał Jan

    2013-11-23

    Protein DataBank file format is used for the majority of biomolecular data available today. Haskell is a lazy functional language that enjoys a high-level class-based type system, a growing collection of useful libraries and a reputation for efficiency. I present a fast library for processing biomolecular data in the Protein Data Bank format. I present benchmarks indicating that this library is faster than other frequently used Protein Data Bank parsing programs. The proposed library also features a convenient iterator mechanism, and a simple API modeled after BioPython. I set a new standard for convenience and efficiency of Protein Data Bank processing in a Haskell library, and release it to open source.

  19. Design of an embedded inverse-feedforward biomolecular tracking controller for enzymatic reaction processes.

    Science.gov (United States)

    Foo, Mathias; Kim, Jongrae; Sawlekar, Rucha; Bates, Declan G

    2017-04-06

    Feedback control is widely used in chemical engineering to improve the performance and robustness of chemical processes. Feedback controllers require a 'subtractor' that is able to compute the error between the process output and the reference signal. In the case of embedded biomolecular control circuits, subtractors designed using standard chemical reaction network theory can only realise one-sided subtraction, rendering standard controller design approaches inadequate. Here, we show how a biomolecular controller that allows tracking of required changes in the outputs of enzymatic reaction processes can be designed and implemented within the framework of chemical reaction network theory. The controller architecture employs an inversion-based feedforward controller that compensates for the limitations of the one-sided subtractor that generates the error signals for a feedback controller. The proposed approach requires significantly fewer chemical reactions to implement than alternative designs, and should have wide applicability throughout the fields of synthetic biology and biological engineering.

  20. Rapid prototyping of nanofluidic systems using size-reduced electrospun nanofibers for biomolecular analysis.

    Science.gov (United States)

    Park, Seung-Min; Huh, Yun Suk; Szeto, Kylan; Joe, Daniel J; Kameoka, Jun; Coates, Geoffrey W; Edel, Joshua B; Erickson, David; Craighead, Harold G

    2010-11-05

    Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.

  1. Unique temporal and spatial biomolecular emission profile on individual zinc oxide nanorods

    Science.gov (United States)

    Singh, Manpreet; Song, Sheng; Hahm, Jong-In

    2013-12-01

    Zinc oxide nanorods (ZnO NRs) have emerged in recent years as extremely useful, optical signal-enhancing platforms in DNA and protein detection. Although the use of ZnO NRs in biodetection has been demonstrated so far in systems involving many ZnO NRs per detection element, their future applications will likely take place in a miniaturized setting while exploiting single ZnO NRs in a low-volume, high-throughput bioanalysis. In this paper, we investigate temporal and spatial characteristics of the biomolecular fluorescence on individual ZnO NR systems. Quantitative and qualitative examinations of the biomolecular intensity and photostability are carried out as a function of two important criteria, the time and position along the long axis (length) of NRs. Photostability profiles are also measured with respect to the position on NRs and compared to those characteristics of biomolecules on polymeric control platforms. Unlike the uniformly distributed signal observed on the control platforms, both the fluorescence intensity and photostability are position-dependent on individual ZnO NRs. We have identified a unique phenomenon of highly localized, fluorescence intensification on the nanorod ends (FINE) of well-characterized, individual ZnO nanostructures. When compared to the polymeric controls, the biomolecular fluorescence intensity and photostability are determined to be higher on individual ZnO NRs regardless of the position on NRs. We have also carried out finite-difference time-domain simulations the results of which are in good agreement with the observed FINE. The outcomes of our investigation will offer a much needed basis for signal interpretation for biodetection devices and platforms consisting of single ZnO NRs and, at the same time, contribute significantly to provide insight in understanding the biomolecular fluorescence observed from ZnO NR ensemble-based systems.Zinc oxide nanorods (ZnO NRs) have emerged in recent years as extremely useful, optical

  2. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    DEFF Research Database (Denmark)

    Soberano de Oliveira, Ana Paula; Patil, Kiran Raosaheb; Nielsen, Jens

    2008-01-01

    is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology......Background: Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem...... with transcriptome data, thereby allowing the identification of key biological features (Reporter Features) around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription...

  3. Design of an embedded inverse-feedforward biomolecular tracking controller for enzymatic reaction processes

    OpenAIRE

    Foo, Mathias; Kim, Jongrae; Sawlekar, Rucha; Bates, Declan G.

    2017-01-01

    Feedback control is widely used in chemical engineering to improve the performance and robustness of chemical processes. Feedback controllers require a ‘subtractor’ that is able to compute the error between the process output and the reference signal. In the case of embedded biomolecular control circuits, subtractors designed using standard chemical reaction network theory can only realise one-sided subtraction, rendering standard controller design approaches inadequate. Here, we show how a b...

  4. Introduction to a Protein Interaction System Used for Quantitative Evaluation of Biomolecular Interactions

    OpenAIRE

    Yamniuk, Aaron

    2013-01-01

    A central goal of molecular biology is the determination of biomolecular function. This comes largely from a knowledge of the non-covalent interactions that biological small and macro-molecules experience. The fundamental mission of the Molecular Interactions Research Group (MIRG) of the ABRF is to show how solution biophysical tools are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core t...

  5. Parity Violation in Chiral Molecules: From Theory towards Spectroscopic Experiment and the Evolution of Biomolecular Homochirality

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    The observation of biomolecular homochirality can be considered as a quasi-fossil of the evolution of life [1], the interpretation of which has been an open question for more than a century, with numerous related hypotheses, but no definitive answers. We shall briefly discuss the current status and the relation to the other two questions. The discovery of parity violation led to important developm...

  6. Changes in biomolecular profile in a single nucleolus during cell fixation.

    Science.gov (United States)

    Kuzmin, Andrey N; Pliss, Artem; Prasad, Paras N

    2014-11-04

    Fixation of biological sample is an essential technique applied in order to "freeze" in time the intracellular molecular content. However, fixation induces changes of the cellular molecular structure, which mask physiological distribution of biomolecules and bias interpretation of results. Accurate, sensitive, and comprehensive characterization of changes in biomolecular composition, occurring during fixation, is crucial for proper analysis of experimental data. Here we apply biomolecular component analysis for Raman spectra measured in the same nucleoli of HeLa cells before and after fixation by either formaldehyde solution or by chilled ethanol. It is found that fixation in formaldehyde does not strongly affect the Raman spectra of nucleolar biomolecular components, but may significantly decrease the nucleolar RNA concentration. At the same time, ethanol fixation leads to a proportional increase (up to 40%) in concentrations of nucleolar proteins and RNA, most likely due to cell shrinkage occurring in the presence of coagulant fixative. Ethanol fixation also triggers changes in composition of nucleolar proteome, as indicated by an overall reduction of the α-helical structure of proteins and increase in the concentration of proteins containing the β-sheet conformation. We conclude that cross-linking fixation is a more appropriate protocol for mapping of proteins in situ. At the same time, ethanol fixation is preferential for studies of RNA-containing macromolecules. We supplemented our quantitative Raman spectroscopic measurements with mapping of the protein and lipid macromolecular groups in live and fixed cells using coherent anti-Stokes Raman scattering nonlinear optical imaging.

  7. Nanogap biosensors for electrical and label-free detection of biomolecular interactions

    International Nuclear Information System (INIS)

    Kyu Kim, Sang; Cho, Hyunmin; Park, Hye-Jung; Kwon, Dohyoung; Min Lee, Jeong; Hyun Chung, Bong

    2009-01-01

    We demonstrate nanogap biosensors for electrical and label-free detection of biomolecular interactions. Parallel fabrication of nanometer distance gaps has been achieved using a silicon anisotropic wet etching technique on a silicon-on-insulator (SOI) wafer with a finely controllable silicon device layer. Since silicon anisotropic wet etching resulted in a trapezoid-shaped structure whose end became narrower during the etching, the nanogap structure was simply fabricated on the device layer of a SOI wafer. The nanogap devices were individually addressable and a gap size of less than 60 nm was obtained. We demonstrate that the nanogap biosensors can electrically detect biomolecular interactions such as biotin/streptavidin and antigen/antibody pairs. The nanogap devices show a current increase when the proteins are bound to the surface. The current increases proportionally depending upon the concentrations of the molecules in the range of 100 fg ml -1 -100 ng ml -1 at 1 V bias. It is expected that the nanogap developed here could be a highly sensitive biosensor platform for label-free detection of biomolecular interactions.

  8. Molecular-dynamics simulations of polymeric surfaces for biomolecular applications

    NARCIS (Netherlands)

    Muntean, S.A.

    2013-01-01

    In-vitro diagnostics plays a very important role in the present healthcare system. It consists of a large variety of medical devices designed to diagnose a medical condition by measuring a target molecule in a sample, such as blood or urine. In vitro is the latin term for in glass and refers here to

  9. PREFACE: 1st Nano-IBCT Conference 2011 - Radiation Damage of Biomolecular Systems: Nanoscale Insights into Ion Beam Cancer Therapy

    Science.gov (United States)

    Huber, Bernd A.; Malot, Christiane; Domaracka, Alicja; Solov'yov, Andrey V.

    2012-07-01

    are indispensable for the optimization of this new therapy. The conference gathered 115 participants originating from 28 countries and addressed a large number of highly relevant aspects concerning ion propagation in biological matter, the production of secondary particles along the ion tracks as electrons, holes and radicals, and their propagation in the biomolecular medium. In particular, the attack of DNA molecules and proteins by electrons and free radicals, the relative importance of direct and indirect damage processes as well as the role of the environment were discussed. Not only were fundamental mechanisms and processes elucidated, but radiobiological scale effects, multi-scale approaches and recent advances in the theoretical description of the underlying complex phenomena were also presented. Aspects linked to the energy deposition (LET), the characteristics of the Bragg peak and new techniques of dosimetry and radiolysis were highlighted. Furthermore, methods for increasing the therapy efficiency by using radio sensitizers and the state-of-the-art of defining precise patient treatment plans, identifying the clinical benefits of this type of therapy, were also addressed. We would like to thank all participants for the lively exchange of ideas and results, thus making this conference a very fruitful event. Furthermore, we appreciate the financial support of the sponsors of this conference, in particular of the COST Action MP1002 financed by ESF. We would also like to express our thanks to all authors of these proceedings, as well as to the reviewers for their time, efforts and recommendations made during the preparation of this volume. Finally, many thanks to U G Huber for a careful proof-read of this manuscript. We look forward to the 2nd Nano-IBCT Conference, which will be held in spring 2013. Caen, 15 March 2012 Bernd A Huber, Christiane Malot, Alicja Domaracka and Andrey V Solov'yov The Editors Nano-IBCT group The PDF also contains details of the

  10. Minimal metabolic pathway structure is consistent with associated biomolecular interactions

    DEFF Research Database (Denmark)

    Bordbar, Aarash; Nagarajan, Harish; Lewis, Nathan E.

    2014-01-01

    Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still predicated on human-defined pathways. Here, we......, effectively doubling the known regulatory roles for Nac and MntR. This study suggests an underlying and fundamental principle in the evolutionary selection of pathway structures; namely, that pathways may be minimal, independent, and segregated....

  11. Chromophoric Dissolved Organic Matter in Southwestern Greenland Lakes

    Science.gov (United States)

    Osburn, C. L.; Giles, M. E.; Underwood, G. J. C.

    2014-12-01

    Dissolved organic matter (DOM) is an important property of Arctic lake ecosystems, originating from allochthonous inputs from catchments and autochthonous production by plankton in the water column. Little is known about the quality of DOM in Arctic lakes that lack substantial inputs from catchments and such lakes are abundant in southwestern Greenland. Colored dissolved organic matter (CDOM), the fraction that absorbs ultraviolet (UV) and visible light, is the controlling factor for the optical properties of many surface waters and as well informs on the quality of DOM. We examined the quality of CDOM in 21 lakes in southwestern Greenland, from the ice sheet to the coast, as part of a larger study examining the role of DOM in regulating microbial communities in these lakes. DOM was size fractioned and absorbance and fluorescence was measured on each size fraction, as well as on bulk DOM. The specific ultraviolet absorbance (SUVA) at 254 nm (SUVA254), computed by normalizing absorption (a254) to dissolved organic carbon (DOC) concentration, provided an estimate of the aromatic carbon content of DOM. SUVA values were generally CDOM fluorescence was used to determine the relative abundance of allochthonous and autochthonous DOM in all size fractions. Younger lakes near the ice sheet and lakes near the coast had lower amounts of CDOM and appeared more microbial in quality. However, lakes centrally located between the ice sheet and the coast had the highest CDOM concentrations and exhibited strong humic fluorescence. Overall distinct differences in CDOM quality were observed between lake locations and among DOM size fractions.

  12. Design, Structure, and Optical Properties of Organic-Inorganic Perovskites Containing an Oligothiophene Chromophore.

    Science.gov (United States)

    Mitzi, David B.; Chondroudis, Konstantinos; Kagan, Cherie R.

    1999-12-27

    A quaterthiophene derivative, 5,5' "-bis(aminoethyl)-2,2':5',2' ':5' ',2' "-quaterthiophene (AEQT), has been selected for incorporation within the layered organic-inorganic perovskite structure. In addition to having an appropriate molecular shape and two tethering aminoethyl groups to bond to the inorganic framework, AEQT is also a dye and can influence the optical properties of lead(II) halide-based perovskites. Crystals of C(20)H(22)S(4)N(2)PbBr(4) were grown from a slowly cooled aqueous solution containing lead(II) bromide and quaterthiophene derivative (AEQT.2HBr) salts. The new layered perovskite adopts a monoclinic (C2/c) subcell with the lattice parameters a = 39.741(2) Å, b = 5.8420(3) Å, c = 11.5734(6) Å, beta = 92.360(1) degrees, and Z = 4. Broad superstructure peaks are observed in the X-ray diffraction data, indicative of a poorly ordered, doubled supercell along both the a and b axes. The quaterthiophene segment of AEQT(2+) is nearly planar, with a syn-anti-syn relationship between adjacent thiophene rings. Each quaterthiophene chromophore is ordered between nearest-neighbor lead(II) bromide sheets in a herringbone arrangement with respect to neighboring quaterthiophenes. Room temperature optical absorption spectra for thermally ablated films of the perovskites (AEQT)PbX(4) (X = Cl, Br, I) exhibit an exciton peak arising from the lead(II) halide sheets, along with absorption from the quaterthiophene moiety. No evidence of the inorganic sheet excitonic transition is observed in the photoluminescence spectra for any of the chromophore-containing perovskites. However, strong quaterthiophene photoluminescence is observed for X = Cl, with an emission peak at approximately lambda(max) = 532 nm. Similar photoluminescence is observed for the X = Br and I materials, but with substantial quenching, as the inorganic layer band gap decreases relative to the chromophore HOMO-LUMO gap.

  13. Absorption by DNA single strands of adenine isolated in vacuo: The role of multiple chromophores

    DEFF Research Database (Denmark)

    Nielsen, L.M.; Pedersen, S.O.; Kirketerp, M.-B.S.

    2012-01-01

    to that for the adenine molecule and the dAMP mononucleotide. Desolvation has little effect on the bandwidth, which implies that inhomogenous broadening of the absorption bands in aqueous solution is of minor importance compared to, e.g., conformational disorder. Finally, at high photon energies, internal conversion...

  14. Characteristics of Chromophoric and Fluorescent Dissolved Organic Matter in the Nordic Seas

    OpenAIRE

    Makarewicz, Anna; Kowalczuk, Piotr; Sagan, Sławomir; Granskog, Mats A.; Pavlov, Alexey K.; Zdun, Agnieszka; Borzycka, Karolina; Zabłocka, Monika

    2018-01-01

    Optical properties of Chromophoric (CDOM) and Fluorescent Dissolved Organic Matter (FDOM) were characterized in the Nordic Seas including the West Spitsbergen Shelf during June–July of 2013, 2014 and 2015. The CDOM absorption coefficient at 350 nm, aCDOM(350) showed significant interannual variation. In 2013, the highest average aCDOM(350) values (aCDOM = 0.30 ± 0.12 m−1) were observed due to the influence of cold and low–saline wat...

  15. Second harmonic generation and photochromic grating in polyurethane films containing diazo isoxazole chromophore

    Science.gov (United States)

    Marański, Krzysztof; Kucharski, Stanisław; Ortyl, Ewelina; Nunzi, Jean-Michel; Ahmadi-Kandjani, Sohrab; Dabos-Seignon, Sylvie; Chan, Siu-Wai; Barille, Regis

    2008-08-01

    The chromophoric intermediate: 2,2'-({4-[( E)-(5-methylisoxazol-3-yl)diazenyl]phenyl}-imino)diethanol was used in polyaddition reaction with di-isocyanate to obtain a new polyurethane polymeric material showing nonlinear optical and photochromic properties. The maximum absorption band of the polymer film was at 418 nm. The illumination of the film with crossed beams of the 488 nm Ar + laser yielded surface relief grating of regular structure. Measurement of the frequency doubling signal with 1064 nm laser indicated the polymer as interesting material for photooptical applications. The measured nonlinear optical coefficient, d33, reached 90.2 pm/V.

  16. Determination of retinal chromophore structure in bacteriorhodopsin with resonance Raman spectroscopy.

    Science.gov (United States)

    Smith, S O; Lugtenburg, J; Mathies, R A

    1985-01-01

    The analysis of the vibrational spectrum of the retinal chromophore in bacteriorhodopsin with isotopic derivatives provides a powerful "structural dictionary" for the translation of vibrational frequencies and intensities into structural information. Of importance for the proton-pumping mechanism is the unambiguous determination of the configuration about the C13=C14 and C=N bonds, and the protonation state of the Schiff base nitrogen. Vibrational studies have shown that in light-adapted BR568 the Schiff base nitrogen is protonated and both the C13=C14 and C=N bonds are in a trans geometry. The formation of K625 involves the photochemical isomerization about only the C13=C14 bond which displaces the Schiff base proton into a different protein environment. Subsequent Schiff base deprotonation produces the M412 intermediate. Thermal reisomerization of the C13=C14 bond and reprotonation of the Schiff base occur in the M412------O640 transition, resetting the proton-pumping mechanism. The vibrational spectra can also be used to examine the conformation about the C--C single bonds. The frequency of the C14--C15 stretching vibration in BR568, K625, L550 and O640 argues that the C14--C15 conformation in these intermediates is s-trans. Conformational distortions of the chromophore have been identified in K625 and O640 through the observation of intense hydrogen out-of-plane wagging vibrations in the Raman spectra (see Fig. 2). These two intermediates are the direct products of chromophore isomerization. Thus it appears that following isomerization in a tight protein binding pocket, the chromophore cannot easily relax to a planar geometry. The analogous observation of intense hydrogen out-of-plane modes in the primary photoproduct in vision (Eyring et al., 1982) suggests that this may be a general phenomenon in protein-bound isomerizations. Future resonance Raman studies should provide even more details on how bacterio-opsin and retinal act in concert to produce an

  17. Bioinspired synthesis of pentalene-based chromophores from an oligoketone chain.

    Science.gov (United States)

    Saito, Yuki; Higuchi, Masayuki; Yoshioka, Shota; Senboku, Hisanori; Inokuma, Yasuhide

    2018-04-24

    We report a bioinspired synthesis of 2,5-dihydropentalene-based chromophores from an aliphatic oligoketone bearing 1,3- and 1,4-diketone subunits. Unlike the natural polyketone sequence, fused five-membered rings were formed via an intramolecular aldol condensation. A subsequent Knoevenagel condensation reaction with malononitrile furnished a multiply cross-conjugated π-system with low-lying LUMO levels. Furthermore, pentalenes obtained from a non-conjugated aliphatic chain exhibited visible absorption and solid-state fluorescence.

  18. Direct and Indirect Electron Emission from the Green Fluorescent Protein Chromophore

    Science.gov (United States)

    Toker, Y.; Rahbek, D. B.; Klærke, B.; Bochenkova, A. V.; Andersen, L. H.

    2012-09-01

    Photoelectron spectra of the deprotonated green fluorescent protein chromophore have been measured in the gas phase at several wavelengths within and beyond the S0-S1 photoabsorption band of the molecule. The vertical detachment energy (VDE) was determined to be 2.68±0.1eV. The data show that the first electronically excited state is bound in the Franck-Condon region, and that electron emission proceeds through an indirect (resonant) electron-emission channel within the corresponding absorption band.

  19. New organic photorefractive material composed of a charge-transporting dendrimer and a stilbene chromophore

    Science.gov (United States)

    Bai, Jaeil; Ducharme, Stephen; Leonov, Alexei G.; Lu, Liu; Takacs, James M.

    1999-10-01

    In this report, we introduce new organic photorefractive composites consisting of charge transporting den-drimers highly doped with a stilbene nonlinear optic chromophore, The purpose of making these composites is to improve charge transport, by reducing inhomogeneity when compared to ordinary polymer-based systems. Because the structure of this material gives us freedom to control the orientation of charge transport agents synthetically, we can study the charge transport mechanism more systematically than in polymers. We discuss this point and present the characterization results for this material.

  20. Wide-range tuning of polymer microring resonators by the photobleaching of CLD-1 chromophores

    Science.gov (United States)

    Poon, Joyce K. S.; Huang, Yanyi; Paloczi, George T.; Yariv, Amnon; Zhang, Cheng; Dalton, Larry R.

    2004-11-01

    We present a simple and effective method for the postfabrication trimming of optical microresonators. We photobleach CLD-1 chromophores to tune the resonance wavelengths of polymer microring resonator optical notch filters. A maximum wavelength shift of -8.73 nm is observed. The resonators are fabricated with a soft-lithography molding technique and have an intrinsic Q value of 2.6×10^4 and a finesse of 9.3. The maximum extinction ratio of the resonator filters is -34 dB, indicating that the critical coupling condition has been satisfied.

  1. Associated depression in pseudophakic patients with intraocular lens with and without chromophore

    Directory of Open Access Journals (Sweden)

    Mendoza-Mendieta ME

    2016-03-01

    Full Text Available María Elena Mendoza-Mendieta, Ana Aurora Lorenzo-Mejía Association to Prevent Blindness in Mexico (APEC, Hospital “Dr Luis Sánchez Bulnes”, Mexico City, Mexico Background: With aging, the crystalline lens turns yellowish, which increases the absorption of wavelengths in the blue electromagnetic spectrum, reducing their photoreception in the retina. Since these wavelengths are the main stimulus in the regulation of the circadian rhythm, progressive reduction in their transmission is associated with chronic sleep disturbances and depression in elderly patients. Cataract extraction improves circadian photoreception at any age. However, lenses that block blue waves have 27% to 38% less melatonin suppression than lenses that block only ultraviolet (UV rays. Purpose: To assess the depression symptoms in subjects who have had bilateral phacoemulsification and intraocular lens (IOL implants, one group with yellow chromophore IOLs and the other group with transparent IOLs were compared. Setting: Association to Prevent Blindness in Mexico (APEC, Hospital “Dr Luis Sánchez Bulnes”. Design: This was an observational, cross-sectional, and single-center study. Materials and methods: Twenty-six subjects between 60 and 80 years of age, with a history of bilateral phacoemulsification and placement of the same type of IOL in both eyes from 4 to 12 months prior to the study, who attended the follow-up visits and agreed to participate in this study, and provided signed informed consent were included in the study. They were asked to answer the short version of the 15-item Geriatric Depression Scale. Results: The average age of the study participants was 72.5±5.94 years. The group without chromophore included 46.1% (n=12 of the patients and the group with chromophore included 53.9% (n=14 of the patients (P=0.088. Conclusion: In the group of patients with IOLs that block the passage of blue light, the depression rate was 21.4%, a rate similar to that

  2. Synthesis and Properties of the p-Sulfonamide Analogue of the Green Fluorescent Protein (GFP) Chromophore: The Mimic of GFP Chromophore with Very Strong N-H Photoacid Strength.

    Science.gov (United States)

    Chen, Yi-Hui; Sung, Robert; Sung, Kuangsen

    2018-04-06

    The para-sulfonamide analogue ( p-TsABDI) of a green fluorescent protein (GFP) chromophore was synthesized to mimic the GFP chromophore. Its S 1 excited-state p K a * value in dimethylsulfoxide (DMSO) is -1.5, which is strong enough to partially protonate dipolar aprotic solvents and causes excited-state proton transfer (ESPT), so it can partially mimic the GFP chromophore to further study the ESPT-related photophysics and the blinking phenomenon of GFP. In comparison with 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) (p K a = 7.4, p K a * = 1.3 in water), p-TsABDI (p K a = 6.7, p K a * = -1.5 in DMSO) is a better photoacid for pH-jump studies.

  3. Biomolecular Mechanisms of Pseudomonas aeruginosa and Escherichia coli Biofilm Formation

    Science.gov (United States)

    Laverty, Garry; Gorman, Sean P.; Gilmore, Brendan F.

    2014-01-01

    Pseudomonas aeruginosa and Escherichia coli are the most prevalent Gram-negative biofilm forming medical device associated pathogens, particularly with respect to catheter associated urinary tract infections. In a similar manner to Gram-positive bacteria, Gram-negative biofilm formation is fundamentally determined by a series of steps outlined more fully in this review, namely adhesion, cellular aggregation, and the production of an extracellular polymeric matrix. More specifically this review will explore the biosynthesis and role of pili and flagella in Gram-negative adhesion and accumulation on surfaces in Pseudomonas aeruginosa and Escherichia coli. The process of biofilm maturation is compared and contrasted in both species, namely the production of the exopolysaccharides via the polysaccharide synthesis locus (Psl), pellicle Formation (Pel) and alginic acid synthesis in Pseudomonas aeruginosa, and UDP-4-amino-4-deoxy-l-arabinose and colonic acid synthesis in Escherichia coli. An emphasis is placed on the importance of the LuxR homologue sdiA; the luxS/autoinducer-II; an autoinducer-III/epinephrine/norepinephrine and indole mediated Quorum sensing systems in enabling Gram-negative bacteria to adapt to their environments. The majority of Gram-negative biofilms consist of polysaccharides of a simple sugar structure (either homo- or heteropolysaccharides) that provide an optimum environment for the survival and maturation of bacteria, allowing them to display increased resistance to antibiotics and predation. PMID:25438014

  4. Biomolecular Mechanisms of Pseudomonas aeruginosa and Escherichia coli Biofilm Formation

    Directory of Open Access Journals (Sweden)

    Garry Laverty

    2014-07-01

    Full Text Available Pseudomonas aeruginosa and Escherichia coli are the most prevalent Gram-negative biofilm forming medical device associated pathogens, particularly with respect to catheter associated urinary tract infections. In a similar manner to Gram-positive bacteria, Gram-negative biofilm formation is fundamentally determined by a series of steps outlined more fully in this review, namely adhesion, cellular aggregation, and the production of an extracellular polymeric matrix. More specifically this review will explore the biosynthesis and role of pili and flagella in Gram-negative adhesion and accumulation on surfaces in Pseudomonas aeruginosa and Escherichia coli. The process of biofilm maturation is compared and contrasted in both species, namely the production of the exopolysaccharides via the polysaccharide synthesis locus (Psl, pellicle Formation (Pel and alginic acid synthesis in Pseudomonas aeruginosa, and UDP-4-amino-4-deoxy-l-arabinose and colonic acid synthesis in Escherichia coli. An emphasis is placed on the importance of the LuxR homologue sdiA; the luxS/autoinducer-II; an autoinducer-III/epinephrine/norepinephrine and indole mediated Quorum sensing systems in enabling Gram-negative bacteria to adapt to their environments. The majority of Gram-negative biofilms consist of polysaccharides of a simple sugar structure (either homo- or heteropolysaccharides that provide an optimum environment for the survival and maturation of bacteria, allowing them to display increased resistance to antibiotics and predation.

  5. The therapy of kidney cancer with biomolecular drugs.

    Science.gov (United States)

    Di Lorenzo, G; Buonerba, C; Biglietto, M; Scognamiglio, F; Chiurazzi, B; Riccardi, F; Cartenì, G

    2010-11-01

    Over the last few years, targeted agents have assumed a predominant role in treatment of metastatic renal cell carcinoma (mRCC). Our aim is to discuss recent developments on this rapidly evolving topic. Sunitinib represents front-line standard treatment for the good- and intermediate prognosis groups of patients with clear cell renal carcinoma. Bevacizumab/interferon and pazopanib have also been FDA-approved as first-line agents, while sorafenib has moved toward second-line and later therapy. Temsirolimus, an mTOR inhibitor, is recommended as front line therapy for patients in the poor-risk group and is the best front-line choice for patients with non-clear cell histology. Another mTOR inhibitor, everolimus, has shown clinical benefit post-tyrosine kinasis inhibitors failure in a phase III study and is considered the standard of care in this setting. Novel prognostic and efficacy markers might help to define most appropriate therapeutic strategy. Best sequence of use of these effective agents in mRCC patients remains up to the discretion of treating physician. In light of the considerable advances in understanding the biology of mRCC, several new drugs have been recently developed, with an increasing number of treatment options. Several markers are under evaluation for diagnostic, prognostic and efficacy purposes. A treatment algorithm, based on the best scientific evidence produce so far, is presented and it will evolve as data from ongoing trials will be available. Copyright © 2010 Elsevier Ltd. All rights reserved.

  6. Plucked Human Hair Shafts and Biomolecular Medical Research

    Directory of Open Access Journals (Sweden)

    Kevin Schembri

    2013-01-01

    Full Text Available The hair follicle is a skin integument at the boundary between an organism and its immediate environment. The biological role of the human hair follicle has lost some of its ancestral importance. However, an indepth investigation of this miniorgan reveals hidden complexity with huge research potential. An essential consideration when dealing with human research is the awareness of potential harm and thus the absolute need not to harm—a rule aptly qualified by the Latin term “primum non nocere” (first do no harm. The plucked hair shaft offers such advantages. The use of stem cells found in hair follicles cells is gaining momentum in the field of regenerative medicine. Furthermore, current diagnostic and clinical applications of plucked hair follicles include their use as autologous and/or three-dimensional epidermal equivalents, together with their utilization as surrogate tissue in pharmacokinetic and pharmacodynamics studies. Consequently, the use of noninvasive diagnostic procedures on hair follicle shafts, posing as a surrogate molecular model for internal organs in the individual patient for a spectrum of human disease conditions, can possibly become a reality in the near future.

  7. Chromophore-assisted light inactivation of pKi-67 leads to inhibition of ribosomal RNA synthesis.

    Science.gov (United States)

    Rahmanzadeh, R; Hüttmann, G; Gerdes, J; Scholzen, T

    2007-06-01

    Expression of the nuclear Ki-67 protein (pKi-67) is strongly associated with cell proliferation. For this reason, antibodies against this protein are widely used as prognostic tools for the assessment of cell proliferation in biopsies from cancer patients. Despite this broad application in histopathology, functional evidence for the physiological role of pKi-67 is still missing. Recently, we proposed a function of pKi-67 in the early steps of ribosomal RNA (rRNA) synthesis. Here, we have examined the involvement of pKi-67 in this process by photochemical inhibition using chromophore-assisted light inactivation (CALI). Anti-pKi-67 antibodies were labelled with the fluorochrome fluorescein 5(6)-isothiocyanate and were irradiated after binding to their target protein. Performing CALI in vitro on cell lysates led to specific cross-linking of pKi-67. Moreover, the upstream binding factor (UBF) necessary for rRNA transcription was also partly subjected to cross-link formation, indicating a close spatial proximity of UBF and pKi-67. CALI in living cells, using micro-injected antibody, caused a striking relocalization of UBF from foci within the nucleoli to spots located at the nucleolar rim or within the nucleoplasm. pKi-67-CALI resulted in dramatic inhibition of RNA polymerase I-dependent nucleolar rRNA synthesis, whereas RNA polymerase II-dependent nucleoplasmic RNA synthesis remained almost unaltered. Our data presented here argue for a crucial role of pKi-67 in RNA polymerase I-dependent nucleolar rRNA synthesis.

  8. Synthesis and Properties of Novel T-Type Polyurethanes Containing 2,5-Dioxynitrostilbenyl Group as a Nonlinear Optical Chromophore

    International Nuclear Information System (INIS)

    Lee, Ju Yeon; Lee, Won Jung; Park, Eun Ju; Bang, Han Bae; Rhee, Bum Ku; Jung, Chang Soo; Lee, Seung Mook; Lee, Jin Hyun

    2003-01-01

    Two approaches to minimize the randomization have been proposed. One is to use crosslinking method and the other is to use high T g polymers such as polyimides. Polyurethane matrix forms extensive hydrogen bond between urethane linkage and increases rigidity preventing the relaxation of induced dipoles. In this work we prepared new T-type polyurethanes containing dioxynitrostilbenyl group as a NLO-chromophore. We selected 2,5-dioxynitrostilbenyl group as NLO-chromophore because it will have a large dipole moment and is rather easy to synthesize. Furthermore 2,5-dioxynitrostilbenyl group constitutes a novel T-type NLO polyurthanes, in which the NLO chromophores are parts of polymer backbones. These T-type NLO polyurethanes are not shown in the literature. After confirming the structure of the resulting polymers we investigated the properties such as T g and second harmonic generation (SHG) activity (d 33 ). We now report the results of the initial phase of the work

  9. A Light-Induced Reaction with Oxygen Leads to Chromophore Decomposition and Irreversible Photobleaching in GFP-Type Proteins.

    Science.gov (United States)

    Grigorenko, Bella L; Nemukhin, Alexander V; Polyakov, Igor V; Khrenova, Maria G; Krylov, Anna I

    2015-04-30

    Photobleaching and photostability of proteins of the green fluorescent protein (GFP) family are crucially important for practical applications of these widely used biomarkers. On the basis of simulations, we propose a mechanism for irreversible bleaching in GFP-type proteins under intense light illumination. The key feature of the mechanism is a photoinduced reaction of the chromophore with molecular oxygen (O2) inside the protein barrel leading to the chromophore's decomposition. Using quantum mechanics/molecular mechanics (QM/MM) modeling we show that a model system comprising the protein-bound Chro(-) and O2 can be excited to an electronic state of the intermolecular charge-transfer (CT) character (Chro(•)···O2(-•)). Once in the CT state, the system undergoes a series of chemical reactions with low activation barriers resulting in the cleavage of the bridging bond between the phenolic and imidazolinone rings and disintegration of the chromophore.

  10. Water-Soluble Triarylborane Chromophores for One- and Two-Photon Excited Fluorescence Imaging of Mitochondria in Cells.

    Science.gov (United States)

    Griesbeck, Stefanie; Zhang, Zuolun; Gutmann, Marcus; Lühmann, Tessa; Edkins, Robert M; Clermont, Guillaume; Lazar, Adina N; Haehnel, Martin; Edkins, Katharina; Eichhorn, Antonius; Blanchard-Desce, Mireille; Meinel, Lorenz; Marder, Todd B

    2016-10-04

    Three water-soluble tetracationic quadrupolar chromophores comprising two three-coordinate boron π-acceptor groups bridged by thiophene-containing moieties were synthesised for biological imaging applications. Compound 3 containing the bulkier 5-(3,5-Me2 C6 H2 )-2,2'-(C4 H2 S)2 -5'-(3,5-Me2 C6 H2 ) bridge is stable over a long period of time, exhibits a high fluorescence quantum yield and strong one- and two-photon absorption (TPA), and has a TPA cross section of 268 GM at 800 nm in water. Confocal laser scanning fluorescence microscopy studies in live cells indicated localisation of the chromophore at the mitochondria; moreover, cytotoxicity measurements proved biocompatibility. Thus, chromophore 3 has excellent potential for one- and two-photon-excited fluorescence imaging of mitochondrial function in cells. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Active and silent chromophore isoforms for phytochrome Pr photoisomerization: An alternative evolutionary strategy to optimize photoreaction quantum yields

    Directory of Open Access Journals (Sweden)

    Yang Yang

    2014-01-01

    Full Text Available Photoisomerization of a protein bound chromophore is the basis of light sensing of many photoreceptors. We tracked Z-to-E photoisomerization of Cph1 phytochrome chromophore PCB in the Pr form in real-time. Two different phycocyanobilin (PCB ground state geometries with different ring D orientations have been identified. The pre-twisted and hydrogen bonded PCBa geometry exhibits a time constant of 30 ps and a quantum yield of photoproduct formation of 29%, about six times slower and ten times higher than that for the non-hydrogen bonded PCBb geometry. This new mechanism of pre-twisting the chromophore by protein-cofactor interaction optimizes yields of slow photoreactions and provides a scaffold for photoreceptor engineering.

  12. The importance of charge-transfer interactions in determining chromophoric dissolved organic matter (CDOM) optical and photochemical properties.

    Science.gov (United States)

    Sharpless, Charles M; Blough, Neil V

    2014-04-01

    Absorption of sunlight by chromophoric dissolved natural organic matter (CDOM) is environmentally significant because it controls photic zone depth and causes photochemistry that affects elemental cycling and contaminant fate. Both the optics (absorbance and fluorescence) and photochemistry of CDOM display unusual properties that cannot easily be ascribed to a superposition of individual chromophores. These include (i) broad, unstructured absorbance that decreases monotonically well into the visible and near IR, (ii) fluorescence emission spectra that all fall into a single envelope regardless of the excitation wavelength, and (iii) photobleaching and photochemical quantum yields that decrease monotonically with increasing wavelength. In contrast to a simple superposition model, these phenomena and others can be reasonably well explained by a physical model in which charge-transfer interactions between electron donating and accepting chromophores within the CDOM control the optical and photophysical properties. This review summarizes current understanding of the processes underlying CDOM photophysics and photochemistry as well as their physical basis.

  13. Interacting with the biomolecular solvent accessible surface via a haptic feedback device

    Directory of Open Access Journals (Sweden)

    Hayward Steven

    2009-10-01

    Full Text Available Abstract Background From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion By using the software, named HaptiMol ISAS (available from http://www.haptimol.co.uk, one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water

  14. Raman spectroscopy detects biomolecular changes associated with nanoencapsulated hesperetin treatment in experimental oral carcinogenesis

    International Nuclear Information System (INIS)

    Gurushankar, K; Gohulkumar, M; Krishnakumar, N; Kumar, Piyush; Murali Krishna, C

    2016-01-01

    Recently it has been shown that Raman spectroscopy possesses great potential in the investigation of biomolecular changes of tumor tissues with therapeutic drug response in a non-invasive and label-free manner. The present study is designed to investigate the antitumor effect of hespertin-loaded nanoparticles (HETNPs) relative to the efficacy of native hesperetin (HET) in modifying the biomolecular changes during 7,12-dimethyl benz(a)anthracene (DMBA)-induced oral carcinogenesis using a Raman spectroscopic technique. Significant differences in the intensity and shape of the Raman spectra between the control and the experimental tissues at 1800–500 cm −1 were observed. Tumor tissues are characterized by an increase in the relative amount of proteins, nucleic acids, tryptophan and phenylalanine and a decrease in the percentage of lipids when compared to the control tissues. Further, oral administration of HET and its nanoparticulates restored the status of the lipids and significantly decreased the levels of protein and nucleic acid content. Treatment with HETNPs showed a more potent antitumor effect than treatment with native HET, which resulted in an overall reduction in the intensity of several biochemical Raman bands in DMBA-induced oral carcinogenesis being observed. Principal component and linear discriminant analysis (PC–LDA), together with leave-one-out cross validation (LOOCV) on Raman spectra yielded diagnostic sensitivities of 100%, 80%, 91.6% and 65% and specificities of 100%, 65%, 60% and 55% for classification of control versus DMBA, DMBA versus DMBA  +  HET, DMBA versus DMBA  +  HETNPs and DMBA  +  HET versus DMBA  +  HETNPs treated tissue groups, respectively. These results further demonstrate that Raman spectroscopy associated with multivariate statistical algorithms could be a valuable tool for developing a comprehensive understanding of the process of biomolecular changes, and could reveal the signatures of the

  15. Insights Into the Bifunctional Aphidicolan-16-ß-ol Synthase Through Rapid Biomolecular Modeling Approaches.

    Science.gov (United States)

    Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B

    2018-01-01

    Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modeling techniques offer an alternative route to study the enzyme's reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modeling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modeling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789, and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modeling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially restricted location of

  16. The use of gold nanoparticle aggregation for DNA computing and logic-based biomolecular detection

    International Nuclear Information System (INIS)

    Lee, In-Hee; Yang, Kyung-Ae; Zhang, Byoung-Tak; Lee, Ji-Hoon; Park, Ji-Yoon; Chai, Young Gyu; Lee, Jae-Hoon

    2008-01-01

    The use of DNA molecules as a physical computational material has attracted much interest, especially in the area of DNA computing. DNAs are also useful for logical control and analysis of biological systems if efficient visualization methods are available. Here we present a quick and simple visualization technique that displays the results of the DNA computing process based on a colorimetric change induced by gold nanoparticle aggregation, and we apply it to the logic-based detection of biomolecules. Our results demonstrate its effectiveness in both DNA-based logical computation and logic-based biomolecular detection

  17. Insights Into the Bifunctional Aphidicolan-16-ß-ol Synthase Through Rapid Biomolecular Modeling Approaches

    Directory of Open Access Journals (Sweden)

    Max Hirte

    2018-04-01

    Full Text Available Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modeling techniques offer an alternative route to study the enzyme's reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modeling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modeling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789, and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modeling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially

  18. Insights into the bifunctional Aphidicolan-16-ß-ol synthase through rapid biomolecular modelling approaches

    Science.gov (United States)

    Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B.

    2018-04-01

    Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modelling techniques offer an alternative route to study the enzyme’s reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modelling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modelling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789 and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modelling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially restricted location

  19. Towards sensitive, high-throughput, biomolecular assays based on fluorescence lifetime

    Science.gov (United States)

    Ioanna Skilitsi, Anastasia; Turko, Timothé; Cianfarani, Damien; Barre, Sophie; Uhring, Wilfried; Hassiepen, Ulrich; Léonard, Jérémie

    2017-09-01

    Time-resolved fluorescence detection for robust sensing of biomolecular interactions is developed by implementing time-correlated single photon counting in high-throughput conditions. Droplet microfluidics is used as a promising platform for the very fast handling of low-volume samples. We illustrate the potential of this very sensitive and cost-effective technology in the context of an enzymatic activity assay based on fluorescently-labeled biomolecules. Fluorescence lifetime detection by time-correlated single photon counting is shown to enable reliable discrimination between positive and negative control samples at a throughput as high as several hundred samples per second.

  20. Conformation of bovine submaxillary mucin layers on hydrophobic surface as studied by biomolecular probes

    DEFF Research Database (Denmark)

    Pakkanen, Kirsi I.; Madsen, Jan Busk; Lee, Seunghwan

    2015-01-01

    In the present study, the conformational changes of bovine submaxillary mucin (BSM) adsorbed on a hydrophobic surface (polystyrene (PS)) as a function of concentration in bulk solution (up to 2mg/mL) have been investigated with biomolecular probe-based approaches, including bicinchoninic acid (BCA),enzyme-linkedimmunosorbentassay(EIA...... solution. Adsorbed masses of BSM onto hydrophobic surface, as probe by BCA, showed a continuously increasing trend up to 2mg/mL. But, the signals from EIA and ELLA, which probe the concentration of available unglycosylatedC-terminals and the central glycosylated regions, respectively, showed complicated...

  1. Super-resolution biomolecular crystallography with low-resolution data.

    Science.gov (United States)

    Schröder, Gunnar F; Levitt, Michael; Brunger, Axel T

    2010-04-22

    X-ray diffraction plays a pivotal role in the understanding of biological systems by revealing atomic structures of proteins, nucleic acids and their complexes, with much recent interest in very large assemblies like the ribosome. As crystals of such large assemblies often diffract weakly (resolution worse than 4 A), we need methods that work at such low resolution. In macromolecular assemblies, some of the components may be known at high resolution, whereas others are unknown: current refinement methods fail as they require a high-resolution starting structure for the entire complex. Determining the structure of such complexes, which are often of key biological importance, should be possible in principle as the number of independent diffraction intensities at a resolution better than 5 A generally exceeds the number of degrees of freedom. Here we introduce a method that adds specific information from known homologous structures but allows global and local deformations of these homology models. Our approach uses the observation that local protein structure tends to be conserved as sequence and function evolve. Cross-validation with R(free) (the free R-factor) determines the optimum deformation and influence of the homology model. For test cases at 3.5-5 A resolution with known structures at high resolution, our method gives significant improvements over conventional refinement in the model as monitored by coordinate accuracy, the definition of secondary structure and the quality of electron density maps. For re-refinements of a representative set of 19 low-resolution crystal structures from the Protein Data Bank, we find similar improvements. Thus, a structure derived from low-resolution diffraction data can have quality similar to a high-resolution structure. Our method is applicable to the study of weakly diffracting crystals using X-ray micro-diffraction as well as data from new X-ray light sources. Use of homology information is not restricted to X

  2. Refractive index modulation in the polyurethane films containing diazo sulfonamide chromophores

    Energy Technology Data Exchange (ETDEWEB)

    Ortyl, E. [Insitute of Organic and Polymer Technology, WrocIaw University of Technology, 50-384 WrocIaw (Poland); Kucharski, S. [Insitute of Organic and Polymer Technology, WrocIaw University of Technology, 50-384 WrocIaw (Poland)]. E-mail: stanislaw.kucharski@pwr.wroc.pl; Gotszalk, T. [Faculty of Microsystem Electronics and Photonics, WrocIaw University of Technology, 50-384 WrocIaw (Poland)

    2005-05-23

    The series of photochromic polyurethanes was obtained by modification of precursor polymers prepared from 4,4'-diphenylmethane diisocyanate (MDI), hexamethylene 1,6-diisocyanate (HDI) or toluene 2,4-diisocyanate (TDI) and N,N'-di-(2-hydroxyethyl) aniline. The precursor polymers were functionalized by an azo-coupling reaction to form the polymers with different degrees of functionalization and various heterocyclic sulfonamide groups. Ellipsometric measurements showed a decrease of the refractive index during illumination of thin polymer films with white light. The change of real part of the refractive index was in the range of 0.0033-0.0296 depending on the polymer kind and chromophore content. It was found that photocurrent was generated in the polymer films deposited onto indium tin oxide (ITO) glass plates. For the polyurethanes containing sulfathiazole groups in side chains the current density was up to 180 nA/cm{sup 2}. The formation of diffraction grating in the polymer films was easily achieved using linearly polarized laser light (532 nm) in a standard two beam coupling (TBC) system. The diffraction efficiency of the first diffraction beam was dependent on the chromophore content reaching ca. 12% for the derivatives of sulfamethoxazole.

  3. Electron transfer in silicon-bridged adjacent chromophores: the source for blue-green emission.

    Science.gov (United States)

    Bayda, Malgorzata; Angulo, Gonzalo; Hug, Gordon L; Ludwiczak, Monika; Karolczak, Jerzy; Koput, Jacek; Dobkowski, Jacek; Marciniak, Bronislaw

    2017-05-10

    Si-Bridged chromophores have been proposed as sources for blue-green emission in several technological applications. The origin of this dual emission is to be found in an internal charge transfer reaction. The current work is an attempt to describe the details of these processes in these kinds of substances, and to design a molecular architecture to improve their performance. Nuclear motions essential for intramolecular charge transfer (ICT) can involve processes from twisted internal moieties to dielectric relaxation of the solvent. To address these issues, we studied ICT between adjacent chromophores in a molecular compound containing N-isopropylcarbazole (CBL) and 1,4-divinylbenzene (DVB) linked by a dimethylsilylene bridge. In nonpolar solvents emission arises from the local excited state (LE) of carbazole whereas in solvents of higher polarity dual emission was detected (LE + ICT). The CT character of the additional emission band was concluded from the linear dependence of the fluorescence maxima on solvent polarity. Electron transfer from CBL to DVB resulted in a large excited-state dipole moment (37.3 D) as determined from a solvatochromic plot and DFT calculations. Steady-state and picosecond time-resolved fluorescence experiments in butyronitrile (293-173 K) showed that the ICT excited state arises from the LE state of carbazole. These results were analyzed and found to be in accordance with an adiabatic version of Marcus theory including solvent relaxation.

  4. Photoproduction of hydrogen peroxide in aqueous solution from model compounds for chromophoric dissolved organic matter (CDOM)

    International Nuclear Information System (INIS)

    Clark, Catherine D.; Bruyn, Warren de; Jones, Joshua G.

    2014-01-01

    Highlights: • CDOM produces hydrogen peroxide in sunlit surface waters. • Quinone moieties have been proposed as the photo-active chromophore in CDOM. • Hydrogen peroxide is produced in irradiated aqueous quinone solutions. • Concentrations and production rates are comparable to humic and fulvic acids. • Optical properties post-irradiation were similar to CDOM. - Abstract: To explore whether quinone moieties are important in chromophoric dissolved organic matter (CDOM) photochemistry in natural waters, hydrogen peroxide (H 2 O 2 ) production and associated optical property changes were measured in aqueous solutions irradiated with a Xenon lamp for CDOM model compounds (dihydroquinone, benzoquinone, anthraquinone, napthoquinone, ubiquinone, humic acid HA, fulvic acid FA). All compounds produced H 2 O 2 with concentrations ranging from 15 to 500 μM. Production rates were higher for HA vs. FA (1.32 vs. 0.176 mM h −1 ); values ranged from 6.99 to 0.137 mM h −1 for quinones. Apparent quantum yields (Θ app ; measure of photochemical production efficiency) were higher for HA vs. FA (0.113 vs. 0.016) and ranged from 0.0018 to 0.083 for quinones. Dihydroquinone, the reduced form of benzoquinone, had a higher production rate and efficiency than its oxidized form. Post-irradiation, quinone compounds had absorption spectra similar to HA and FA and 3D-excitation–emission matrix fluorescence spectra (EEMs) with fluorescent peaks in regions associated with CDOM

  5. Unmixing chromophores in human skin with a 3D multispectral optoacoustic mesoscopy system

    Science.gov (United States)

    Schwarz, Mathias; Aguirre, Juan; Soliman, Dominik; Buehler, Andreas; Ntziachristos, Vasilis

    2016-03-01

    The absorption of visible light by human skin is governed by a number of natural chromophores: Eumelanin, pheomelanin, oxyhemoglobin, and deoxyhemoglobin are the major absorbers in the visible range in cutaneous tissue. Label-free quantification of these tissue chromophores is an important step of optoacoustic (photoacoustic) imaging towards clinical application, since it provides relevant information in diseases. In tumor cells, for instance, there are metabolic changes (Warburg effect) compared to healthy cells, leading to changes in oxygenation in the environment of tumors. In malignant melanoma changes in the absorption spectrum have been observed compared to the spectrum of nonmalignant nevi. So far, optoacoustic imaging has been applied to human skin mostly in single-wavelength mode, providing anatomical information but no functional information. In this work, we excited the tissue by a tunable laser source in the spectral range from 413-680 nm with a repetition rate of 50 Hz. The laser was operated in wavelengthsweep mode emitting consecutive pulses at various wavelengths that allowed for automatic co-registration of the multispectral datasets. The multispectral raster-scan optoacoustic mesoscopy (MSOM) system provides a lateral resolution of melanin, oxyhemoglobin, and deoxyhemoglobin, three-dimensional absorption maps of all three absorbers were calculated from the multispectral dataset.

  6. On the Role of London Dispersion Forces in Biomolecular Structure Determination

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Kubař, T.; Hobza, Pavel

    2011-01-01

    Roč. 115, č. 24 (2011), s. 8038-8046 ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA ČR GAP208/11/0295 Grant - others:Korea Science and Ingineering Foundation(KR) R32-2008-000-10180-0; European Scince Found(XE) CZ.1.05/2.1.00/03.0058 Institutional research plan: CEZ:AV0Z40550506 Keywords : dispersion interaction * DNA * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.696, year: 2011

  7. [Study on optical characteristics of chromophoric dissolved organic matter (CDOM) in rainwater by fluorescence excitation-emission matrix and absorbance spectroscopy].

    Science.gov (United States)

    Cheng, Yuan-yue; Guo, Wei-dong; Long, Ai-min; Chen, Shao-yong

    2010-09-01

    The optical characteristics of chromophoric dissolved organic matter (CDOM) were determined in rain samples collected in Xiamen Island, during a rainy season in 2007, using fluorescence excitation-emission matrix spectroscopy associated with UV-Vis absorbance spectra. Results showed that the absorbance spectra of CDOM in rain samples decreased exponentially with wavelength. The absorbance coefficient at 300 nm [a(300)] ranged from 0.27 to 3.45 m(-1), which would be used as an index of CDOM abundance, and the mean value was 1.08 m(-1). The content of earlier stage of precipitation events was higher than that of later stage of precipitation events, which implied that anthropogenic sources or atmospheric pollution or air mass types were important contributors to CDOM levels in precipitation. EEMs spectra showed 4 types of fluorescence signals (2 humic-like fluorescence peaks and 2 protein-like fluorescence peaks) in rainwater samples, and there were significant positive correlations of peak A with C and peak B with S, showing their same sources or some relationship of the two humic-like substance and the two protein-like substance. The strong positive correlations of the two humic-like fluorescence peaks with a(300), suggested that the chromophores responsible for absorbance might be the same as fluorophores responsible for fluorescence. Results showed that the presence of highly absorbing and fluorescing CDOM in rainwater is of significant importance in atmospheric chemistry and might play a previously unrecognized role in the wavelength dependent spectral attenuation of solar radiation by atmospheric waters.

  8. A compact imaging spectroscopic system for biomolecular detections on plasmonic chips.

    Science.gov (United States)

    Lo, Shu-Cheng; Lin, En-Hung; Wei, Pei-Kuen; Tsai, Wan-Shao

    2016-10-17

    In this study, we demonstrate a compact imaging spectroscopic system for high-throughput detection of biomolecular interactions on plasmonic chips, based on a curved grating as the key element of light diffraction and light focusing. Both the curved grating and the plasmonic chips are fabricated on flexible plastic substrates using a gas-assisted thermal-embossing method. A fiber-coupled broadband light source and a camera are included in the system. Spectral resolution within 1 nm is achieved in sensing environmental index solutions and protein bindings. The detected sensitivities of the plasmonic chip are comparable with a commercial spectrometer. An extra one-dimensional scanning stage enables high-throughput detection of protein binding on a designed plasmonic chip consisting of several nanoslit arrays with different periods. The detected resonance wavelengths match well with the grating equation under an air environment. Wavelength shifts between 1 and 9 nm are detected for antigens of various concentrations binding with antibodies. A simple, mass-productive and cost-effective method has been demonstrated on the imaging spectroscopic system for real-time, label-free, highly sensitive and high-throughput screening of biomolecular interactions.

  9. Biomolecular solid state NMR with magic-angle spinning at 25K.

    Science.gov (United States)

    Thurber, Kent R; Tycko, Robert

    2008-12-01

    A magic-angle spinning (MAS) probe has been constructed which allows the sample to be cooled with helium, while the MAS bearing and drive gases are nitrogen. The sample can be cooled to 25K using roughly 3 L/h of liquid helium, while the 4-mm diameter rotor spins at 6.7 kHz with good stability (+/-5 Hz) for many hours. Proton decoupling fields up to at least 130 kHz can be applied. This helium-cooled MAS probe enables a variety of one-dimensional and two-dimensional NMR experiments on biomolecular solids and other materials at low temperatures, with signal-to-noise proportional to 1/T. We show examples of low-temperature (13)C NMR data for two biomolecular samples, namely the peptide Abeta(14-23) in the form of amyloid fibrils and the protein HP35 in frozen glycerol/water solution. Issues related to temperature calibration, spin-lattice relaxation at low temperatures, paramagnetic doping of frozen solutions, and (13)C MAS NMR linewidths are discussed.

  10. ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design.

    Science.gov (United States)

    Wood, Christopher W; Heal, Jack W; Thomson, Andrew R; Bartlett, Gail J; Ibarra, Amaurys Á; Brady, R Leo; Sessions, Richard B; Woolfson, Derek N

    2017-10-01

    The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users. Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico. ISAMBARD addresses a standing issue in protein design, namely, how to introduce backbone variability in a controlled manner. This is achieved through the generalization of tools for parametric modelling, describing the overall shape of proteins geometrically, and without input from experimentally determined structures. This will allow backbone conformations for entire folds and assemblies not observed in nature to be generated de novo, that is, to access the 'dark matter of protein-fold space'. We anticipate that ISAMBARD will find broad applications in biomolecular design, biotechnology and synthetic biology. A current stable build can be downloaded from the python package index (https://pypi.python.org/pypi/isambard/) with development builds available on GitHub (https://github.com/woolfson-group/) along with documentation, tutorial material and all the scripts used to generate the data described in this paper. d.n.woolfson@bristol.ac.uk or chris.wood@bristol.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  11. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

    Science.gov (United States)

    van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J

    2016-02-22

    The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  12. Single-molecule imaging and manipulation of biomolecular machines and systems.

    Science.gov (United States)

    Iino, Ryota; Iida, Tatsuya; Nakamura, Akihiko; Saita, Ei-Ichiro; You, Huijuan; Sako, Yasushi

    2018-02-01

    Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. A new approach to implement absorbing boundary condition in biomolecular electrostatics.

    Science.gov (United States)

    Goni, Md Osman

    2013-01-01

    This paper discusses a novel approach to employ the absorbing boundary condition in conjunction with the finite-element method (FEM) in biomolecular electrostatics. The introduction of Bayliss-Turkel absorbing boundary operators in electromagnetic scattering problem has been incorporated by few researchers. However, in the area of biomolecular electrostatics, this boundary condition has not been investigated yet. The objective of this paper is twofold. First, to solve nonlinear Poisson-Boltzmann equation using Newton's method and second, to find an efficient and acceptable solution with minimum number of unknowns. In this work, a Galerkin finite-element formulation is used along with a Bayliss-Turkel absorbing boundary operator that explicitly accounts for the open field problem by mapping the Sommerfeld radiation condition from the far field to near field. While the Bayliss-Turkel condition works well when the artificial boundary is far from the scatterer, an acceptable tolerance of error can be achieved with the second order operator. Numerical results on test case with simple sphere show that the treatment is able to reach the same level of accuracy achieved by the analytical method while using a lower grid density. Bayliss-Turkel absorbing boundary condition (BTABC) combined with the FEM converges to the exact solution of scattering problems to within discretization error.

  14. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems

    International Nuclear Information System (INIS)

    Zhou, Peipei; Cai, Shuiming; Liu, Zengrong; Chen, Luonan; Wang, Ruiqi

    2013-01-01

    To understand how a complex biomolecular network functions, a decomposition or a reconstruction process of the network is often needed so as to provide new insights into the regulatory mechanisms underlying various dynamical behaviors and also to gain qualitative knowledge of the network. Unfortunately, it seems that there are still no general rules on how to decompose a complex network into simple modules. An alternative resolution is to decompose a complex network into small modules or subsystems with specified functions such as switches and oscillators and then integrate them by analyzing the interactions between them. The main idea of this approach can be illustrated by considering a bidirectionally coupled network in this paper, i.e., coupled Toggle switch and Repressilator, and analyzing the occurrence of various dynamics, although the theoretical principle may hold for a general class of networks. We show that various biomolecular signals can be shaped by regulating the coupling between the subsystems. The approach presented here can be expected to simplify and analyze even more complex biological networks

  15. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Peipei [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China); Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China); Cai, Shuiming [Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China); Liu, Zengrong [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China); Chen, Luonan [Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Center for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Collaborative Research Center for Innovative Mathematical Modeling, Institute of Industrial Science, University of Tokyo, Tokyo 153-8505 (Japan); Wang, Ruiqi [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China)

    2013-05-15

    To understand how a complex biomolecular network functions, a decomposition or a reconstruction process of the network is often needed so as to provide new insights into the regulatory mechanisms underlying various dynamical behaviors and also to gain qualitative knowledge of the network. Unfortunately, it seems that there are still no general rules on how to decompose a complex network into simple modules. An alternative resolution is to decompose a complex network into small modules or subsystems with specified functions such as switches and oscillators and then integrate them by analyzing the interactions between them. The main idea of this approach can be illustrated by considering a bidirectionally coupled network in this paper, i.e., coupled Toggle switch and Repressilator, and analyzing the occurrence of various dynamics, although the theoretical principle may hold for a general class of networks. We show that various biomolecular signals can be shaped by regulating the coupling between the subsystems. The approach presented here can be expected to simplify and analyze even more complex biological networks.

  16. Optimal number of coarse-grained sites in different components of large biomolecular complexes.

    Science.gov (United States)

    Sinitskiy, Anton V; Saunders, Marissa G; Voth, Gregory A

    2012-07-26

    The computational study of large biomolecular complexes (molecular machines, cytoskeletal filaments, etc.) is a formidable challenge facing computational biophysics and biology. To achieve biologically relevant length and time scales, coarse-grained (CG) models of such complexes usually must be built and employed. One of the important early stages in this approach is to determine an optimal number of CG sites in different constituents of a complex. This work presents a systematic approach to this problem. First, a universal scaling law is derived and numerically corroborated for the intensity of the intrasite (intradomain) thermal fluctuations as a function of the number of CG sites. Second, this result is used for derivation of the criterion for the optimal number of CG sites in different parts of a large multibiomolecule complex. In the zeroth-order approximation, this approach validates the empirical rule of taking one CG site per fixed number of atoms or residues in each biomolecule, previously widely used for smaller systems (e.g., individual biomolecules). The first-order corrections to this rule are derived and numerically checked by the case studies of the Escherichia coli ribosome and Arp2/3 actin filament junction. In different ribosomal proteins, the optimal number of amino acids per CG site is shown to differ by a factor of 3.5, and an even wider spread may exist in other large biomolecular complexes. Therefore, the method proposed in this paper is valuable for the optimal construction of CG models of such complexes.

  17. Investigating biomolecular recognition at the cell surface using atomic force microscopy.

    Science.gov (United States)

    Wang, Congzhou; Yadavalli, Vamsi K

    2014-05-01

    Probing the interaction forces that drive biomolecular recognition on cell surfaces is essential for understanding diverse biological processes. Force spectroscopy has been a widely used dynamic analytical technique, allowing measurement of such interactions at the molecular and cellular level. The capabilities of working under near physiological environments, combined with excellent force and lateral resolution make atomic force microscopy (AFM)-based force spectroscopy a powerful approach to measure biomolecular interaction forces not only on non-biological substrates, but also on soft, dynamic cell surfaces. Over the last few years, AFM-based force spectroscopy has provided biophysical insight into how biomolecules on cell surfaces interact with each other and induce relevant biological processes. In this review, we focus on describing the technique of force spectroscopy using the AFM, specifically in the context of probing cell surfaces. We summarize recent progress in understanding the recognition and interactions between macromolecules that may be found at cell surfaces from a force spectroscopy perspective. We further discuss the challenges and future prospects of the application of this versatile technique. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Chromophore-Dependent Intramolecular Exciton-Vibrational Coupling in the FMO Complex: Quantification and Importance for Exciton Dynamics.

    Science.gov (United States)

    Padula, Daniele; Lee, Myeong H; Claridge, Kirsten; Troisi, Alessandro

    2017-11-02

    In this paper, we adopt an approach suitable for monitoring the time evolution of the intramolecular contribution to the spectral density of a set of identical chromophores embedded in their respective environments. We apply the proposed method to the Fenna-Matthews-Olson (FMO) complex, with the objective to quantify the differences among site-dependent spectral densities and the impact of such differences on the exciton dynamics of the system. Our approach takes advantage of the vertical gradient approximation to reduce the computational demands of the normal modes analysis. We show that the region of the spectral density that is believed to strongly influence the exciton dynamics changes significantly in the timescale of tens of nanoseconds. We then studied the impact of the intramolecular vibrations on the exciton dynamics by considering a model of FMO in a vibronic basis and neglecting the interaction with the environment to isolate the role of the intramolecular exciton-vibration coupling. In agreement with the assumptions in the literature, we demonstrate that high frequency modes at energy much larger than the excitonic energy splitting have negligible influence on exciton dynamics despite the large exciton-vibration coupling. We also find that the impact of including the site-dependent spectral densities on exciton dynamics is not very significant, indicating that it may be acceptable to apply the same spectral density on all sites. However, care needs to be taken for the description of the exciton-vibrational coupling in the low frequency part of intramolecular modes because exciton dynamics is more susceptible to low frequency modes despite their small Huang-Rhys factors.

  19. Effect of intercalation and chromophore arrangement on the linear and nonlinear optical properties of model aminopyridine push–pull molecules

    Czech Academy of Sciences Publication Activity Database

    Bureš, F.; Cvejn, D.; Melánová, Klára; Beneš, L.; Svoboda, Jan; Zima, Vítězslav; Pytela, O.; Mikysek, T.; Růžičková, Z.; Kityk, I. V.; Wojciechowski, A.; AlZayed, N.

    2016-01-01

    Roč. 4, č. 3 (2016), s. 468-478 ISSN 2050-7526 R&D Projects: GA ČR(CZ) GA13-01061S Institutional support: RVO:61389013 Keywords : push-pull chromophore * intercalation * layered phosphates Subject RIV: CA - Inorganic Chemistry Impact factor: 5.256, year: 2016

  20. Photochemical degradation of chromophoric-dissolved organic matter exposed to simulated UV-B and natural solar radiation

    NARCIS (Netherlands)

    Zhang, Y.; Liu, M.; Qin, B.; Feng, S.

    2009-01-01

    Photochemical degradation of chromophoric-dissolved organic matter (CDOM) by UV-B radiation decreases CDOM absorption in the UV region and fluorescence intensity, and alters CDOM composition. CDOM absorption, fluorescence, and the spectral slope indicating the CDOM composition were studied using

  1. Synthesis and Properties of Novel Polyurethane Containing Nitrophenylazocatecholic Group as NLO Chromophore

    International Nuclear Information System (INIS)

    Song, Mi Young; Kim, Mi Sung; Lee, Ju Yeon

    2012-01-01

    The promise of NLO polymers lies in their higher nonlinear optical activity, faster response time, and easy fabrication into electro-optic devices. In the developments of NLO polymers for electrooptic device applications, stabilization of electrically induced dipole alignment is one of important considerations; in this context, two approaches to minimize the randomization have been proposed, namely the use of cross-linked systems and the utilization of polymers with high glass transition temperature (T g ) such as polyimides. A polyurethane matrix forms extensive hydrogen bonding between urethane linkages, with increased rigidity preventing the relaxation of induced dipoles. Polyurethanes functionalized with hemicyanine and thiophene ring in side chain show an enhanced thermal stability of aligned dipoles. Polyurethanes with NLO chromophores, whose dipole moments are aligned transverse to the main chains, show large second-order nonlinearity with good thermal stability

  2. Symmetry Breaking in Platinum Acetylide Chromophores Studied by Femtosecond Two-Photon Absorption Spectroscopy

    Science.gov (United States)

    2014-02-01

    used hyper- Raman and hyper-Rayleigh scattering to show that in some nominally centrosymmetric metal- free chromophores the inversion symmetry could be...67 618 320 1300 654 1300 NH2 742 18 53 590 30 160 782 93 51 602 160 650 644 420 OCH3 722 16 16 560 57 120 774 57 66 604 190 660 646 300 t-butyl 714...420 644 220 F 706 5.9 1.6 560 85 85 772 53 89 600 60 340 644 170 CF3 714 6.4 22 586 31 110 792 120 210 602 87 440 650 250 CN 732 29 28 590 32 120 814

  3. Synthesis of Dendrimer Containing Dialkylated-fluorene Unit as a Core Chromophore via Click Chemistry

    International Nuclear Information System (INIS)

    Han, Seung Choul; Lee, Jae Wook; Jin, Sung Ho

    2012-01-01

    The convergent synthetic strategy for the emissive dendrimers having the chromophore at core via the coppercatalyzed 1,3-dipolar cycloaddition reaction between alkyne and azide was described. 2,7-Diazido-9,9-dioctyl- 9H-fluorene, designed to serve as the core in dendrimer, was stitched with the alkyne-functionalized Frechettype and PAMAM dendrons by the click chemistry leading to the formation of the corresponding fluorescent dendrimers in high yields. The preliminary photoluminescence studies indicated that 2,7-diazido-9,9-dioctyl- 9H-fluorene showed no fluorescence due to the quenching effect from the electron-rich α-nitrogen of the azido group but the dendrimers fluoresced due to the elimination of the quenching through the formation of the triazole ring

  4. Tracing global biogeochemical cycles and meridional overturning circulation using chromophoric dissolved organic matter

    Science.gov (United States)

    Nelson, Norman B.; Siegel, David A.; Carlson, Craig A.; Swan, Chantal M.

    2010-02-01

    Basin-scale distributions of light absorption by chromophoric dissolved organic matter (CDOM) are positively correlated (R2 > 0.8) with apparent oxygen utilization (AOU) within the top kilometer of the Pacific and Indian Oceans. However, a much weaker correspondence is found for the Atlantic (R2 organic matter from sinking particles. The observed meridional-depth sections of CDOM result from a balance between biogeochemical processes (autochthonous production and solar bleaching) and the meridional overturning circulation. Rapid mixing in the Atlantic dilutes CDOM in the interior and implies that the time scale for CDOM accumulation is greater than ˜50 years. CDOM emerges as a unique tracer for diagnosing changes in biogeochemistry and the overturning circulation, similar to dissolved oxygen, with the additional feature that it can be quantified from satellite observation.

  5. Picosecond absorption studies of photoinduced charge separation in polyelectrolyte bound aromatic chromophores

    Science.gov (United States)

    Shand, M. A.; Rodgers, M. A. J.; Webber, S. E.

    1991-02-01

    Picosecond absorption studies of photoinduced electron transfer between aromatic chromophores bound to polymethacrylic acid (P) and methylviologen (MV 2+ have been carried out in aqueous solution. The diphenylanthracene copolymer/viologen system at pH 2.8 shows the corresponding redox products DPA + rad and MV + rad arising from the singlet state of DPA with a forward rate constant of electron transfer of 2.6 × 10 9 s -1. At pH 9.0 the quenching of the S 1 state of DPA occurs with no charge separated products being observed. The pyrene copolymer shows no evidence of charge separated products at any pH in the range 2.8-9.0. It is proposed that the differences in the radical pair kinetics arise from differences in the degree of binding of the ground state complexes formed by the donor and acceptor species.

  6. Depth profiling of laser-heated chromophores in biological tissues by pulsed photothermal radiometry

    International Nuclear Information System (INIS)

    Milner, T.E.; Goodman, D.M.; Tanenbaum, B.S.; Nelson, J.S.

    1995-01-01

    A solution method is proposed to the inverse problem of determining the unknown initial temperature distribution in a laser-exposed test material from measurements provided by infrared radiometry. A Fredholm integral equation of the first kind is derived that relates the temporal evolution of the infrared signal amplitude to the unknown initial temperature distribution in the exposed test material. The singular-value decomposition is used to demonstrate the severely ill-posed nature of the derived inverse problem. Three inversion methods are used to estimate solutions for the initial temperature distribution. A nonnegatively constrained conjugate-gradient algorithm using early termination is found superior to unconstrained inversion methods and is applied to image the depth of laser-heated chromophores in human skin. Key words: constrained conjugate gradients, ill-posed problem, infrared radiometry, laser surgery, nonnegative, singular-value decomposition

  7. Dimeric fluorescent energy transfer dyes comprising asymmetric cyanine azole-indolenine chromophores

    Science.gov (United States)

    Glazer, Alexander N.; Benson, Scott C.

    1998-01-01

    Novel fluorescent heterodimeric DNA-staining energy transfer dyes are provided combining asymmetric cyanine azole-indolenine dyes, which provide for strong DNA affinity, large Stokes shifts and emission in the red region of the spectrum. The dyes find particular application in gel electrophoresis and for labels which may be bound to a variety of compositions in a variety of contexts. Kits and individual compounds are provided, where the kits find use for simultaneous detection of a variety of moieties, particularly using a single narrow wavelength irradiation source. The individual compounds are characterized by high donor quenching and high affinity to dsDNA as a result of optimizing the length of the linking group separating the two chromophores.

  8. Band-engineering of TiO2 as a wide-band gap semiconductor using organic chromophore dyes

    Science.gov (United States)

    Wahyuningsih, S.; Kartini, I.; Ramelan, A. H.; Saputri, L. N. M. Z.; Munawaroh, H.

    2017-07-01

    Bond-engineering as applied to semiconductor materials refers to the manipulation of the energy bands in order to control charge transfer processes in a device. When the device in question is a photoelectrochemical cell, the charges affected by drift become the focus of the study. The ideal band gap of semiconductors for enhancement of photocatalyst activity can be lowered to match with visible light absorption and the location of conduction Band (CB) should be raised to meet the reducing capacity. Otherwise, by the addition of the chromofor organic dyes, the wide-band gab can be influences by interacation resulting between TiO2 surface and the dyes. We have done the impruvisation wide-band gap of TiO2 by the addition of organic chromophore dye, and the addition of transition metal dopand. The TiO2 morphology influence the light absorption as well as the surface modification. The organic chromophore dye was syntesized by formation complexes compound of Co(PAR)(SiPA)(PAR)= 4-(2-piridylazoresorcinol), SiPA = Silyl propil amine). The result showed that the chromophore groups adsorbed onto TiO2 surface can increase the visible light absorption of wide-band gab semiconductor. Initial absorption of a chromophore will affect light penetration into the material surfaces. The use of photonic material as a solar cell shows this phenomenon clearly from the IPCE (incident photon to current conversion efficiency) measurement data. Organic chromophore dyes of Co(PAR)(SiPA) exhibited the long wavelength absorption character compared to the N719 dye (from Dyesol).

  9. Native fluorescence detection of biomolecular and pharmaceutical compounds in capillary electrophoresis: detector designs, performance and applications: A review

    NARCIS (Netherlands)

    de Kort, B.J.; de Jong, G.J.; Somsen, G.W.

    2013-01-01

    This review treats the coupling of capillary electrophoresis (CE) with fluorescence detection (Flu) for the analysis of natively fluorescent biomolecular and pharmaceutical compounds. CE-Flu combines the excellent separation efficiency of CE with the high selectivity and sensitivity of Flu. In

  10. Investigation of the Human Disease Osteogenesis Imperfecta: A Research-Based Introduction to Concepts and Skills in Biomolecular Analysis

    Science.gov (United States)

    Mate, Karen; Sim, Alistair; Weidenhofer, Judith; Milward, Liz; Scott, Judith

    2013-01-01

    A blended approach encompassing problem-based learning (PBL) and structured inquiry was used in this laboratory exercise based on the congenital disease Osteogenesis imperfecta (OI), to introduce commonly used techniques in biomolecular analysis within a clinical context. During a series of PBL sessions students were presented with several…

  11. Electrochemical sensor for multiplex screening of genetically modified DNA: identification of biotech crops by logic-based biomolecular analysis.

    Science.gov (United States)

    Liao, Wei-Ching; Chuang, Min-Chieh; Ho, Ja-An Annie

    2013-12-15

    Genetically modified (GM) technique, one of the modern biomolecular engineering technologies, has been deemed as profitable strategy to fight against global starvation. Yet rapid and reliable analytical method is deficient to evaluate the quality and potential risk of such resulting GM products. We herein present a biomolecular analytical system constructed with distinct biochemical activities to expedite the computational detection of genetically modified organisms (GMOs). The computational mechanism provides an alternative to the complex procedures commonly involved in the screening of GMOs. Given that the bioanalytical system is capable of processing promoter, coding and species genes, affirmative interpretations succeed to identify specified GM event in terms of both electrochemical and optical fashions. The biomolecular computational assay exhibits detection capability of genetically modified DNA below sub-nanomolar level and is found interference-free by abundant coexistence of non-GM DNA. This bioanalytical system, furthermore, sophisticates in array fashion operating multiplex screening against variable GM events. Such a biomolecular computational assay and biosensor holds great promise for rapid, cost-effective, and high-fidelity screening of GMO. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Small-angle X-ray scattering investigations of biomolecular confinement, loading, and release from liquid-crystalline nanochannel assemblies

    Czech Academy of Sciences Publication Activity Database

    Angelova, A.; Angelov, Borislav; Garamus, V. M.; Couvreur, P.; Lesieur, S.

    2012-01-01

    Roč. 3, č. 3 (2012), s. 445-457 ISSN 1948-7185 Institutional research plan: CEZ:AV0Z40500505 Keywords : nanochannels * biomolecular nanostructures * SAXS Subject RIV: CD - Macromolecular Chemistry Impact factor: 6.585, year: 2012

  13. Chromophore dynamics in the PYP photocycle from femtosecond stimulated Raman spectroscopy.

    Science.gov (United States)

    Creelman, Mark; Kumauchi, Masato; Hoff, Wouter D; Mathies, Richard A

    2014-01-23

    Femtosecond stimulated Raman spectroscopy (FSRS) is used to examine the structural dynamics of the para-hydroxycinnamic acid (HCA) chromophore during the first 300 ps of the photoactive yellow protein (PYP) photocycle, as the system transitions from its vertically excited state to the early ground state cis intermediate, I0. A downshift in both the C7═C8 and C1═O stretches upon photoexcitation reveals that the chromophore has shifted to an increasingly quinonic form in the excited state, indicating a charge shift from the phenolate moiety toward the C9═O carbonyl, which continues to increase for 170 fs. In addition, there is a downshift in the C9═O carbonyl out-of-plane vibration on an 800 fs time scale as PYP transitions from its excited state to I0, indicating that weakening of the hydrogen bond with Cys69 and out-of-plane rotation of the C9═O carbonyl are key steps leading to photoproduct formation. HOOP intensity increases on a 3 ps time scale during the formation of I0, signifying distortion about the C7═C8 bond. Once on the I0 surface, the C7═C8 and C1═O stretches blue shift, indicating recovery of charge to the phenolate, while persistent intensity in the HOOP and carbonyl out-of-plane modes reveal HCA to be a cissoid structure with significant distortion about the C7═C8 bond and of C9═O out of the molecular plane.

  14. [Photodegradation of chromophoric dissolved organic matter from Jiulong River Estuary under natural solar radiation].

    Science.gov (United States)

    Guo, Wei-dong; Cheng, Yuan-yue

    2008-06-01

    Low salinity water sample collected from Jiulong River Estuary filtered using 0.2 microm Millipore filter was exposed to natural solar radiation from 10:00 to 16:00 each day during one week period in early and late May, 2005. Photodegradation of fluorescence and absorption properties of CDOM (chromophoric dissolved organic matter) was observed. The results showed that humic-like fluorescence (lambda Ex/lambda Em = 350/450 nm), tryptophan-like fluorescence (lambda Ex/lambda Em = 225/350 nm) and absorption coefficient of CDOM can be significantly photodegraded during short-term solar exposure in early summer. These photodegradation processes followed the first-order dynamic equation. The degradation half time of humic-like fluorescence, tryptophan-like fluorescence and a (280) were calculated as 3.5-5.1 d, 3.0-4.5 d and 6.3 d. The absorption loss spectra of CDOM indicated that the solar UV radiation was responsible for the photochemical degradation of CDOM. The loss of humic-like fluorescence (70%) was obviously higher than loss of a (280) (about 40%), suggesting that photobleaching ability of CDOM fluorophores were much stronger than CDOM chromophores. However, the correlation relationship between humic-like fluorescence and absorption coefficient are still kept. A250/A350 of CDOM increased till the end of radiation experiment compared with the control group, suggesting photodegradation may decrease the average molecular size of CDOM. These findings show that terrestrial CDOM can be transformed and removed by photochemical decomposition after transport into the sea, and photodegradation might be an important sink for terrestrial CDOM.

  15. Effects of Clear Kefir on Biomolecular Aspects of Glycemic Status of Type 2 Diabetes Mellitus (T2DM Patients in Bandung, West Java [Study on Human Blood Glucose, c Peptide and Insulin

    Directory of Open Access Journals (Sweden)

    Judiono J

    2014-08-01

    Full Text Available Background: Diabetes Mellitus (DM triggers an excessive reaction of free-radicals. It increases reactive oxygen species and reduces antioxidants status as well as the β cell damage. Clear kefir was used for DM therapies, however it limited biomolecular exploration of its bioactive roles. Research aimed to investigate the effects of clear kefir on the biomolecular nature of the glycemic status of T2DM in Bandung. Methods: The randomized pretest-posttest control group was conducted by 106 T2DM patients. Research was done in several hospitals in Bandung and Cimahi, West Java from 2012–2013. Samples were divided randomly into three groups: (1 T2DM with HbA1c 7 fed standard diet and supplemented 200 ml/day by clear kefir, (3 T2DM with HbA1c was fed a standard diet as a control group. Dose response was obtained from a preeliminary vivo study, and then converted to human dosage by year 2011. Intervention was effectively done for 30 days. HbA1c was measured by HPLC. Fasting blood glucose (FBG and Postprandial blood glucose levels (PBG were measured by enzymes levels. C Peptide and insulin were measured by Elisa. Data was analyzed by a statictics programme by significance p<0,05. Study was approved by ethic committee. Results : HbA1c was significantly reduced in delta level (p<0.01 and FBG (p<0.015 among kefir groups. PBG was not significantly reduced among groups. C-Peptide was significantly increased in delta level, except in control group (p<0.014. Insulin was reduced significantly, except in control group (p<0.003. Conclusions : Supplementation of clear kefir reduced blood glucose levels (HbA1c, FBG, PBG and increased c-peptide. Clear kefir’s biomolecular mechanisms and chemistry characterization is a challenge for future studies.

  16. Evidences of long lived cages in functionalized polymers: Effects on chromophore dynamic and spectroscopic properties

    Science.gov (United States)

    Prampolini, Giacomo; Monti, Susanna; De Mitri, Nicola; Barone, Vincenzo

    2014-05-01

    action on the dye, can be evinced from the analysis of selected dynamic properties, related to NfO-TEMPO translational and rotational motions and to the residence times of the neighboring groups into the first neighbors shell. All the details for the calculations of the latter three properties are also defined in the Supporting Information. As far as the dye translational dynamics is concerned, the mean square displacement (MSD) of the probe in the two different environments was monitored as a function of time and shown with solid lines in Figure 3. When the probe is grafted onto the polymer (orange line), the MSD reveals a sub-diffusive regime which is identified by the plateau visible in the logarithmic scale the Figure referenced above. This is a typical signature of a β-relaxation, that takes place from the end of the pure ballistic dynamics (hundreds of femtoseconds) to the onset of the linear behavior (visible after around 100 ps). It could be speculated that this trend might be due on the one hand, to the intrinsic sub-diffusive character of the dynamics of the polymer bundle which is transmitted to the dye through the grafting process, and on the other hand, to the polymer cage around the probe which prevents it from reaching a true diffusive regime. This analysis can be extended to the re-orientational processes, by investigating the relaxation of the main molecular axes of the dye (α,β,γ). To this end, the auto correlation function of the first Legendre polynomial (P1) of one (β) of the tumbling axes is plotted vs time and shown in Figure 3. A qualitatively similar behavior was found for the other axes. The different role played by the two embeddings appears clearly from the comparison of the two data sets. Indeed, while in the less structured solvent (toluene), a relatively fast reorientation of the dye takes place, and the P1 function drops below 0.5 after ∼10 ps, in the other case (polymer) a neat plateau again appears in the 1-100 ps range, and the

  17. Piezoelectric tuning fork biosensors for the quantitative measurement of biomolecular interactions

    International Nuclear Information System (INIS)

    Gonzalez, Laura; Maria Benito, Angel; Puig-Vidal, Manel; Otero, Jorge; Rodrigues, Mafalda; Pérez-García, Lluïsa

    2015-01-01

    The quantitative measurement of biomolecular interactions is of great interest in molecular biology. Atomic force microscopy (AFM) has proved its capacity to act as a biosensor and determine the affinity between biomolecules of interest. Nevertheless, the detection scheme presents certain limitations when it comes to developing a compact biosensor. Recently, piezoelectric quartz tuning forks (QTFs) have been used as laser-free detection sensors for AFM. However, only a few studies along these lines have considered soft biological samples, and even fewer constitute quantified molecular recognition experiments. Here, we demonstrate the capacity of QTF probes to perform specific interaction measurements between biotin–streptavidin complexes in buffer solution. We propose in this paper a variant of dynamic force spectroscopy based on representing adhesion energies E (aJ) against pulling rates v (nm s"–"1). Our results are compared with conventional AFM measurements and show the great potential of these sensors in molecular interaction studies. (paper)

  18. XML-based approaches for the integration of heterogeneous bio-molecular data.

    Science.gov (United States)

    Mesiti, Marco; Jiménez-Ruiz, Ernesto; Sanz, Ismael; Berlanga-Llavori, Rafael; Perlasca, Paolo; Valentini, Giorgio; Manset, David

    2009-10-15

    The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

  19. Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies

    International Nuclear Information System (INIS)

    Zhou Pei; Wagner, Gerhard

    2010-01-01

    Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR. We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs.

  20. RPYFMM: Parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations

    Science.gov (United States)

    Guan, W.; Cheng, X.; Huang, J.; Huber, G.; Li, W.; McCammon, J. A.; Zhang, B.

    2018-06-01

    RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a linear combination of four Laplace interactions, each of which is evaluated using the adaptive fast multipole method (FMM) (Greengard and Rokhlin, 1997) where the exponential expansions are applied to diagonalize the multipole-to-local translation operators. RPYFMM offers a unified execution on both shared and distributed memory computers by leveraging the DASHMM library (DeBuhr et al., 2016, 2018). Preliminary numerical results show that the interactions for a molecular system of 15 million particles (beads) can be computed within one second on a Cray XC30 cluster using 12,288 cores, while achieving approximately 54% strong-scaling efficiency.

  1. Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation.

    Science.gov (United States)

    Seibert, Jakob; Bannwarth, Christoph; Grimme, Stefan

    2017-08-30

    A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, nonequilibrium structure and conformational, as well as purely quantum mechanical effects like charge-transfer or exciton-coupling, are included. Different from other contemporary approaches, the entire system is treated quantum mechanically and neither fragmentation nor system-specific adjustment is necessary. Among the systems considered are a large DNA fragment, oligopeptides, and even entire proteins in an implicit solvent. We propose the method in tandem with experimental spectroscopy or X-ray studies for the elucidation of complex (bio)molecular structures including metallo-proteins like myoglobin.

  2. Frequency-scanning MALDI linear ion trap mass spectrometer for large biomolecular ion detection.

    Science.gov (United States)

    Lu, I-Chung; Lin, Jung Lee; Lai, Szu-Hsueh; Chen, Chung-Hsuan

    2011-11-01

    This study presents the first report on the development of a matrix-assisted laser desorption ionization (MALDI) linear ion trap mass spectrometer for large biomolecular ion detection by frequency scan. We designed, installed, and tested this radio frequency (RF) scan linear ion trap mass spectrometer and its associated electronics to dramatically extend the mass region to be detected. The RF circuit can be adjusted from 300 to 10 kHz with a set of operation amplifiers. To trap the ions produced by MALDI, a high pressure of helium buffer gas was employed to quench extra kinetic energy of the heavy ions produced by MALDI. The successful detection of the singly charged secretory immunoglobulin A ions indicates that the detectable mass-to-charge ratio (m/z) of this system can reach ~385 000 or beyond.

  3. New hyperbranched polytriazoles containing isolation chromophore moieties derived from AB4 monomers through click chemistry under copper(I) catalysis: improved optical transparency and enhanced NLO effects.

    Science.gov (United States)

    Wu, Wenbo; Ye, Cheng; Yu, Gui; Liu, Yunqi; Qin, Jingui; Li, Zhen

    2012-04-02

    By modifying a synthetic procedure, two new hyperbranched polytriazoles (HP1 and HP2) containing isolation chromophores were synthesized successfully through click chemistry reactions under copper(I) catalysis. For the first time, these two polymers were derived from an AB(4)-type monomer, although they contain different end-capping chromophores. They are soluble in normal polar organic solvents and are well characterized. Thanks to the presence of the isolation chromophore, the two polymers demonstrate good nonlinear optical (NLO) properties and optical transparency, making them promising candidates for practical applications. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics

    Science.gov (United States)

    Sinitskiy, Anton V.; Pande, Vijay S.

    2018-01-01

    Markov state models (MSMs) have been widely used to analyze computer simulations of various biomolecular systems. They can capture conformational transitions much slower than an average or maximal length of a single molecular dynamics (MD) trajectory from the set of trajectories used to build the MSM. A rule of thumb claiming that the slowest implicit time scale captured by an MSM should be comparable by the order of magnitude to the aggregate duration of all MD trajectories used to build this MSM has been known in the field. However, this rule has never been formally proved. In this work, we present analytical results for the slowest time scale in several types of MSMs, supporting the above rule. We conclude that the slowest implicit time scale equals the product of the aggregate sampling and four factors that quantify: (1) how much statistics on the conformational transitions corresponding to the longest implicit time scale is available, (2) how good the sampling of the destination Markov state is, (3) the gain in statistics from using a sliding window for counting transitions between Markov states, and (4) a bias in the estimate of the implicit time scale arising from finite sampling of the conformational transitions. We demonstrate that in many practically important cases all these four factors are on the order of unity, and we analyze possible scenarios that could lead to their significant deviation from unity. Overall, we provide for the first time analytical results on the slowest time scales captured by MSMs. These results can guide further practical applications of MSMs to biomolecular dynamics and allow for higher computational efficiency of simulations.

  5. A biomolecular recognition approach for the functionalization of cellulose with gold nanoparticles.

    Science.gov (United States)

    Almeida, A; Rosa, A M M; Azevedo, A M; Prazeres, D M F

    2017-09-01

    Materials with new and improved functionalities can be obtained by modifying cellulose with gold nanoparticles (AuNPs) via the in situ reduction of a gold precursor or the deposition or covalent immobilization of pre-synthesized AuNPs. Here, we present an alternative biomolecular recognition approach to functionalize cellulose with biotin-AuNPs that relies on a complex of 2 recognition elements: a ZZ-CBM3 fusion that combines a carbohydrate-binding module (CBM) with the ZZ fragment of the staphylococcal protein A and an anti-biotin antibody. Paper and cellulose microparticles with AuNPs immobilized via the ZZ-CBM3:anti-biotin IgG supramolecular complex displayed an intense red color, whereas essentially no color was detected when AuNPs were deposited over the unmodified materials. Scanning electron microscopy analysis revealed a homogeneous distribution of AuNPs when immobilized via ZZ-CBM3:anti-biotin IgG complexes and aggregation of AuNPs when deposited over paper, suggesting that color differences are due to interparticle plasmon coupling effects. The approach could be used to functionalize paper substrates and cellulose nanocrystals with AuNPs. More important, however, is the fact that the occurrence of a biomolecular recognition event between the CBM-immobilized antibody and its specific, AuNP-conjugated antigen is signaled by red color. This opens up the way for the development of simple and straightforward paper/cellulose-based tests where detection of a target analyte can be made by direct use of color signaling. Copyright © 2017 John Wiley & Sons, Ltd.

  6. A hydrogel-based versatile screening platform for specific biomolecular recognition in a well plate format.

    Science.gov (United States)

    Beer, Meike V; Rech, Claudia; Diederichs, Sylvia; Hahn, Kathrin; Bruellhoff, Kristina; Möller, Martin; Elling, Lothar; Groll, Jürgen

    2012-04-01

    Precise determination of biomolecular interactions in high throughput crucially depends on a surface coating technique that allows immobilization of a variety of interaction partners in a non-interacting environment. We present a one-step hydrogel coating system based on isocyanate functional six-arm poly(ethylene oxide)-based star polymers for commercially available 96-well microtiter plates that combines a straightforward and robust coating application with versatile bio-functionalization. This system generates resistance to unspecific protein adsorption and cell adhesion, as demonstrated with fluorescently labeled bovine serum albumin and primary human dermal fibroblasts (HDF), and high specificity for the assessment of biomolecular recognition processes when ligands are immobilized on this surface. One particular advantage is the wide range of biomolecules that can be immobilized and convert the per se inert coating into a specifically interacting surface. We here demonstrate the immobilization and quantification of a broad range of biochemically important ligands, such as peptide sequences GRGDS and GRGDSK-biotin, the broadly applicable coupler molecule biocytin, the protein fibronectin, and the carbohydrates N-acetylglucosamine and N-acetyllactosamine. A simplified protocol for an enzyme-linked immunosorbent assay was established for the detection and quantification of ligands on the coating surface. Cell adhesion on the peptide and protein-modified surfaces was assessed using HDF. All coatings were applied using a one-step preparation technique, including bioactivation, which makes the system suitable for high-throughput screening in a format that is compatible with the most routinely used testing systems.

  7. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics

    KAUST Repository

    Sobhy, M. A.

    2011-11-07

    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and versatile multi-color excitation and emission fluorescence instrument for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact, where two inverted microscopes share a laser combiner module with six individual laser sources that extend from 400 to 640 nm. Nonetheless, each microscope can independently and in a flexible manner select the combinations, sequences, and intensities of the excitation wavelengths. This high flexibility is achieved by the replacement of conventional mechanical shutters with acousto-optic tunable filter (AOTF). The use of AOTF provides major advancement by controlling the intensities, duration, and selection of up to eight different wavelengths with microsecond alternation time in a transparent and easy manner for the end user. To our knowledge this is the first time AOTF is applied to wide-field total internal reflection fluorescence (TIRF) microscopy even though it has been commonly used in multi-wavelength confocal microscopy. The laser outputs from the combiner module are coupled to the microscopes by two sets of four single-mode optic fibers in order to allow for the optimization of the TIRF angle for each wavelength independently. The emission is split into two or four spectral channels to allow for the simultaneous detection of up to four different fluorophores of wide selection and using many possible excitation and photoactivation schemes. We demonstrate the performance of this new setup by conducting two-color alternating excitation single-molecule fluorescence resonance energy

  8. Optical properties and composition changes in chromophoric dissolved organic matter along trophic gradients: Implications for monitoring and assessing lake eutrophication.

    Science.gov (United States)

    Zhang, Yunlin; Zhou, Yongqiang; Shi, Kun; Qin, Boqiang; Yao, Xiaolong; Zhang, Yibo

    2017-12-26

    Chromophoric dissolved organic matter (CDOM) is an important optically active substance in aquatic environments and plays a key role in light attenuation and in the carbon, nitrogen and phosphorus biogeochemical cycles. Although the optical properties, abundance, sources, cycles, compositions and remote sensing estimations of CDOM have been widely reported in different aquatic environments, little is known about the optical properties and composition changes in CDOM along trophic gradients. Therefore, we collected 821 samples from 22 lakes along a trophic gradient (oligotrophic to eutrophic) in China from 2004 to 2015 and determined the CDOM spectral absorption and nutrient concentrations. The total nitrogen (TN), total phosphorus (TP), and chlorophyll a (Chla) concentrations and the Secchi disk depth (SDD) ranged from 0.02 to 24.75 mg/L, 0.002-3.471 mg/L, 0.03-882.66 μg/L, and 0.05-17.30 m, respectively. The trophic state index (TSI) ranged from 1.55 to 98.91 and covered different trophic states, from oligotrophic to hyper-eutrophic. The CDOM absorption coefficient at 254 nm (a(254)) ranged from 1.68 to 92.65 m -1 . Additionally, the CDOM sources and composition parameters, including the spectral slope and relative molecular size value, exhibited a substantial variability from the oligotrophic level to other trophic levels. The natural logarithm value of the CDOM absorption, lna(254), is highly linearly correlated with the TSI (r 2  = 0.92, p 10 m -1 , respectively. The results suggested that the CDOM absorption coefficient a(254) might be a more sensitive single indicator of the trophic state than TN, TP, Chla and SDD. Therefore, we proposed a CDOM absorption coefficient and determined the threshold for defining the trophic state of a lake. Several advantages of measuring and estimating CDOM, including rapid experimental measurements, potential in situ optical sensor measurements and large-spatial-scale remote sensing estimations, make it

  9. Spatiotemporal Characterization of Chromophoric Dissolved Organic Matter (CDOM and CDOM-DOC Relationships for Highly Polluted Rivers

    Directory of Open Access Journals (Sweden)

    Sijia Li

    2016-09-01

    Full Text Available Spectral characteristics of CDOM (Chromophoric dissolved organic matter in water columns are a key parameter for bio-optical modeling. Knowledge of CDOM optical properties and spatial discrepancy based on the relationship between water quality and spectral parameters in the Yinma River watershed with in situ data collected from highly polluted waters are exhibited in this study. Based on the comprehensive index method, the riverine waters showed serious contamination; especially the chemical oxygen demand (COD, iron (Fe, manganese (Mn, mercury (Hg and dissolved oxygen (DO were out of range of the contamination warning. Dissolved organic carbon (DOC and total suspended matter (TSM with prominent non-homogenizing were significantly high in the riverine waters, but chlorophyll-a (Chl-a was the opposite. The ternary phase diagram showed that non-algal particle absorption played an important role in total non-water light absorption (>50% in most sampling locations, and mean contributions of CDOM were 13% and 22% in the summer and autumn, respectively. The analysis of the ratio of absorption at 250–365 nm (E250:365 and the spectral slope (S275–295 indicated that CDOM had higher aromaticity and molecular weight in autumn than in summer, which is consistent with the results of water quality and the CDOM relative contribution rate. Redundancy analysis (RDA indicated that the environmental variables OSM (Organic suspended matter had a strong correlation with CDOM absorption, followed by heavy metals, e.g., Mn, Hg and Cr6+. However, for the specific UV absorbance (SUVA254, the seasonal values showed opposite results compared with the reported literature. The potential reasons were that more UDOM (uncolored dissolved organic matter from human sources (wastewater effluent existed in the waters. Terrigenous inputs simultaneously are in relation to the aCDOM(440-DOC relationship with the correlation coefficient of 0.90 in the summer (two-tailed, p < 0

  10. Light transmission through intraocular lenses with or without yellow chromophore (blue light filter) and its potential influence on functional vision in everyday environmental conditions.

    Science.gov (United States)

    Owczarek, Grzegorz; Gralewicz, Grzegorz; Skuza, Natalia; Jurowski, Piotr

    2016-01-01

    In this research the factors used to evaluate the light transmission through two types of acrylic hydrophobic intraocular lenses, one that contained yellow chromophore that blocks blue light transmission and the other which did not contain that filter, were defined according to various light condition, e.g., daylight and at night. The potential influence of light transmission trough intraocular lenses with or without yellow chromophore on functional vision in everyday environmental conditions was analysed.

  11. Report on result 1998. Research and development on fusion area. Part 3 (biomolecular mechanism and design); 1998 nendo seika hokokusho. Yugo ryoiki kenkyu kaihatsu daisan bunsatsu (bimolecular mechanism and design)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-03-01

    An organism is a molecular mechanical system consisting of nucleic acid, peptide and protein having a self-forming and a self-repairing function. For the purpose of creating cells, tissues and molecular mechanism alternating these biological functions, their basic technology was developed. Concretely, studies were made on three-dimensional cellular structural module engineering and biomolecular mechanism and design. Studies on biological soft tissue resulted in success by giving atmospheric glow discharge treatment to the inner surface of a tubular PVC. An artificial vitreous body was created using PVA hydrogels. In addition, liver cells were successfully cultured for the first time in the world. Studies on biological hard tissue revealed that osteopontin plays a role of a trigger for the initial differentiation of the osteoblast cell. Further, a basic experiment was carried out on the initial response of the cartilage cell. In the research on the molecular mechanism, examination was made on the mechanism of a double-head molecular motor. Examination was also made on the adjustment of the hydrogenase LB film as an electricity/hydrogen energy conversion element and on the biomolecular mechanism and design. (NEDO)

  12. Absorption features of chromophoric dissolved organic matter (CDOM) and tracing implication for dissolved organic carbon (DOC) in Changjiang Estuary, China

    OpenAIRE

    Zhang, X. Y.; Chen, X.; Deng, H.; Du, Y.; Jin, H. Y.

    2013-01-01

    Chromophoric dissolved organic matter (CDOM) represents the light absorbing fraction of dissolved organic carbon (DOC). Studies have shown that the optical properties of CDOM can be used to infer the distribution and diffusion characteristics of DOC in the estuary and coastal zone. The inversion of DOC concentrations from remote sensing has been implemented in certain regions. In this study we investigate the potential of tracing DOC from CDOM by the measure...

  13. Spatiotemporal Characterization of Chromophoric Dissolved Organic Matter (CDOM) and CDOM-DOC Relationships for Highly Polluted Rivers

    OpenAIRE

    Sijia Li; Jiquan Zhang; Guangyi Mu; Hanyu Ju; Rui Wang; Danjun Li; Ali Hassan Shabbir

    2016-01-01

    Spectral characteristics of CDOM (Chromophoric dissolved organic matter) in water columns are a key parameter for bio-optical modeling. Knowledge of CDOM optical properties and spatial discrepancy based on the relationship between water quality and spectral parameters in the Yinma River watershed with in situ data collected from highly polluted waters are exhibited in this study. Based on the comprehensive index method, the riverine waters showed serious contamination; especially the chemical...

  14. Delineating the relationship between chromophoric dissolved organic matter (CDOM) variability and biogeochemical parameters in a shallow continental shelf

    OpenAIRE

    Sourav Das; Sugata Hazra; Aneesh A. Lotlikar; Isha Das; Sandip Giri; Abhra Chanda; Anirban Akhand; Sourav Maity; T. Srinivasa Kumar

    2016-01-01

    Absorption coefficient of chromophoric dissolved organic matter (CDOM) at 440 nm [aCDOM (440)], sea surface salinity (SSS), total suspended matter (TSM) and chlorophyll-a (chl-a) were measured during October, 2014 to March, 2015 in the shallow continental shelf waters of the Hugli Estuary, adjacent to West Bengal coast, India. The primary objective of the study was to characterize the relationship between aCDOM (440) and the above mentioned biogeochemical parameters. Upon analyzing the result...

  15. Synthesis and solution aggregation studies of a suite of mixed neutral and zwitterionic chromophores for second-order nonlinear optics.

    Science.gov (United States)

    Peddie, Victoria; Anderson, Jack; Harvey, Joanne E; Smith, Gerald J; Kay, Andrew

    2014-11-07

    We report details of the synthesis of a series of bi- and trichromophores. These compounds contain mixtures of chromophores that have zwitterionic (ZWI) and neutral ground state (NGS) components covalently attached to each other. The neutral ground state moieties are based on dyes with aniline donors--such as Disperse Red 1--whereas the zwitterionic components are derived from chromophores with pro-aromatic donors such as 1,4-dihydropyridinylidene. By combining both ZWI and NGS components, we aim to develop novel compounds for nonlinear optics in which there is an enhancement of the overall hyperpolarizability coupled with a decrease in the net dipole moment. Thus, this approach should eliminate the electrostatic effects that result when only one type of chromophore is used, and so reduce the likelihood of undesirable aggregation occurring. This, in turn, should enable us to realize organic materials with large macroscopic optical nonlinearities. An analysis of the UV-vis results suggests that there is a strong dependence on solvent polarity that determines whether the embedded constituents should be treated as discrete elements; in low polarity solvents, there appear to be strong intramolecular interactions occurring, particularly when a 1,4-quinolinylidene-based donor is used in the ZWI component.

  16. Fluorescence characteristics of chromophoric dissolved organic matter in shallow water along the Zhejiang coasts, southeast China.

    Science.gov (United States)

    Gao, Lei; Fan, Daidu; Li, Daoji; Cai, Jingong

    2010-04-01

    Twenty-eight surface water samples from rivers, muddy intertidal flats, sand shores, and bedrock coasts were collected along the Zhejiang coastline in southeast China. In addition, three samples from the Changjiang (Yangtze River) were collected for comparison. CDOM (chromophoric dissolved organic matter) absorption and fluorescence excitation-emission matrix (EEM) spectroscopy, as well as nutrients and DOC were measured in these samples. According to salinity, nutrient, and DOC constituents, the 28 Zhejiang samples were categorized into four groups, i.e. highly-polluted, river derived, muddy-flat derived, and saltwater dominated ones. Among the six parameters (two humic-like and two protein-like peak intensities in fluorescence EEM contours, absorption at 300 nm, and DOC concentration) for the Zhejiang samples, any two of them were positively correlated. The submarine groundwater discharge, rather than local rivers, might have provided most of the freshwater that interacted with the saltwater during the mixing process. The high protein-like EEM peaks in samples from muddy salt marshes and rivers were probably caused by terrestrial inputs, land-based pollution, and local biological activities in combination. Copyright 2009. Published by Elsevier Ltd.

  17. New Homogeneous Chromophore/Catalyst Concepts for the Solar-Driven Reduction of Carbon Dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Hopkins, Michael D. [The University of Chicago, Chicago, IL (United States)

    2015-06-22

    One of the major scientific and technical challenges of this century is to develop chemical means to store solar energy in the form of fuels. This can be accomplished by developing light-absorbing and catalytic compounds that function cooperatively to rearrange the chemical bonds of feedstocks in a way that allows solar energy to be stored and released on demand. The research conducted during this project was directed toward addressing fundamental questions that underlie the conversion of CO2 to a solar fuel using homogeneous molecular systems. The research focused particularly on developing methods for extracting the reducing equivalents for these photochemical conversions from H2, which is a renewable molecule sourced to water. The research followed two main lines. One effort focused on understanding the general principles that govern how light-absorbing molecules interact with independent H2 oxidation and CO2 reduction catalysts to produce a functional cycle for driving the energy-storing reverse water-gas-shift reaction with light. The second effort centered on developing the excited-state properties and H2 activation chemistry of tungsten–alkylidyne complexes. These chromophores were found to be powerful excited-state reducing agents, which could be incorporated into light-light-harvesting assemblies, and to hold the potential to be regenerated using H2.

  18. DFT calculations on spectroscopic and structural properties of a NLO chromophore

    Science.gov (United States)

    Altürk, Sümeyye; Avci, Davut; Tamer, Ömer; Atalay, Yusuf

    2016-03-01

    The molecular geometry optimization, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of 2-(1'-(4'''-Methoxyphenyl)-5'-(thien-2″-yl)pyrrol-2'-yl)-1,3-benzothiazole as potential nonlinear optical (NLO) material were calculated using density functional theory (DFT) HSEh1PBE method with 6-311G(d,p) basis set. The best of our knowledge, this study have not been reported to date. Additionally, a detailed vibrational study was performed on the basis of potential energy distribution (PED) using VEDA program. It is noteworthy that NMR chemical shifts are quite useful for understanding the relationship between the molecular structure and electronic properties of molecules. The computed IR and NMR spectra were used to determine the types of the experimental bands observed. Predicted values of structural and spectroscopic parameters of the chromophore were compared with each other so as to display the effects of the different substituents on the spectroscopic and structural properties. Obtained data showed that there is an agreement between the predicted and experimental data.

  19. Resonance Raman spectra of the copper-sulfur chromophores in Achromobacter cycloclastes nitrite reductase.

    Science.gov (United States)

    Dooley, D M; Moog, R S; Liu, M Y; Payne, W J; LeGall, J

    1988-10-15

    Resonance Raman spectroscopy at ambient temperature and 77 K has been used to probe the structures of the copper sites in Achromobacter cycloclastes nitrite reductase. This enzyme contains three copper ions per protein molecule and has two principal electronic absorption bands with lambda max values of 458 and 585 nm. Comparisons between the resonance Raman spectra of nitrite reductase and blue copper proteins establish that both the 458 and 585 nm bands are associated with Cu(II)-S(Cys) chromophores. A histidine ligand probably is also present. Different sets of vibrational frequencies are observed with 457.9 nm (ambient) or 476.1 nm (77 K) excitation as compared with 590 nm (ambient) or 593 nm (77 K) excitation. Excitation profiles indicate that the 458 and 585 nm absorption bands are associated with separate [Cu(II)-S(Cys)N(His)] sites or with inequivalent and uncoupled cysteine ligands in the same site. The former possibility is considered to be more likely.

  20. Determination of the absorption coefficient of chromophoric dissolved organic matter from underway spectrophotometry.

    Science.gov (United States)

    Dall'Olmo, Giorgio; Brewin, Robert J W; Nencioli, Francesco; Organelli, Emanuele; Lefering, Ina; McKee, David; Röttgers, Rüdiger; Mitchell, Catherine; Boss, Emmanuel; Bricaud, Annick; Tilstone, Gavin

    2017-11-27

    Measurements of the absorption coefficient of chromophoric dissolved organic matter (ay) are needed to validate existing ocean-color algorithms. In the surface open ocean, these measurements are challenging because of low ay values. Yet, existing global datasets demonstrate that ay could contribute between 30% to 50% of the total absorption budget in the 400-450 nm spectral range, thus making accurate measurement of ay essential to constrain these uncertainties. In this study, we present a simple way of determining ay using a commercially-available in-situ spectrophotometer operated in underway mode. The obtained ay values were validated using independent collocated measurements. The method is simple to implement, can provide measurements with very high spatio-temporal resolution, and has an accuracy of about 0.0004 m -1 and a precision of about 0.0025 m -1 when compared to independent data (at 440 nm). The only limitation for using this method at sea is that it relies on the availability of relatively large volumes of ultrapure water. Despite this limitation, the method can deliver the ay data needed for validating and assessing uncertainties in ocean-colour algorithms.

  1. Enhanced Indirect Photochemical Transformation of Histidine and Histamine through Association with Chromophoric Dissolved Organic Matter.

    Science.gov (United States)

    Chu, Chiheng; Lundeen, Rachel A; Remucal, Christina K; Sander, Michael; McNeill, Kristopher

    2015-05-05

    Photochemical transformations greatly affect the stability and fate of amino acids (AAs) in sunlit aquatic ecosystems. Whereas the direct phototransformation of dissolved AAs is well investigated, their indirect photolysis in the presence of chromophoric dissolved organic matter (CDOM) is poorly understood. In aquatic systems, CDOM may act both as sorbent for AAs and as photosensitizer, creating microenvironments with high concentrations of photochemically produced reactive intermediates, such as singlet oxygen (1O2). This study provides a systematic investigation of the indirect photochemical transformation of histidine (His) and histamine by 1O2 in solutions containing CDOM as a function of solution pH. Both His and histamine showed pH-dependent enhanced phototransformation in the CDOM systems as compared to systems in which model, low-molecular-weight 1O2 sensitizers were used. Enhanced reactivity resulted from sorption of His and histamine to CDOM and thus exposure to elevated 1O2 concentrations in the CDOM microenvironment. The extent of reactivity enhancement depended on solution pH via its effects on the protonation state of His, histamine, and CDOM. Sorption-enhanced reactivity was independently supported by depressed rate enhancements in the presence of a cosorbate that competitively displaced His and histamine from CDOM. Incorporating sorption and photochemical transformation processes into a reaction rate prediction model improved the description of the abiotic photochemical transformation rates of His in the presence of CDOM.

  2. Photoproduction of hydrogen peroxide in aqueous solution from model compounds for chromophoric dissolved organic matter (CDOM).

    Science.gov (United States)

    Clark, Catherine D; de Bruyn, Warren; Jones, Joshua G

    2014-02-15

    To explore whether quinone moieties are important in chromophoric dissolved organic matter (CDOM) photochemistry in natural waters, hydrogen peroxide (H2O2) production and associated optical property changes were measured in aqueous solutions irradiated with a Xenon lamp for CDOM model compounds (dihydroquinone, benzoquinone, anthraquinone, napthoquinone, ubiquinone, humic acid HA, fulvic acid FA). All compounds produced H2O2 with concentrations ranging from 15 to 500 μM. Production rates were higher for HA vs. FA (1.32 vs. 0.176 mM h(-1)); values ranged from 6.99 to 0.137 mM h(-1) for quinones. Apparent quantum yields (Θ app; measure of photochemical production efficiency) were higher for HA vs. FA (0.113 vs. 0.016) and ranged from 0.0018 to 0.083 for quinones. Dihydroquinone, the reduced form of benzoquinone, had a higher production rate and efficiency than its oxidized form. Post-irradiation, quinone compounds had absorption spectra similar to HA and FA and 3D-excitation-emission matrix fluorescence spectra (EEMs) with fluorescent peaks in regions associated with CDOM. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Characterization of chromophoric dissolved organic matter (CDOM) in rainwater using fluorescence spectrophotometry.

    Science.gov (United States)

    Salve, P R; Lohkare, H; Gobre, T; Bodhe, G; Krupadam, R J; Ramteke, D S; Wate, S R

    2012-02-01

    The fluorescence excitation-emission matrix of Chromophoric dissolved organic matter (CDOM) samples from rainwater collected at Rameswaram, Tamilnadu, India are analysed. Total five peaks were observed for humic/marine and protein likes substances respectively. The peak A and C intensities varies form 1.98 ± 0.28 and 0.97 ± 0.11 QSU respectively represents humic like substances. The peak B and T intensities varies from 3.94 ± 0.75 and 7.42 ± 1.43 QSU showed association of protein like substances whereas peak M intensities varies from 1.92 ± 0.37 QSU indicates marine contribution. Among the fluorophores, the following sequence were observed as T > B > A > M > C which indicates dominance of Tryptophan like substances in rainwater. The average peak T/C ratios was observed as 7.88 ± 2.2 indicates microbial contamination by Tryptophan-like substances with the high biological activity and low volatility.

  4. Mixing behavior of chromophoric dissolved organic matter in the Pearl River Estuary in spring

    Science.gov (United States)

    Lei, Xia; Pan, Jiayi; Devlin, Adam T.

    2018-02-01

    Mixing behavior of chromophoric dissolved organic matter (CDOM) in the Pearl River Estuary (PRE) and relevant hydrodynamic parameters such as horizontal transport and vertical mixing are identified and discussed based on a set of sampling data obtained during a cruise in May 2014. Using a theoretical conservative mixing model, the surface CDOM in the PRE in spring is classified into two groups by the CDOM absorption-spectral slope relationship (a(300) vs S(275-295)): First, terrigenous CDOM under a non-conservative mixing condition, and removal processes such as photobleaching are suggested to happen; second, marine CDOM behaves conservatively during mixing. The mixing of CDOM at the bottom is shown to be conservative. Controlled by the two-layer gravitational circulation in the PRE, the northern and western estuary shows higher CDOM absorption and lower spectral slope than the southern and eastern estuary, and the surface CDOM presents higher absorption and lower spectral slope than the bottom. Horizontal transport is hypothesized to be the dominant hydrodynamic mechanism affecting CDOM variation and mixing behavior in the PRE, while the vertical mixing has less influence.

  5. Molecular hyperpolarizabilities of push–pull chromophores: A comparison between theoretical and experimental results

    Energy Technology Data Exchange (ETDEWEB)

    Capobianco, A. [Dipartimento di Fisica E.R. Caianiello, Università di Salerno, via ponte don Melillo, I-84084 Fisciano (Italy); Centore, R. [Dipartimento di Chimica P. Corradini, Università di Napoli, via Cintia, I-80126 Napoli (Italy); Noce, C. [Dipartimento di Fisica E.R. Caianiello, Università di Salerno, via ponte don Melillo, I-84084 Fisciano (Italy); Peluso, A., E-mail: apeluso@unisa.it [Dipartimento di Chimica e Biologia, Università di Salerno, via ponte don Melillo, I-84084 Fisciano (Italy)

    2013-01-16

    Highlights: ► Electro-optical determined and MP2/DFT computed NLO properties have been compared. ► Significant dependence of dipole moments of elongated NLO chromophores on conformations has been found. ► A thorough comparison between MP2 and DFT/TD-DFT computational approaches has been carried out. ► The two-state model overestimates hyperpolarizability. - Abstract: Electric dipole moments and static first order hyperpolarizabilities of two push–pull molecules with an extended π electron systems have been evaluated at different computational levels and compared with the results of electro-optical absorption measurements, based on the two state model. Calculations show that: (i) the dipole moments of such elongated systems depend significantly on conformation, a thorough conformational search is necessary for a meaningful comparison between theoretical and experimental results; (ii) DFT methods, in particular CAM-B3LYP and M05-2X, yield dipole moments which compare well with those obtained by post Hartree–Fock methods (MP2) and by EOA measurements; (iii) theoretical first order hyperpolarizabilities are largely underestimated, both by MP2 and DFT methods, possibly because of the failure of two state model used in electro-optical measurements.

  6. Crystallographic Structure of Xanthorhodopsin, the Light-Driven Proton Pump With a Dual Chromophore

    International Nuclear Information System (INIS)

    Luecke, H.; Schobert, B.; Stagno, J.; Imasheva, E.S.; Wang, J.M.; Balashov, S.P.; Lanyi, J.K

    2008-01-01

    Homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. We determined the structure of this eubacterial membrane protein-carotenoid complex by X-ray diffraction, to 1.9-(angstrom) resolution. Although it contains 7 transmembrane helices like bacteriorhodopsin and archaerhodopsin, the structure of xanthorhodopsin is considerably different from the 2 archaeal proteins. The crystallographic model for this rhodopsin introduces structural motifs for proton transfer during the reaction cycle, particularly for proton release, that are dramatically different from those in other retinal-based transmembrane pumps. Further, it contains a histidine-aspartate complex for regulating the pK a of the primary proton acceptor not present in archaeal pumps but apparently conserved in eubacterial pumps. In addition to aiding elucidation of a more general proton transfer mechanism for light-driven energy transducers, the structure defines also the geometry of the carotenoid and the retinal. The close approach of the 2 polyenes at their ring ends explains why the efficiency of the excited-state energy transfer is as high as ∼45%, and the 46 o angle between them suggests that the chromophore location is a compromise between optimal capture of light of all polarization angles and excited-state energy transfer

  7. A new strategy for imaging biomolecular events through interactions between liquid crystals and oil-in-water emulsions.

    Science.gov (United States)

    Hu, Qiong-Zheng; Jang, Chang-Hyun

    2012-11-21

    In this study, we demonstrate a new strategy to image biomolecular events through interactions between liquid crystals (LCs) and oil-in-water emulsions. The optical response had a dark appearance when a nematic LC, 4-cyano-4'-pentylbiphenyl (5CB), is in contact with emulsion droplets of glyceryl trioleate (GT). In contrast, the optical response had a bright appearance when 5CB is in contact with GT emulsions decorated with surfactants such as sodium oleate. Since lipase can hydrolyze GT and produce oleic acid, the optical response also displays a bright appearance after 5CB has been in contact with a mixture of lipase and GT emulsions. These results indicate the feasibility of monitoring biomolecular events through interactions between LCs and oil-in-water emulsions.

  8. Tibialis anterior muscle needle biopsy and sensitive biomolecular methods: a useful tool in myotonic dystrophy type 1

    Directory of Open Access Journals (Sweden)

    S. Iachettini

    2015-10-01

    Full Text Available Myotonic dystrophy type 1 (DM1 is a neuromuscular disorder caused by a CTG repeat expansion in 3’UTR of DMPK gene. This mutation causes accumulation of toxic RNA in nuclear foci leading to splicing misregulation of specific genes. In view of future clinical trials with antisense oligonucleotides in DM1 patients, it is important to set up sensitive and minimally-invasive tools to monitor the efficacy of treatments on skeletal muscle. A tibialis anterior (TA muscle sample of about 60 mg was obtained from 5 DM1 patients and 5 healthy subjects through a needle biopsy. A fragment of about 40 mg was used for histological examination and a fragment of about 20 mg was used for biomolecular analysis. The TA fragments obtained with the minimally-invasive needle biopsy technique is enough to perform all the histopathological and biomolecular evaluations useful to monitor a clinical trial on DM1 patients.

  9. Dynamic and label-free high-throughput detection of biomolecular interactions based on phase-shift interferometry

    Science.gov (United States)

    Li, Qiang; Huang, Guoliang; Gan, Wupeng; Chen, Shengyi

    2009-08-01

    Biomolecular interactions can be detected by many established technologies such as fluorescence imaging, surface plasmon resonance (SPR)[1-4], interferometry and radioactive labeling of the analyte. In this study, we have designed and constructed a label-free, real-time sensing platform and its operating imaging instrument that detects interactions using optical phase differences from the accumulation of biological material on solid substrates. This system allows us to monitor biomolecular interactions in real time and quantify concentration changes during micro-mixing processes by measuring the changes of the optical path length (OPD). This simple interferometric technology monitors the optical phase difference resulting from accumulated biomolecular mass. A label-free protein chip that forms a 4×4 probe array was designed and fabricated using a commercial microarray robot spotter on solid substrates. Two positive control probe lines of BSA (Bovine Serum Albumin) and two experimental human IgG and goat IgG was used. The binding of multiple protein targets was performed and continuously detected by using this label-free and real-time sensing platform.

  10. A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design.

    Science.gov (United States)

    Alford, Rebecca F; Leaver-Fay, Andrew; Gonzales, Lynda; Dolan, Erin L; Gray, Jeffrey J

    2017-12-01

    Computational biology is an interdisciplinary field, and many computational biology research projects involve distributed teams of scientists. To accomplish their work, these teams must overcome both disciplinary and geographic barriers. Introducing new training paradigms is one way to facilitate research progress in computational biology. Here, we describe a new undergraduate program in biomolecular structure prediction and design in which students conduct research at labs located at geographically-distributed institutions while remaining connected through an online community. This 10-week summer program begins with one week of training on computational biology methods development, transitions to eight weeks of research, and culminates in one week at the Rosetta annual conference. To date, two cohorts of students have participated, tackling research topics including vaccine design, enzyme design, protein-based materials, glycoprotein modeling, crowd-sourced science, RNA processing, hydrogen bond networks, and amyloid formation. Students in the program report outcomes comparable to students who participate in similar in-person programs. These outcomes include the development of a sense of community and increases in their scientific self-efficacy, scientific identity, and science values, all predictors of continuing in a science research career. Furthermore, the program attracted students from diverse backgrounds, which demonstrates the potential of this approach to broaden the participation of young scientists from backgrounds traditionally underrepresented in computational biology.

  11. Toxicity evaluation of PEDOT/biomolecular composites intended for neural communication electrodes

    International Nuclear Information System (INIS)

    Asplund, M; Thaning, E; Von Holst, H; Lundberg, J; Sandberg-Nordqvist, A C; Kostyszyn, B; Inganaes, O

    2009-01-01

    Electrodes coated with the conducting polymer poly(3,4-ethylene dioxythiophene) (PEDOT) possess attractive electrochemical properties for stimulation or recording in the nervous system. Biomolecules, added as counter ions in electropolymerization, could further improve the biomaterial properties, eliminating the need for surfactant counter ions in the process. Such PEDOT/biomolecular composites, using heparin or hyaluronic acid, have previously been investigated electrochemically. In the present study, their biocompatibility is evaluated. An agarose overlay assay using L929 fibroblasts, and elution and direct contact tests on human neuroblastoma SH-SY5Y cells are applied to investigate cytotoxicity in vitro. PEDOT:heparin was further evaluated in vivo through polymer-coated implants in rodent cortex. No cytotoxic response was seen to any of the PEDOT materials tested. The examination of cortical tissue exposed to polymer-coated implants showed extensive glial scarring irrespective of implant material (Pt:polymer or Pt). However, quantification of immunological response, through distance measurements from implant site to closest neuron and counting of ED1+ cell density around implant, was comparable to those of platinum controls. These results indicate that PEDOT:heparin surfaces were non-cytotoxic and show no marked difference in immunological response in cortical tissue compared to pure platinum controls.

  12. Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions.

    Science.gov (United States)

    Lu, Benzhuo; Holst, Michael J; McCammon, J Andrew; Zhou, Y C

    2010-09-20

    In this paper we developed accurate finite element methods for solving 3-D Poisson-Nernst-Planck (PNP) equations with singular permanent charges for electrodiffusion in solvated biomolecular systems. The electrostatic Poisson equation was defined in the biomolecules and in the solvent, while the Nernst-Planck equation was defined only in the solvent. We applied a stable regularization scheme to remove the singular component of the electrostatic potential induced by the permanent charges inside biomolecules, and formulated regular, well-posed PNP equations. An inexact-Newton method was used to solve the coupled nonlinear elliptic equations for the steady problems; while an Adams-Bashforth-Crank-Nicolson method was devised for time integration for the unsteady electrodiffusion. We numerically investigated the conditioning of the stiffness matrices for the finite element approximations of the two formulations of the Nernst-Planck equation, and theoretically proved that the transformed formulation is always associated with an ill-conditioned stiffness matrix. We also studied the electroneutrality of the solution and its relation with the boundary conditions on the molecular surface, and concluded that a large net charge concentration is always present near the molecular surface due to the presence of multiple species of charged particles in the solution. The numerical methods are shown to be accurate and stable by various test problems, and are applicable to real large-scale biophysical electrodiffusion problems.

  13. Cytoscape: a software environment for integrated models of biomolecular interaction networks.

    Science.gov (United States)

    Shannon, Paul; Markiel, Andrew; Ozier, Owen; Baliga, Nitin S; Wang, Jonathan T; Ramage, Daniel; Amin, Nada; Schwikowski, Benno; Ideker, Trey

    2003-11-01

    Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

  14. A Starting Point for Fluorescence-Based Single-Molecule Measurements in Biomolecular Research

    Directory of Open Access Journals (Sweden)

    Alexander Gust

    2014-09-01

    Full Text Available Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.

  15. A Quick-responsive DNA Nanotechnology Device for Bio-molecular Homeostasis Regulation.

    Science.gov (United States)

    Wu, Songlin; Wang, Pei; Xiao, Chen; Li, Zheng; Yang, Bing; Fu, Jieyang; Chen, Jing; Wan, Neng; Ma, Cong; Li, Maoteng; Yang, Xiangliang; Zhan, Yi

    2016-08-10

    Physiological processes such as metabolism, cell apoptosis and immune responses, must be strictly regulated to maintain their homeostasis and achieve their normal physiological functions. The speed with which bio-molecular homeostatic regulation occurs directly determines the ability of an organism to adapt to conditional changes. To produce a quick-responsive regulatory system that can be easily utilized for various types of homeostasis, a device called nano-fingers that facilitates the regulation of physiological processes was constructed using DNA origami nanotechnology. This nano-fingers device functioned in linked open and closed phases using two types of DNA tweezers, which were covalently coupled with aptamers that captured specific molecules when the tweezer arms were sufficiently close. Via this specific interaction mechanism, certain physiological processes could be simultaneously regulated from two directions by capturing one biofactor and releasing the other to enhance the regulatory capacity of the device. To validate the universal application of this device, regulation of the homeostasis of the blood coagulant thrombin was attempted using the nano-fingers device. It was successfully demonstrated that this nano-fingers device achieved coagulation buffering upon the input of fuel DNA. This nano-device could also be utilized to regulate the homeostasis of other types of bio-molecules.

  16. New Distributed Multipole Methods for Accurate Electrostatics for Large-Scale Biomolecular Simultations

    Science.gov (United States)

    Sagui, Celeste

    2006-03-01

    An accurate and numerically efficient treatment of electrostatics is essential for biomolecular simulations, as this stabilizes much of the delicate 3-d structure associated with biomolecules. Currently, force fields such as AMBER and CHARMM assign ``partial charges'' to every atom in a simulation in order to model the interatomic electrostatic forces, so that the calculation of the electrostatics rapidly becomes the computational bottleneck in large-scale simulations. There are two main issues associated with the current treatment of classical electrostatics: (i) how does one eliminate the artifacts associated with the point-charges (e.g., the underdetermined nature of the current RESP fitting procedure for large, flexible molecules) used in the force fields in a physically meaningful way? (ii) how does one efficiently simulate the very costly long-range electrostatic interactions? Recently, we have dealt with both of these challenges as follows. In order to improve the description of the molecular electrostatic potentials (MEPs), a new distributed multipole analysis based on localized functions -- Wannier, Boys, and Edminston-Ruedenberg -- was introduced, which allows for a first principles calculation of the partial charges and multipoles. Through a suitable generalization of the particle mesh Ewald (PME) and multigrid method, one can treat electrostatic multipoles all the way to hexadecapoles all without prohibitive extra costs. The importance of these methods for large-scale simulations will be discussed, and examplified by simulations from polarizable DNA models.

  17. Bookshelf: a simple curation system for the storage of biomolecular simulation data.

    Science.gov (United States)

    Vohra, Shabana; Hall, Benjamin A; Holdbrook, Daniel A; Khalid, Syma; Biggin, Philip C

    2010-01-01

    Molecular dynamics simulations can now routinely generate data sets of several hundreds of gigabytes in size. The ability to generate this data has become easier over recent years and the rate of data production is likely to increase rapidly in the near future. One major problem associated with this vast amount of data is how to store it in a way that it can be easily retrieved at a later date. The obvious answer to this problem is a database. However, a key issue in the development and maintenance of such a database is its sustainability, which in turn depends on the ease of the deposition and retrieval process. Encouraging users to care about meta-data is difficult and thus the success of any storage system will ultimately depend on how well used by end-users the system is. In this respect we suggest that even a minimal amount of metadata if stored in a sensible fashion is useful, if only at the level of individual research groups. We discuss here, a simple database system which we call 'Bookshelf', that uses python in conjunction with a mysql database to provide an extremely simple system for curating and keeping track of molecular simulation data. It provides a user-friendly, scriptable solution to the common problem amongst biomolecular simulation laboratories; the storage, logging and subsequent retrieval of large numbers of simulations. Download URL: http://sbcb.bioch.ox.ac.uk/bookshelf/

  18. Biochemical Stability Analysis of Nano Scaled Contrast Agents Used in Biomolecular Imaging Detection of Tumor Cells

    Science.gov (United States)

    Kim, Jennifer; Kyung, Richard

    Imaging contrast agents are materials used to improve the visibility of internal body structures in the imaging process. Many agents that are used for contrast enhancement are now studied empirically and computationally by researchers. Among various imaging techniques, magnetic resonance imaging (MRI) has become a major diagnostic tool in many clinical specialties due to its non-invasive characteristic and its safeness in regards to ionizing radiation exposure. Recently, researchers have prepared aqueous fullerene nanoparticles using electrochemical methods. In this paper, computational simulations of thermodynamic stabilities of nano scaled contrast agents that can be used in biomolecular imaging detection of tumor cells are presented using nanomaterials such as fluorescent functionalized fullerenes. In addition, the stability and safety of different types of contrast agents composed of metal oxide a, b, and c are tested in the imaging process. Through analysis of the computational simulations, the stabilities of the contrast agents, determined by optimized energies of the conformations, are presented. The resulting numerical data are compared. In addition, Density Functional Theory (DFT) is used in order to model the electron properties of the compound.

  19. Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays.

    Science.gov (United States)

    Hager, Roland; Burns, Jonathan R; Grydlik, Martyna J; Halilovic, Alma; Haselgrübler, Thomas; Schäffler, Friedrich; Howorka, Stefan

    2016-06-01

    The biofunctionalization of nanopatterned surfaces with DNA origami nanostructures is an important topic in nanobiotechnology. An unexplored challenge is, however, to co-immobilize proteins with DNA origami at pre-determined substrate sites in high contrast relative to the nontarget areas. The immobilization should, in addition, preferably be achieved on a transparent substrate to allow ultrasensitive optical detection. If successful, specific co-binding would be a step towards stoichiometrically defined arrays with few to individual protein molecules per site. Here, we successfully immobilize with high specificity positively charged avidin proteins and negatively charged DNA origami nanoplates on 100 nm-wide carbon nanoislands while suppressing undesired adsorption to surrounding nontarget areas. The arrays on glass slides achieve unprecedented selectivity factors of up to 4000 and allow ultrasensitive fluorescence read-out. The co-immobilization onto the nanoislands leads to layered biomolecular architectures, which are functional because bound DNA origami influences the number of capturing sites on the nanopatches for other proteins. The novel hybrid DNA origami-protein nanoarrays allow the fabrication of versatile research platforms for applications in biosensing, biophysics, and cell biology, and, in addition, represent an important step towards single-molecule protein arrays. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Charge patterns as templates for the assembly of layered biomolecular structures.

    Science.gov (United States)

    Naujoks, Nicola; Stemmer, Andreas

    2006-08-01

    Electric fields are used to guide the assembly of biomolecules in predefined geometric patterns on solid substrates. Local surface charges serve as templates to selectively position proteins on thin-film polymeric electret layers, thereby creating a basis for site-directed layered assembly of biomolecular structures. Charge patterns are created using the lithographic capabilities of an atomic force microscope, namely by applying voltage pulses between a conductive tip and the sample. Samples consist of a poly(methyl methacrylate) layer on a p-doped silicon support. Subsequently, the sample is developed in a water-in-oil emulsion, consisting of a dispersed aqueous phase containing biotin-modified immunoglobulinG molecules, and a continuous nonpolar, insulating oil phase. The electrostatic fields cause a net force of (di)electrophoretic nature on the droplet, thereby guiding the proteins to the predefined locations. Due to the functionalization of the immunoglobulinG molecules with biotin-groups, these patterns can now be used to initiate the localized layer-by-layer assembly of biomolecules based on the avidin-biotin mechanism. By binding 40 nm sized biotin-labelled beads to the predefined locations via a streptavidin linker, we verify the functionality of the previously deposited immunoglobulinG-biotin. All assembly steps following the initial deposition of the immunoglobulinG from emulsion can conveniently be conducted in aqueous solutions. Results show that pattern definition is maintained after immersion into aqueous solution.

  1. Solving the 0/1 Knapsack Problem by a Biomolecular DNA Computer

    Directory of Open Access Journals (Sweden)

    Hassan Taghipour

    2013-01-01

    Full Text Available Solving some mathematical problems such as NP-complete problems by conventional silicon-based computers is problematic and takes so long time. DNA computing is an alternative method of computing which uses DNA molecules for computing purposes. DNA computers have massive degrees of parallel processing capability. The massive parallel processing characteristic of DNA computers is of particular interest in solving NP-complete and hard combinatorial problems. NP-complete problems such as knapsack problem and other hard combinatorial problems can be easily solved by DNA computers in a very short period of time comparing to conventional silicon-based computers. Sticker-based DNA computing is one of the methods of DNA computing. In this paper, the sticker based DNA computing was used for solving the 0/1 knapsack problem. At first, a biomolecular solution space was constructed by using appropriate DNA memory complexes. Then, by the application of a sticker-based parallel algorithm using biological operations, knapsack problem was resolved in polynomial time.

  2. Correlated Heterospectral Lipidomics for Biomolecular Profiling of Remyelination in Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Mads S. Bergholt

    2017-12-01

    Full Text Available Analyzing lipid composition and distribution within the brain is important to study white matter pathologies that present focal demyelination lesions, such as multiple sclerosis. Some lesions can endogenously re-form myelin sheaths. Therapies aim to enhance this repair process in order to reduce neurodegeneration and disability progression in patients. In this context, a lipidomic analysis providing both precise molecular classification and well-defined localization is crucial to detect changes in myelin lipid content. Here we develop a correlated heterospectral lipidomic (HSL approach based on coregistered Raman spectroscopy, desorption electrospray ionization mass spectrometry (DESI-MS, and immunofluorescence imaging. We employ HSL to study the structural and compositional lipid profile of demyelination and remyelination in an induced focal demyelination mouse model and in multiple sclerosis lesions from patients ex vivo. Pixelwise coregistration of Raman spectroscopy and DESI-MS imaging generated a heterospectral map used to interrelate biomolecular structure and composition of myelin. Multivariate regression analysis enabled Raman-based assessment of highly specific lipid subtypes in complex tissue for the first time. This method revealed the temporal dynamics of remyelination and provided the first indication that newly formed myelin has a different lipid composition compared to normal myelin. HSL enables detailed molecular myelin characterization that can substantially improve upon the current understanding of remyelination in multiple sclerosis and provides a strategy to assess remyelination treatments in animal models.

  3. Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets.

    Directory of Open Access Journals (Sweden)

    Mary E Prendergast

    Full Text Available Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus and black rat (Rattus rattus. Our approach included ancient DNA (aDNA analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS collagen fingerprinting, and direct AMS (accelerator mass spectrometry radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation.

  4. Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets.

    Science.gov (United States)

    Prendergast, Mary E; Buckley, Michael; Crowther, Alison; Frantz, Laurent; Eager, Heidi; Lebrasseur, Ophélie; Hutterer, Rainer; Hulme-Beaman, Ardern; Van Neer, Wim; Douka, Katerina; Veall, Margaret-Ashley; Quintana Morales, Eréndira M; Schuenemann, Verena J; Reiter, Ella; Allen, Richard; Dimopoulos, Evangelos A; Helm, Richard M; Shipton, Ceri; Mwebi, Ogeto; Denys, Christiane; Horton, Mark; Wynne-Jones, Stephanie; Fleisher, Jeffrey; Radimilahy, Chantal; Wright, Henry; Searle, Jeremy B; Krause, Johannes; Larson, Greger; Boivin, Nicole L

    2017-01-01

    Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our approach included ancient DNA (aDNA) analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation.

  5. Review of Transducer Principles for Label-Free Biomolecular Interaction Analysis

    Directory of Open Access Journals (Sweden)

    Janos Vörös

    2011-07-01

    Full Text Available Label-free biomolecular interaction analysis is an important technique to study the chemical binding between e.g., protein and protein or protein and small molecule in real-time. The parameters obtained with this technique, such as the affinity, are important for drug development. While the surface plasmon resonance (SPR instruments are most widely used, new types of sensors are emerging. These developments are generally driven by the need for higher throughput, lower sample consumption or by the need of complimentary information to the SPR data. This review aims to give an overview about a wide range of sensor transducers, the working principles and the peculiarities of each technology, e.g., concerning the set-up, sensitivity, sensor size or required sample volume. Starting from optical technologies like the SPR and waveguide based sensors, acoustic sensors like the quartz crystal microbalance (QCM and the film bulk acoustic resonator (FBAR, calorimetric and electrochemical sensors are covered. Technologies long established in the market are presented together with those newly commercially available and with technologies in the early development stage. Finally, the commercially available instruments are summarized together with their sensitivity and the number of sensors usable in parallel and an outlook for potential future developments is given.

  6. Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications.

    Science.gov (United States)

    Shrot, Yoav; Frydman, Lucio

    2011-04-01

    A topic of active investigation in 2D NMR relates to the minimum number of scans required for acquiring this kind of spectra, particularly when these are dictated by sampling rather than by sensitivity considerations. Reductions in this minimum number of scans have been achieved by departing from the regular sampling used to monitor the indirect domain, and relying instead on non-uniform sampling and iterative reconstruction algorithms. Alternatively, so-called "ultrafast" methods can compress the minimum number of scans involved in 2D NMR all the way to a minimum number of one, by spatially encoding the indirect domain information and subsequently recovering it via oscillating field gradients. Given ultrafast NMR's simultaneous recording of the indirect- and direct-domain data, this experiment couples the spectral constraints of these orthogonal domains - often calling for the use of strong acquisition gradients and large filter widths to fulfill the desired bandwidth and resolution demands along all spectral dimensions. This study discusses a way to alleviate these demands, and thereby enhance the method's performance and applicability, by combining spatial encoding with iterative reconstruction approaches. Examples of these new principles are given based on the compressed-sensed reconstruction of biomolecular 2D HSQC ultrafast NMR data, an approach that we show enables a decrease of the gradient strengths demanded in this type of experiments by up to 80%. Copyright © 2011 Elsevier Inc. All rights reserved.

  7. Biomolecular Nano-Flow-Sensor to Measure Near-Surface Flow

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    Noji Hiroyuki

    2009-01-01

    Full Text Available Abstract We have proposed and experimentally demonstrated that the measurement of the near-surface flow at the interface between a liquid and solid using a 10 nm-sized biomolecular motor of F1-ATPase as a nano-flow-sensor. For this purpose, we developed a microfluidic test-bed chip to precisely control the liquid flow acting on the F1-ATPase. In order to visualize the rotation of F1-ATPase, several hundreds nanometer-sized particle was immobilized at the rotational axis of F1-ATPase to enhance the rotation to be detected by optical microscopy. The rotational motion of F1-ATPase, which was immobilized on an inner surface of the test-bed chip, was measured to obtain the correlation between the near-surface flow and the rotation speed of F1-ATPase. As a result, we obtained the relationship that the rotation speed of F1-ATPase was linearly decelerated with increasing flow velocity. The mechanism of the correlation between the rotation speed and the near-surface flow remains unclear, however the concept to use biomolecule as a nano-flow-sensor was proofed successfully. (See supplementary material 1 Electronic supplementary material The online version of this article (doi:10.1007/s11671-009-9479-3 contains supplementary material, which is available to authorized users. Click here for file

  8. A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design.

    Directory of Open Access Journals (Sweden)

    Rebecca F Alford

    2017-12-01

    Full Text Available Computational biology is an interdisciplinary field, and many computational biology research projects involve distributed teams of scientists. To accomplish their work, these teams must overcome both disciplinary and geographic barriers. Introducing new training paradigms is one way to facilitate research progress in computational biology. Here, we describe a new undergraduate program in biomolecular structure prediction and design in which students conduct research at labs located at geographically-distributed institutions while remaining connected through an online community. This 10-week summer program begins with one week of training on computational biology methods development, transitions to eight weeks of research, and culminates in one week at the Rosetta annual conference. To date, two cohorts of students have participated, tackling research topics including vaccine design, enzyme design, protein-based materials, glycoprotein modeling, crowd-sourced science, RNA processing, hydrogen bond networks, and amyloid formation. Students in the program report outcomes comparable to students who participate in similar in-person programs. These outcomes include the development of a sense of community and increases in their scientific self-efficacy, scientific identity, and science values, all predictors of continuing in a science research career. Furthermore, the program attracted students from diverse backgrounds, which demonstrates the potential of this approach to broaden the participation of young scientists from backgrounds traditionally underrepresented in computational biology.

  9. REVIEW ARTICLE: How do biomolecular systems speed up and regulate rates?

    Science.gov (United States)

    Zhou, Huan-Xiang

    2005-09-01

    The viability of a biological system depends upon careful regulation of the rates of various processes. These rates have limits imposed by intrinsic chemical or physical steps (e.g., diffusion). These limits can be expanded by interactions and dynamics of the biomolecules. For example, (a) a chemical reaction is catalyzed when its transition state is preferentially bound to an enzyme; (b) the folding of a protein molecule is speeded up by specific interactions within the transition-state ensemble and may be assisted by molecular chaperones; (c) the rate of specific binding of a protein molecule to a cellular target can be enhanced by mechanisms such as long-range electrostatic interactions, nonspecific binding and folding upon binding; (d) directional movement of motor proteins is generated by capturing favorable Brownian motion through intermolecular binding energy; and (e) conduction and selectivity of ions through membrane channels are controlled by interactions and the dynamics of channel proteins. Simple physical models are presented here to illustrate these processes and provide a unifying framework for understanding speed attainment and regulation in biomolecular systems.

  10. Pre-Clinical Tests of an Integrated CMOS Biomolecular Sensor for Cardiac Diseases Diagnosis.

    Science.gov (United States)

    Lee, Jen-Kuang; Wang, I-Shun; Huang, Chi-Hsien; Chen, Yih-Fan; Huang, Nien-Tsu; Lin, Chih-Ting

    2017-11-26

    Coronary artery disease and its related complications pose great threats to human health. In this work, we aim to clinically evaluate a CMOS field-effect biomolecular sensor for cardiac biomarkers, cardiac-specific troponin-I (cTnI), N -terminal prohormone brain natriuretic peptide (NT-proBNP), and interleukin-6 (IL-6). The CMOS biosensor is implemented via a standard commercialized 0.35 μm CMOS process. To validate the sensing characteristics, in buffer conditions, the developed CMOS biosensor has identified the detection limits of IL-6, cTnI, and NT-proBNP as being 45 pM, 32 pM, and 32 pM, respectively. In clinical serum conditions, furthermore, the developed CMOS biosensor performs a good correlation with an enzyme-linked immuno-sorbent assay (ELISA) obtained from a hospital central laboratory. Based on this work, the CMOS field-effect biosensor poses good potential for accomplishing the needs of a point-of-care testing (POCT) system for heart disease diagnosis.

  11. A coarse-grained model for the simulations of biomolecular interactions in cellular environments

    International Nuclear Information System (INIS)

    Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

    2014-01-01

    The interactions of bio-molecules constitute the key steps of cellular functions. However, in vivo binding properties differ significantly from their in vitro measurements due to the heterogeneity of cellular environments. Here we introduce a coarse-grained model based on rigid-body representation to study how factors such as cellular crowding and membrane confinement affect molecular binding. The macroscopic parameters such as the equilibrium constant and the kinetic rate constant are calibrated by adjusting the microscopic coefficients used in the numerical simulations. By changing these model parameters that are experimentally approachable, we are able to study the kinetic and thermodynamic properties of molecular binding, as well as the effects caused by specific cellular environments. We investigate the volumetric effects of crowded intracellular space on bio-molecular diffusion and diffusion-limited reactions. Furthermore, the binding constants of membrane proteins are currently difficult to measure. We provide quantitative estimations about how the binding of membrane proteins deviates from soluble proteins under different degrees of membrane confinements. The simulation results provide biological insights to the functions of membrane receptors on cell surfaces. Overall, our studies establish a connection between the details of molecular interactions and the heterogeneity of cellular environments

  12. A variational approach to moment-closure approximations for the kinetics of biomolecular reaction networks

    Science.gov (United States)

    Bronstein, Leo; Koeppl, Heinz

    2018-01-01

    Approximate solutions of the chemical master equation and the chemical Fokker-Planck equation are an important tool in the analysis of biomolecular reaction networks. Previous studies have highlighted a number of problems with the moment-closure approach used to obtain such approximations, calling it an ad hoc method. In this article, we give a new variational derivation of moment-closure equations which provides us with an intuitive understanding of their properties and failure modes and allows us to correct some of these problems. We use mixtures of product-Poisson distributions to obtain a flexible parametric family which solves the commonly observed problem of divergences at low system sizes. We also extend the recently introduced entropic matching approach to arbitrary ansatz distributions and Markov processes, demonstrating that it is a special case of variational moment closure. This provides us with a particularly principled approximation method. Finally, we extend the above approaches to cover the approximation of multi-time joint distributions, resulting in a viable alternative to process-level approximations which are often intractable.

  13. High-Throughput, Protein-Targeted Biomolecular Detection Using Frequency-Domain Faraday Rotation Spectroscopy.

    Science.gov (United States)

    Murdock, Richard J; Putnam, Shawn A; Das, Soumen; Gupta, Ankur; Chase, Elyse D Z; Seal, Sudipta

    2017-03-01

    A clinically relevant magneto-optical technique (fd-FRS, frequency-domain Faraday rotation spectroscopy) for characterizing proteins using antibody-functionalized magnetic nanoparticles (MNPs) is demonstrated. This technique distinguishes between the Faraday rotation of the solvent, iron oxide core, and functionalization layers of polyethylene glycol polymers (spacer) and model antibody-antigen complexes (anti-BSA/BSA, bovine serum albumin). A detection sensitivity of ≈10 pg mL -1 and broad detection range of 10 pg mL -1 ≲ c BSA ≲ 100 µg mL -1 are observed. Combining this technique with predictive analyte binding models quantifies (within an order of magnitude) the number of active binding sites on functionalized MNPs. Comparative enzyme-linked immunosorbent assay (ELISA) studies are conducted, reproducing the manufacturer advertised BSA ELISA detection limits from 1 ng mL -1 ≲ c BSA ≲ 500 ng mL -1 . In addition to the increased sensitivity, broader detection range, and similar specificity, fd-FRS can be conducted in less than ≈30 min, compared to ≈4 h with ELISA. Thus, fd-FRS is shown to be a sensitive optical technique with potential to become an efficient diagnostic in the chemical and biomolecular sciences. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Developing the Biomolecular Screening Facility at the EPFL into the Chemical Biology Screening Platform for Switzerland.

    Science.gov (United States)

    Turcatti, Gerardo

    2014-05-01

    The Biomolecular Screening Facility (BSF) is a multidisciplinary laboratory created in 2006 at the Ecole Polytechnique Federale de Lausanne (EPFL) to perform medium and high throughput screening in life sciences-related projects. The BSF was conceived and developed to meet the needs of a wide range of researchers, without privileging a particular biological discipline or therapeutic area. The facility has the necessary infrastructure, multidisciplinary expertise and flexibility to perform large screening programs using small interfering RNAs (siRNAs) and chemical collections in the areas of chemical biology, systems biology and drug discovery. In the framework of the National Centres of Competence in Research (NCCR) Chemical Biology, the BSF is hosting 'ACCESS', the Academic Chemical Screening Platform of Switzerland that provides the scientific community with chemical diversity, screening facilities and know-how in chemical genetics. In addition, the BSF started its own applied research axes that are driven by innovation in thematic areas related to preclinical drug discovery and discovery of bioactive probes.

  15. BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

    International Nuclear Information System (INIS)

    Markley, John L.; Ulrich, Eldon L.; Berman, Helen M.; Henrick, Kim; Nakamura, Haruki; Akutsu, Hideo

    2008-01-01

    We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. All PDB depositions of structures based on NMR data must now be accompanied by experimental restraints. A scheme has been devised that allows depositors to specify a representative structure and to define residues within that structure found experimentally to be largely unstructured. The BMRB now accepts coordinate sets representing three-dimensional structural models based on experimental NMR data of molecules of biological interest that fall outside the guidelines of the Protein Data Bank (i.e., the molecule is a peptide with 23 or fewer residues, a polynucleotide with 3 or fewer residues, a polysaccharide with 3 or fewer sugar residues, or a natural product), provided that the coordinates are accompanied by representation of the covalent structure of the molecule (atom connectivity), assigned NMR chemical shifts, and the structural restraints used in generating model. The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems

  16. Characteristics and sources analysis of riverine chromophoric dissolved organic matter in Liaohe River, China.

    Science.gov (United States)

    Shao, Tiantian; Song, Kaishan; Jacinthe, Pierre-Andre; Du, Jia; Zhao, Ying; Ding, Zhi; Guan, Ying; Bai, Zhang

    2016-12-01

    Chromophoric dissolved organic matter (CDOM) in riverine systems can be affected by environmental conditions and land-use, and thus could provide important information regarding human activities in surrounding landscapes. The optical properties of water samples collected at 42 locations across the Liaohe River (LHR, China) watershed were examined using UV-Vis and fluorescence spectroscopy to determine CDOM characteristics, composition and sources. Total nitrogen (TN) and total phosphorus (TP) concentrations at all sampling sites exceeded the GB3838-2002 (national quality standards for surface waters, China) standard for Class V waters of 2.0 mg N/L and 0.4 mg P/L respectively, while trophic state index (TSI M ) indicated that all the sites investigated were mesotrophic, 64% of which were eutrophic at the same time. Redundancy analysis showed that total suspended matter (TSM), dissolved organic carbon (DOC), and turbidity had a strong correlation with CDOM, while the other parameters (Chl a, TN, TP and TSI M ) exhibited weak correlations with CDOM absorption. High spectral slope values and low SUVA254 (the specific UV absorption) values indicated that CDOM in the LHR was primarily comprised of low molecular weight organic substances. Analysis of excitation-emission matrices contour plots showed that CDOM in water samples collected from upstream locations exhibited fulvic-acid-like characteristics whereas protein-like substances were most likely predominant in samples collected in estuarine areas and downstream from large cities. These patterns were interpreted as indicative of water pollution from urban and industrial activities in several downstream sections of the LHR watershed.

  17. Dissolved organic carbon and chromophoric dissolved organic matter properties of rivers in the USA

    Science.gov (United States)

    Spencer, Robert G. M.; Butler, Kenna D.; Aiken, George R.

    2012-09-01

    Dissolved organic carbon (DOC) concentration and chromophoric dissolved organic matter (CDOM) parameters were measured over a range of discharge in 30 U.S. rivers, covering a diverse assortment of fluvial ecosystems in terms of watershed size and landscape drained. Relationships between CDOM absorption at a range of wavelengths (a254, a350, a440) and DOC in the 30 watersheds were found to correlate strongly and positively for the majority of U.S. rivers. However, four rivers (Colorado, Colombia, Rio Grande and St. Lawrence) exhibited statistically weak relationships between CDOM absorption and DOC. These four rivers are atypical, as they either drain from the Great Lakes or experience significant impoundment of water within their watersheds, and they exhibited values for dissolved organic matter (DOM) parameters indicative of autochthonous or anthropogenic sources or photochemically degraded allochthonous DOM and thus a decoupling between CDOM and DOC. CDOM quality parameters in the 30 rivers were found to be strongly correlated to DOM compositional metrics derived via XAD fractionation, highlighting the potential for examining DOM biochemical quality from CDOM measurements. This study establishes the ability to derive DOC concentration from CDOM absorption for the majority of U.S. rivers, describes characteristics of riverine systems where such an approach is not valid, and emphasizes the possibility of examining DOM composition and thus biogeochemical function via CDOM parameters. Therefore, the usefulness of CDOM measurements, both laboratory-based analyses and in situ instrumentation, for improving spatial and temporal resolution of DOC fluxes and DOM dynamics in future studies is considerable in a range of biogeochemical studies.

  18. Conformational heterogeneity of the Pfr chromophore in plant and cyanobacterial phytochromes

    Directory of Open Access Journals (Sweden)

    Francisco eVelazquez Escobar

    2015-07-01

    Full Text Available Phytochromes are biological photoreceptors that can be reversibly photoconverted between a dark and photoactivated state. The underlying reaction sequences are initiated by the photoisomerisation of the tetrapyrrole cofactor, which in plant and cyanobacterial phytochromes are a phytochromobilin (PB and a phycocyanobilin (PCB, respectively. The transition between the two states represents an on/off-switch of the output module activating or deactivating downstream physiological processes. In addition, the photoactivated state, i.e. Pfr in canonical phytochromes, can be thermally reverted to the dark state (Pr. The present study aimed to improve our understanding of the specific reactivity of various PB- and PCB-binding phytochromes in the Pfr state by analyzing the cofactor structure by vibrational spectroscopic techniques. Resonance Raman (RR spectroscopy revealed two Pfr conformers (Pfr-I and Pfr-II forming a temperature-dependent conformational equilibrium. The two sub-states - found in all phytochromes studied, albeit with different relative contributions - differ in structural details of the C-D and A-B methine bridges. In the Pfr-I sub-state the torsion between the rings C and D is larger by ca. 10o compared to Pfr-II. This structural difference is presumably related to different hydrogen bonding interactions of ring D as revealed by time-resolved IR spectroscopic studies of the cyanobacterial phytochrome Cph1. The transitions between the two sub-states are evidently too fast (i.e., nanosecond time scale to be resolved by NMR spectroscopy which could not detect a structural heterogeneity of the chromophore in Pfr. The implications of the present findings for the dark reversion of the Pfr state are discussed.

  19. Looking at the Green Fluorescent Protein (GFP) chromophore from a different perspective: A computational insight

    Science.gov (United States)

    Paul, Bijan Kumar; Guchhait, Nikhil

    2013-02-01

    In the present contribution Density Functional Theory (DFT) has been applied to explore molecular dipole moment, frontier molecular orbital (FMO) features, chemical hardness, and the molecular electrostatic potential surface (MEPS) characteristics for optimized molecular geometry of the Green Fluorescent Protein (GFP) chromophore p-hydroxybenzylideneimidazolinone (HBDI) both in its protonated (neutral) and deprotonated (anion) forms. The distribution of atomic charges over the entire molecular framework as obtained from Natural Bond Orbital (NBO) analysis is found to faithfully replicate the predictions from the MEP map in respect of reactivity map of HBDI (neutral and anion) and possible sites for hydrogen bonding interactions etc. The three dimensional MEP map encompassing the entire molecule yields a reliable reactivity map of HBDI molecule also displaying the most probable regions for non-covalent interactions. The differential distribution of the electrostatic potential over the neutral and anionic species of HBDI is authentically reflected on MEP map and NBO charge distribution analysis. Thermodynamic properties such as heat capacity, thermal energy, enthalpy, entropy have been calculated and the correlation of the various thermodynamic functions with temperature has been established for neutral molecule. More importantly, however, the computational approach has been employed to unveil the nonlinear optical (NLO) properties of protonated (neutral) and deprotonated (anion) HBDI. Also in an endeavor to achieve a fuller understanding on this aspect the effect of basis set on the NLO properties of the title molecule has been investigated. Our computations delineate the discernible differences in NLO properties between the neutral and anionic species of HBDI whereby indicating the possibility of development of photoswitchable NLO device.

  20. Distribution and spectral characteristics of chromophoric dissolved organic matter in a coastal bay in northern China.

    Science.gov (United States)

    Li, Guiju; Liu, Jing; Ma, Yulan; Zhao, Ruihua; Hu, Suzheng; Li, Yijie; Wei, Hao; Xie, Huixiang

    2014-08-01

    The absorption spectra of chromophoric dissolved organic matter (CDOM), along with general physical, chemical and biological variables, were determined in the Bohai Bay, China, in the springs of 2011 and 2012. The absorption coefficient of CDOM at 350 nm (a350) in surface water ranged from 1.00 to 1.83 m⁻¹ (mean: 1.35 m⁻¹) in May 2011 and from 0.78 to 1.92 m⁻¹ (mean: 1.19 m⁻¹) in April 2012. Little surface-bottom difference was observed due to strong vertical mixing. The a350 was weakly anti-correlated to salinity but positively correlated to chlorophyll a (Chl-a) concentration. A shoulder over 260-290 nm, suggestive of biogenic molecules, superimposed the overall pattern of exponentially decreasing CDOM absorption with wavelength. The wavelength distribution of the absorption spectral slope manifested a pronounced peak at ca. 300 nm characteristic of algal-derived CDOM. All a250/a365 ratios exceeded 6, corresponding to CDOM molecular weights (Mw) of less than 1 kDa. Spectroscopically, CDOM in the Bohai Bay differed substantively from that in the Haihe River, the bay's dominant source of land runoff; photobleaching of the riverine CDOM enlarged the difference. Results point to marine biological production being the principal source of CDOM in the Bohai Bay during the sampling seasons. Relatively low runoff, fast dilution, and selective photodegradation are postulated to be among the overarching elements responsible for the lack of terrigenous CDOM signature in the bay water. Copyright © 2014. Published by Elsevier B.V.

  1. Dissolved organic carbon and chromophoric dissolved organic matter properties of rivers in the USA

    Science.gov (United States)

    Spencer, Robert G.M.; Butler, Kenna D.; Aiken, George R.

    2012-01-01

    Dissolved organic carbon (DOC) concentration and chromophoric dissolved organic matter (CDOM) parameters were measured over a range of discharge in 30 U.S. rivers, covering a diverse assortment of fluvial ecosystems in terms of watershed size and landscape drained. Relationships between CDOM absorption at a range of wavelengths (a254, a350, a440) and DOC in the 30 watersheds were found to correlate strongly and positively for the majority of U.S. rivers. However, four rivers (Colorado, Colombia, Rio Grande and St. Lawrence) exhibited statistically weak relationships between CDOM absorption and DOC. These four rivers are atypical, as they either drain from the Great Lakes or experience significant impoundment of water within their watersheds, and they exhibited values for dissolved organic matter (DOM) parameters indicative of autochthonous or anthropogenic sources or photochemically degraded allochthonous DOM and thus a decoupling between CDOM and DOC. CDOM quality parameters in the 30 rivers were found to be strongly correlated to DOM compositional metrics derived via XAD fractionation, highlighting the potential for examining DOM biochemical quality from CDOM measurements. This study establishes the ability to derive DOC concentration from CDOM absorption for the majority of U.S. rivers, describes characteristics of riverine systems where such an approach is not valid, and emphasizes the possibility of examining DOM composition and thus biogeochemical function via CDOM parameters. Therefore, the usefulness of CDOM measurements, both laboratory-based analyses and in situ instrumentation, for improving spatial and temporal resolution of DOC fluxes and DOM dynamics in future studies is considerable in a range of biogeochemical studies.

  2. Characterization and spacial distribution variability of chromophoric dissolved organic matter (CDOM) in the Yangtze Estuary.

    Science.gov (United States)

    Wang, Ying; Zhang, Di; Shen, Zhenyao; Chen, Jing; Feng, Chenghong

    2014-01-01

    The spatial characteristics and the quantity and quality of the chromophoric dissolved organic matter (CDOM) in the Yangtze Estuary, based on the abundance, degree of humification and sources, were studied using 3D fluorescence excitation emission matrix spectra (F-EEMs) with parallel factor and principal component analysis (PARAFAC-PCA). The results indicated that the CDOM abundance decreased and the aromaticity increased from the upstream to the downstream areas of the estuary. Higher CDOM abundance and degrees of humification were observed in the pore water than that in the surface and bottom waters. Two humic-like components (C1 and C3) and one tryptophan-like component (C2) were identified using the PARAFAC model. The separation of the samples by PCA highlighted the differences in the DOM properties. Components C1 and C3 concurrently displayed positive factor 1 loadings with nearly zero factor 2 loadings, while C2 showed highly positive factor 2 loadings. The C1 and C3 were very similar and exhibited a direct relationship with A355 and DOC. The CDOM in the pore water increased along the river to the coastal area, which was mainly influenced by C1 and C3 and was significantly derived from sediment remineralization and deposition from the inflow of the Yangtze River. The CDOM in the surface and bottom waters was dominated by C2, especially in the inflows of multiple tributaries that were affected by intensive anthropogenic activities. The microbial degradation of exogenous wastes from the tributary inputs and shoreside discharges were dominant sources of the CDOM in the surface and bottom waters. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Vectorial photoinduced energy transfer between boron-dipyrromethene (Bodipy) chromophores across a fluorene bridge.

    Science.gov (United States)

    Puntoriero, Fausto; Nastasi, Francesco; Campagna, Sebastiano; Bura, Thomas; Ziessel, Raymond

    2010-08-02

    A series of novel multichromophoric, luminescent compounds has been prepared, and their absorption spectra, luminescence properties (both at 77 K in rigid matrix and at 298 K in fluid solution), and photoinduced intercomponent energy-transfer processes have been studied. The series contains two new multichromophoric systems 1 and 2, each one containing two different boron-dipyrromethene (Bodipy) subunits and one bridging fluorene species, and two fluorene-Bodipy bichromophoric species, 6 and 7. Three monochromophoric compounds, 3, 4, and 5, used as precursors in the synthetic process, were also fully characterized. The absorption spectra of the multichromophoric compounds are roughly the summation of the absorption spectra of their individual components, thus demonstrating the supramolecular nature of the assemblies. Luminescence studies show that quantitative energy transfer occurs in 6 and 7 from the fluorene chromophore to the Bodipy dyes. Luminescence studies, complemented by transient-absorption spectroscopy studies, also indicate that efficient inter-Bodipy energy transfer across the rigid fluorene spacer takes place in 1 and 2, with rate constants, evaluated by several experimental methods, between 2.0 and 7.0 x 10(9) s(-1). Such an inter-Bodipy energy transfer appears to be governed by the Förster mechanism. By taking advantage of the presence of various protonable sites in the substituents of the lower-energy Bodipy subunit of 1 and 2, the effect of protonation on the energy-transfer rates has also been investigated. The results suggest that control of energy-transfer rate and efficiency of inter-Bodipy energy transfer in this type of systems can be achieved by an external, reversible input.

  4. On the mechanism of non-radiative decay of blue fluorescent protein chromophore: New insight from the excited-state molecular dynamics simulations and potential energy calculations

    Science.gov (United States)

    Zhao, Li; Liu, Jian-Yong; Zhou, Pan-Wang

    2017-11-01

    A detailed theoretical investigation based on the ab initio on-the-fly surface hopping dynamics simulations and potential energy surfaces calculations has been performed to unveil the mechanism of the photoinduced non-adiabatic relaxation process of the isolated blue fluorescent protein (BFP) chromophore in gas phase. The data analysis presents that the dominant reaction coordinate of the BFP chromophore is driven by a rotation motion around the CC double bridging bond, which is in remarkable difference with a previous result which supports a Hula-Twist rotation pattern. Such behavior is consistent with the double bond rotation pattern of the GFP neutral chromophore. In addition, the dynamics simulations give an estimated decay time of 1.1 ps for the S1 state, which is agrees well with the experimental values measured in proteins. The present work offers a straightforward understanding for the decay mechanism of the BFP chromophore and suggestions of the photochemical properties of analogous protein chromophores. We hope the current work would be helpful for further exploration of the BFP photochemical and photophysical properties in various environments, and can provide guidance and prediction for rational design of the fluorescent proteins catering for different demands.

  5. The Major Chromophore Arising from Glucose Degradation and Oxidative Stress Occurrence during Lens Proteins Glycation Induced by Glucose

    Directory of Open Access Journals (Sweden)

    Felipe Ávila

    2017-12-01

    Full Text Available Glucose autoxidation has been proposed as a key reaction associated with deleterious effects induced by hyperglycemia in the eye lens. Little is known about chromophores generated during glucose autoxidation. In this study, we analyzed the effect of oxidative and dicarbonyl stress in the generation of a major chromophore arising from glucose degradation (GDC and its association with oxidative damage in lens proteins. Glucose (5 mM was incubated with H2O2 (0.5–5 mM, Cu2+ (5–50 μM, glyoxal (0.5–5 mM or methylglyoxal (0.5–5 mM at pH 7.4, 5% O2, 37 °C, from 0 to 30 days. GDC concentration increased with incubation time, as well as when incubated in the presence of H2O2 and/or Cu2+, which were effective even at the lowest concentrations. Dicarbonylic compounds did not increase the levels of GDC during incubations. 1H, 13C and FT-IR spectra from the purified fraction containing the chromophore (detected by UV/vis spectroscopy showed oxidation products of glucose, including gluconic acid. Lens proteins solutions (10 mg/mL incubated with glucose (30 mM presented increased levels of carboxymethyl-lysine and hydrogen peroxide that were associated with GDC increase. Our results suggest a possible use of GDC as a marker of autoxidative reactions occurring during lens proteins glycation induced by glucose.

  6. Single Frequency Impedance Analysis on Reduced Graphene Oxide Screen-Printed Electrode for Biomolecular Detection.

    Science.gov (United States)

    Rajesh; Singal, Shobhita; Kotnala, Ravinder K

    2017-10-01

    A biofunctionalized reduced graphene oxide (rGO)-modified screen-printed carbon electrode (SPCE) was constructed as an immunosensor for C-reactive protein (CRP) detection, a biomarker released in early stage acute myocardial infarction. A different approach of single frequency analysis (SFA) study was utilized for the biomolecular sensing, by monitoring the response in phase angle changes obtained at an optimized frequency resulting from antigen-antibody interactions. A set of measurements were carried out to optimize a frequency where a maximum change in phase angle was observed, and in this case, we found it at around 10 Hz. The bioelectrode was characterized by contact angle measurements, scanning electron microscopy, and electrochemical techniques. A concentration-dependent response of immunosensor to CRP with the change in phase angle, at a fixed frequency of 10 Hz, was found to be in the range of 10 ng mL -1 to 10 μg mL -1 in PBS and was fit quantitative well with the Hill-Langmuir equation. Based on the concentration-response data, the dissociation constant (K d ) was found to be 3.5 nM (with a Hill coefficient n = 0.57), which indicated a negative cooperativity with high anti-CRP (antibody)-CRP (antigen) binding at the electrode surface. A low-frequency analysis of sensing with an ease of measurement on a disposable electroactive rGO-modified electrode with high selectivity and sensitivity makes it a potential tool for biological sensors.

  7. Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research

    Science.gov (United States)

    Ilić, Nataša; Pilarczyk, Götz; Lee, Jin-Ho; Logeswaran, Abiramy; Borroni, Aurora Paola; Krufczik, Matthias; Theda, Franziska; Waltrich, Nadine; Bestvater, Felix; Hildenbrand, Georg; Cremer, Christoph; Blank, Michael

    2017-01-01

    Understanding molecular interactions and regulatory mechanisms in tumor initiation, progression, and treatment response are key requirements towards advanced cancer diagnosis and novel treatment procedures in personalized medicine. Beyond decoding the gene expression, malfunctioning and cancer-related epigenetic pathways, investigations of the spatial receptor arrangements in membranes and genome organization in cell nuclei, on the nano-scale, contribute to elucidating complex molecular mechanisms in cells and tissues. By these means, the correlation between cell function and spatial organization of molecules or molecular complexes can be studied, with respect to carcinogenesis, tumor sensitivity or tumor resistance to anticancer therapies, like radiation or antibody treatment. Here, we present several new applications for bio-molecular nano-probes and super-resolution, laser fluorescence localization microscopy and their potential in life sciences, especially in biomedical and cancer research. By means of a tool-box of fluorescent antibodies, green fluorescent protein (GFP) tagging, or specific oligonucleotides, we present tumor relevant re-arrangements of Erb-receptors in membranes, spatial organization of Smad specific ubiquitin protein ligase 2 (Smurf2) in the cytosol, tumor cell characteristic heterochromatin organization, and molecular re-arrangements induced by radiation or antibody treatment. The main purpose of this article is to demonstrate how nano-scaled distance measurements between bio-molecules, tagged by appropriate nano-probes, can be applied to elucidate structures and conformations of molecular complexes which are characteristic of tumorigenesis and treatment responses. These applications open new avenues towards a better interpretation of the spatial organization and treatment responses of functionally relevant molecules, at the single cell level, in normal and cancer cells, offering new potentials for individualized medicine. PMID:28956810

  8. Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research

    Directory of Open Access Journals (Sweden)

    Michael Hausmann

    2017-09-01

    Full Text Available Understanding molecular interactions and regulatory mechanisms in tumor initiation, progression, and treatment response are key requirements towards advanced cancer diagnosis and novel treatment procedures in personalized medicine. Beyond decoding the gene expression, malfunctioning and cancer-related epigenetic pathways, investigations of the spatial receptor arrangements in membranes and genome organization in cell nuclei, on the nano-scale, contribute to elucidating complex molecular mechanisms in cells and tissues. By these means, the correlation between cell function and spatial organization of molecules or molecular complexes can be studied, with respect to carcinogenesis, tumor sensitivity or tumor resistance to anticancer therapies, like radiation or antibody treatment. Here, we present several new applications for bio-molecular nano-probes and super-resolution, laser fluorescence localization microscopy and their potential in life sciences, especially in biomedical and cancer research. By means of a tool-box of fluorescent antibodies, green fluorescent protein (GFP tagging, or specific oligonucleotides, we present tumor relevant re-arrangements of Erb-receptors in membranes, spatial organization of Smad specific ubiquitin protein ligase 2 (Smurf2 in the cytosol, tumor cell characteristic heterochromatin organization, and molecular re-arrangements induced by radiation or antibody treatment. The main purpose of this article is to demonstrate how nano-scaled distance measurements between bio-molecules, tagged by appropriate nano-probes, can be applied to elucidate structures and conformations of molecular complexes which are characteristic of tumorigenesis and treatment responses. These applications open new avenues towards a better interpretation of the spatial organization and treatment responses of functionally relevant molecules, at the single cell level, in normal and cancer cells, offering new potentials for individualized medicine.

  9. Applications of atomic force microscopy to the studies of biomaterials in biomolecular systems

    Science.gov (United States)

    Ma, Xiang

    Atomic force microscopy (AFM) is a unique tool for the studies of nanoscale structures and interactions. In this dissertation, I applied AFM to study transitions among multiple states of biomaterials in three different microscopic biomolecular systems: MukB-dependent DNA condensation, holdfast adhesion, and virus elasticity. To elucidate the mechanism of MukB-dependent DNA condensation, I have studied the conformational changes of MukB proteins as indicators for the strength of interactions between MukB, DNA and other molecular factors, such as magnesium and ParC proteins, using high-resolution AFM imaging. To determine the physical origins of holdfast adhesion, I have investigated the dynamics of adhesive force development of the holdfast, employing AFM force spectroscopy. By measuring rupture forces between the holdfast and the substrate, I showed that the holdfast adhesion is strongly time-dependent and involves transformations at multiple time scales. Understanding the mechanisms of adhesion force development of the holdfast will be critical for future engineering of holdfasts properties for various applications. Finally, I have examined the elasticity of self-assembled hepatitis B virus-like particles (HBV VLPs) and brome mosaic virus (BMV) in response to changes of pH and salinity, using AFM nanoindentation. The distributions of elasticity were mapped on a single particle level and compared between empty, RNA- and gold-filled HBV VLPs. I found that a single HBV VLP showed heterogeneous distribution of elasticity and a two-step buckling transition, suggesting a discrete property of HBV capsids. For BMV, I have showed that viruses containing different RNA molecules can be distinguished by mechanical measurements, while they are indistinguishable by morphology. I also studied the effect of pH on the elastic behaviors of three-particle BMV and R3/4 BMV. This study can yield insights into RNA presentation/release mechanisms, and could help us to design novel drug

  10. Perspectives of biomolecular NMR in drug discovery: the blessing and curse of versatility

    International Nuclear Information System (INIS)

    Jahnke, Wolfgang

    2007-01-01

    The versatility of NMR and its broad applicability to several stages in the drug discovery process is well known and generally considered one of the major strengths of NMR (Pellecchia et al., Nature Rev Drug Discov 1:211-219, 2002; Stockman and Dalvit, Prog Nucl Magn Reson Spectrosc 41:187-231, 2002; Lepre et al., Comb Chem High throughput screen 5:583-590, 2002; Wyss et al., Curr Opin Drug Discov Devel 5:630-647, 2002; Jahnke and Widmer, Cell Mol Life Sci 61:580-599, 2004; Huth et al., Methods Enzymol 394:549-571, 2005b; Klages et al., Mol Biosyst 2:318-332, 2006; Takeuchi and Wagner, Curr Opin Struct Biol 16:109-117, 2006; Zartler and Shapiro, Curr Pharm Des 12:3963-3972, 2006). Indeed, NMR is the only biophysical technique which can detect and quantify molecular interactions, and at the same time provide detailed structural information with atomic level resolution. NMR should therefore be ideally suited and widely requested as a tool for drug discovery research, and numerous examples of drug discovery projects which have substantially benefited from NMR contributions or were even driven by NMR have been described in the literature. However, not all pharmaceutical companies have rigorously implemented NMR as integral tool of their research processes. Some companies invest with limited resources, and others do not use biomolecular NMR at all. This discrepancy in assessing the value of a technology is striking, and calls for clarification-under which circumstances can NMR provide added value to the drug discovery process? What kind of contributions can NMR make, and how is it implemented and integrated for maximum impact? This perspectives article suggests key areas of impact for NMR, and a model of integrating NMR with other technologies to realize synergies and maximize their value for drug discovery

  11. Sop-GPU: accelerating biomolecular simulations in the centisecond timescale using graphics processors.

    Science.gov (United States)

    Zhmurov, A; Dima, R I; Kholodov, Y; Barsegov, V

    2010-11-01

    Theoretical exploration of fundamental biological processes involving the forced unraveling of multimeric proteins, the sliding motion in protein fibers and the mechanical deformation of biomolecular assemblies under physiological force loads is challenging even for distributed computing systems. Using a C(α)-based coarse-grained self organized polymer (SOP) model, we implemented the Langevin simulations of proteins on graphics processing units (SOP-GPU program). We assessed the computational performance of an end-to-end application of the program, where all the steps of the algorithm are running on a GPU, by profiling the simulation time and memory usage for a number of test systems. The ∼90-fold computational speedup on a GPU, compared with an optimized central processing unit program, enabled us to follow the dynamics in the centisecond timescale, and to obtain the force-extension profiles using experimental pulling speeds (v(f) = 1-10 μm/s) employed in atomic force microscopy and in optical tweezers-based dynamic force spectroscopy. We found that the mechanical molecular response critically depends on the conditions of force application and that the kinetics and pathways for unfolding change drastically even upon a modest 10-fold increase in v(f). This implies that, to resolve accurately the free energy landscape and to relate the results of single-molecule experiments in vitro and in silico, molecular simulations should be carried out under the experimentally relevant force loads. This can be accomplished in reasonable wall-clock time for biomolecules of size as large as 10(5) residues using the SOP-GPU package. © 2010 Wiley-Liss, Inc.

  12. SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces.

    Science.gov (United States)

    Kochanczyk, Marek; Hlavacek, William S; Lipniacki, Tomasz

    2017-11-15

    Rule-based modeling is a powerful approach for studying biomolecular site dynamics. Here, we present SPATKIN, a general-purpose simulator for rule-based modeling in two spatial dimensions. The simulation algorithm is a lattice-based method that tracks Brownian motion of individual molecules and the stochastic firing of rule-defined reaction events. Because rules are used as event generators, the algorithm is network-free, meaning that it does not require to generate the complete reaction network implied by rules prior to simulation. In a simulation, each molecule (or complex of molecules) is taken to occupy a single lattice site that cannot be shared with another molecule (or complex). SPATKIN is capable of simulating a wide array of membrane-associated processes, including adsorption, desorption and crowding. Models are specified using an extension of the BioNetGen language, which allows to account for spatial features of the simulated process. The C ++ source code for SPATKIN is distributed freely under the terms of the GNU GPLv3 license. The source code can be compiled for execution on popular platforms (Windows, Mac and Linux). An installer for 64-bit Windows and a macOS app are available. The source code and precompiled binaries are available at the SPATKIN Web site (http://pmbm.ippt.pan.pl/software/spatkin). spatkin.simulator@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  13. Acceptor number-dependent ultrafast photo-physical properties of push-pull chromophores using time-resolved methods

    Science.gov (United States)

    Chi, Xiao-Chun; Wang, Ying-Hui; Gao, Yu; Sui, Ning; Zhang, Li-Quan; Wang, Wen-Yan; Lu, Ran; Ji, Wen-Yu; Yang, Yan-Qiang; Zhang, Han-Zhuang

    2018-04-01

    Three push-pull chromophores comprising a triphenylamine (TPA) as electron-donating moiety and functionalized β-diketones as electron acceptor units are studied by various spectroscopic techniques. The time-correlated single-photon counting data shows that increasing the number of electron acceptor units accelerates photoluminescence relaxation rate of compounds. Transient spectra data shows that intramolecular charge transfer (ICT) takes place from TPA units to β-diketones units after photo-excitation. Increasing the number of electron acceptor units would prolong the generation process of ICT state, and accelerate the excited molecule reorganization process and the relaxation process of ICT state.

  14. Ethyne-linked push-pull chromophores: implications of crystal structure and molecular electronics on the quadric nonlinear activity

    Czech Academy of Sciences Publication Activity Database

    Kautny, P.; Kriegner, H.; Bader, D.; Dušek, Michal; Reider, G.A.; Froehlich, J.; Stoeger, B.

    2017-01-01

    Roč. 17, č. 8 (2017), s. 4124-4136 ISSN 1528-7483 R&D Projects: GA ČR(CZ) GA15-12653S; GA MŠk LO1603 EU Projects: European Commission(XE) CZ.2.16/3.1.00/24510 Institutional support: RVO:68378271 Keywords : ethyne-linked materials * nonlinear optical chromophores * molecular structure * optical activity Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 4.055, year: 2016

  15. Chiral 1,2- and 1,3-diol-functionalized chromophores as Lego building blocks for coupled structures.

    Science.gov (United States)

    Spange, Stefan; Hofmann, Katja; Walfort, Bernhard; Rüffer, Tobias; Lang, Heinrich

    2005-10-14

    Chiral nitroanilines containing 1,2- or 1,3-diol functionalities have been synthesized by nucleophilic aromatic substitution of fluoronitroanilines with 1-aminopropane-2,3-diols and 2-aminopropane-1,3-diol in the melt. X-ray structure analyses confirm retention of the configuration of the chiral center. The novel chromophores are suitable to link reversibly to various substituted arylboronic acids which allows the construction of new solvatochromic sensor molecules suitable to response to solvent and anion coordination by fluoride. The solvatochromism of the new compounds has been studied using the Kamlet-Taft LSE relationship.

  16. Scanning number and brightness yields absolute protein concentrations in live cells: a crucial parameter controlling functional bio-molecular interaction networks.

    Science.gov (United States)

    Papini, Christina; Royer, Catherine A

    2018-02-01

    Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation. Clearly, a mechanistic understanding of any given high level biological function requires a quantitative characterization of the principal bio-molecular interactions involved and how these may change dynamically. Such information can be obtained using fluctation analysis, in particular scanning number and brightness, and used to build and test mechanistic models of the functional network to define which characteristics are the most important for its regulation.

  17. Evolução biomolecular homoquiral: a origem e a amplificação da quiralidade nas moléculas da vida Homochiral biomolecular evolution: the origin and the amplification of chirality in life molecules

    Directory of Open Access Journals (Sweden)

    José Augusto R. Rodrigues

    2010-01-01

    Full Text Available The fact that biologically relevant molecules exist only as one of the two enantiomers is a fascinating example of complete symmetry breaking of chirality and has long intrigued our curiosity. The origin of this selective chirality has remained a fundamental enigma with regard to the origin of life since the time of Pasteur, 160 years ago. The symmetry breaking processes, which include autocatalytic crystallization, asymmetric autocatalysis, spontaneous crystallization, adsorption and polymerization of amino acids on mineral surfaces, provide new insights into the origin of biomolecular homochirality.

  18. Absorption and Fluorescence Properties of Chromophoric Dissolved Organic Matter Produced by Algae.

    Science.gov (United States)

    Peng, Tong; Lu, Xiao-lan; Su, Rong-guo; Zhang, Dong-mei

    2015-09-01

    Four kinds of diatom (Chaetoceros curvisetus, Phaeodactylum tricornutum, Nitzschia closterium f. minutissima and Navicula halophile) and two kinds of dinoflagellates (Prorocentrum donghaiense and Gymnodinium) were cultured under laboratory conditions. Variations of optical properties of chromophoric dissolved organic matter (CDOM) were studied with absorption and fluorescence excitation-emission matrix spectroscopy(EEM) during growth of marine microalgae in incubation experiment. Absorption spectrum revealed absorption coefficient a(355) (CDOM absorption coefficients at 355 nm) of 6 kinds of marine microalgae above increased by 64.8%, 242.3%, 535.1%, 903.2%, 836% and 196.4%, respectively. Simultaneously, the absorption spectral slope (Sg), determined between 270 and 350 nm, representing the size of molecular weight of CDOM and humic-like composition, decreased by 8.7%, 34.6%, 39.4%, 53.1%, 46.7%, and 35.7%, respectively. Applying parallel factor analysis (PARAFAC) together with EEM got four components of CDOM: C1(Ex/Em=350(260) nm/450 nm), C2 (Ex/Em=260(430) nm/525 nm), C3 (Ex/Em=325 nm/400 nm) and C4(Ex/Em=275 nm/325 nm), which were relative to three humic-like and one protein-like fluorescent components of Nitzschia closterium f. minutissima and Navicula halophile. In incubation experiment, fluorescence intensity of these four components during growth of Nitzschia closterium f. minutissima increased by, respectively, 8.68, 24.9, 7.19 and 39.8 times, and those of Navicula halophile increased by 2.64, 0.07, 4.39 and 12.4 times, respectively. Significant relationships were found between the fluorescence intensity of four components of CDOM, a(355) and Sg. All results demonstrated that both content and molecular weight of CDOM produced by diatom and dinoflagellate studied in incubation experiment increased, but these two parameters changed more obviously of the diatom than those of dinoflagellate; the proportion of humic-like components in the composition of CDOM

  19. Beyond the Förster formulation for resonance energy transfer: the role of dark states.

    Science.gov (United States)

    Sissa, C; Manna, A K; Terenziani, F; Painelli, A; Pati, S K

    2011-07-28

    Resonance Energy Transfer (RET) is investigated in pairs of charge-transfer (CT) chromophores. CT chromophores are an interesting class of π conjugated chromophores decorated with one or more electron-donor and acceptor groups in polar (D-π-A), quadrupolar (D-π-A-π-D or A-π-D-π-A) or octupolar (D(-π-A)(3) or A(-π-D)(3)) structures. Essential-state models accurately describe low-energy linear and nonlinear spectra of CT-chromophores and proved very useful to describe spectroscopic effects of electrostatic interchromophore interactions in multichromophoric assemblies. Here we apply the same approach to describe RET between CT-chromophores. The results are quantitatively validated by an extensive comparison with time-dependent density functional theory (TDDFT) calculations, confirming that essential-state models offer a simple and reliable approach for the calculation of electrostatic interchromophore interactions. This is an important result since it sets the basis for more refined treatments of RET: essential-state models are in fact easily extended to account for molecular vibrations in truly non-adiabatic approaches and to account for inhomogeneous broadening effects due to polar solvation. Optically forbidden (dark) states of quadrupolar and octupolar chromophores offer an interesting opportunity to verify the reliability of the dipolar approximation. In striking contrast with the dipolar approximation that strictly forbids RET towards or from dark states, our results demonstrate that dark states can take an active role in RET with interaction energies that, depending on the relative orientation of the chromophores, can be even larger than those relevant to allowed states. Essential-state models, whose predictions are quantitatively confirmed by TDDFT results, allow us to relate RET interaction energies towards allowed and dark states to the supramolecular symmetry of the RET-pair, offering reliable design strategies to optimize RET-interactions. This

  20. Lake and sea populations of Mysis relicta (Crustacea, Mysida with different visual-pigment absorbance spectra use the same A1 chromophore.

    Directory of Open Access Journals (Sweden)

    Nikolai Belikov

    Full Text Available Glacial-relict species of the genus Mysis (opossum shrimps inhabiting both fresh-water lakes and brackish sea waters in northern Europe show a consistent lake/sea dichotomy in eye spectral sensitivity. The absorbance peak (λmax recorded by microspectrophotometry in isolated rhabdoms is invariably 20-30 nm red-shifted in "lake" compared with "sea" populations. The dichotomy holds across species, major opsin lineages and light environments. Chromophore exchange from A1 to A2 (retinal → 3,4-didehydroretinal is a well-known mechanism for red-shifting visual pigments depending on environmental conditions or stages of life history, present not only in fishes and amphibians, but in some crustaceans as well. We tested the hypothesis that the lake/sea dichotomy in Mysis is due to the use of different chromophores, focussing on two populations of M. relicta from, respectively, a Finnish lake and the Baltic Sea. They are genetically very similar, having been separated for less than 10 kyr, and their rhabdoms show a typical lake/sea difference in λmax (554 nm vs. 529 nm. Gene sequencing has revealed no differences translating into amino acid substitutions in the transmembrane parts of their opsins. We determined the chromophore identity (A1 or A2 in the eyes of these two populations by HPLC, using as standards pure chromophores A1 and A2 as well as extracts from bovine (A1 and goldfish (A2 retinas. We found that the visual-pigment chromophore in both populations is A1 exclusively. Thus the spectral difference between these two populations of M. relicta is not due to the use of different chromophores. We argue that this conclusion is likely to hold for all populations of M. relicta as well as its European sibling species.

  1. Winter to spring variations of chromophoric dissolved organic matter in a temperate estuary (Po River, northern Adriatic Sea).

    Science.gov (United States)

    Berto, D; Giani, M; Savelli, F; Centanni, E; Ferrari, C R; Pavoni, B

    2010-07-01

    The light absorbing fraction of dissolved organic carbon (DOC), known as chromophoric dissolved organic matter (CDOM) showed wide seasonal variations in the temperate estuarine zone in front of the Po River mouth. DOC concentrations increased from winter through spring mainly as a seasonal response to increasing phytoplankton production and thermohaline stratification. The monthly dependence of the CDOM light absorption by salinity and chlorophyll a concentrations was explored. In 2003, neither DOC nor CDOM were linearly correlated with salinity, due to an exceptionally low Po river inflow. Though the CDOM absorbance coefficients showed a higher content of chromophoric dissolved organic matter in 2004 with respect to 2003, the spectroscopic features confirmed that the qualitative nature of CDOM was quite similar in both years. CDOM and DOC underwent a conservative mixing, only after relevant Po river freshets, and a change in optical features with an increase of the specific absorption coefficient was observed, suggesting a prevailing terrestrial origin of dissolved organic matter. Published by Elsevier Ltd.

  2. Synthesis and photochemical properties of a novel iron-sulfur-nitrosyl cluster derivatized with the pendant chromophore protoporphyrin IX.

    Science.gov (United States)

    Conrado, Christa L; Wecksler, Stephen; Egler, Christian; Magde, Douglas; Ford, Peter C

    2004-09-06

    The novel Roussin red-salt ester (PPIX-RSE) with a pendant porphyrin chromophore was prepared and investigated as a precursor for the photochemical generation of nitric oxide. PPIX-RSE has the general formula Fe(2)(NO)(4)[(mu-S,mu-S')P] (where (S,S')P is the bis(2-thiolatoethyl) diester of protoporphyrin IX. The photoexcitation of PPIX-RSE with 436- or 546-nm light in an aerated chloroform solution led to the photodecomposition of the cluster with the respective quantum yields (5.2 +/- 0.7) x 10(-4) and (2.5 +/- 0.5 x 10(-4)) and the concomitant release of NO. PPIX-RSE is a significantly more effective NO generator at longer wavelength excitation than are other Fe(2)(mu-SR)(2)(NO)(4) esters for which R is a simple alkyl group such as CH(3)CH(2)- because of the much higher absorptivity of the pendant PPIX chromophore at these wavelengths and a modestly higher quantum yield. Fluorescence intensity and lifetime data indicate that the photoexcited porphyrin of PPIX-RSE is largely quenched by the energy transfer to the Fe(2)S(2)(NO)(4) cluster's core. However, a small fraction of this emission is not quenched, and it is proposed that PPIX-RSE may exist in solution as two conformers.

  3. Occlusion of chromophore oxides by Sol-Gel methods: Application to the synthesis of hematite-silica red pigments

    Directory of Open Access Journals (Sweden)

    Vicent, J. B.

    2000-02-01

    Full Text Available Heteromorphic pigments present the chromophore particle occluded in an encapsulating matrix which is thermally stable and insoluble in glazes. The occluded chromophore compound is also insoluble in the host matrix. In this work the mechanisms of formation of this type of pigments are analyzed and the occlusion of hematite into silica matrix is discussed. The formation of this hematite-silica red pigment follows a sintering-coarsening mechanism, and, consequently, the control of both hematite particles nucleation and their crystal growth results to be decisive to obtain a good coloring effectiveness.

    En los pigmentos heteromórficos la partícula de cromóforo es ocluida en una matriz encapsuladora estable tanto termicamente como frente a los vidriados. El compuesto cromóforo ocluido y la matriz no coloreada son insolubles. En este trabajo se analiza los diferentes mecanismos de formación de estos pigmentos heteromórficos y se estudia la oclusión de hematita en sílice mediante métodos sol-gel acuoso. El pigmento sigue un mecanismo de sinterización-crecimiento cristalino por lo que es muy importante controlar el momento de nucleación y la velocidad de crecimiento de las partículas de hematita en el seno de la matriz.

  4. Predicting dissolved lignin phenol concentrations in the coastal ocean from chromophoric dissolved organic matter (CDOM absorption coefficients

    Directory of Open Access Journals (Sweden)

    Cédric G. Fichot

    2016-02-01

    Full Text Available Dissolved lignin is a well-established biomarker of terrigenous dissolved organic matter (DOM in the ocean, and a chromophoric component of DOM. Although evidence suggests there is a strong linkage between lignin concentrations and chromophoric DOM (CDOM absorption coefficients in coastal waters, the characteristics of this linkage and the existence of a relationship that is applicable across coastal oceans remain unclear. Here, 421 paired measurements of dissolved lignin concentrations (sum of 9 lignin phenols and CDOM absorption coefficients (ag(λ were used to examine their relationship along the river-ocean continuum (0-37 salinity and across contrasting coastal oceans (sub-tropical, temperate, high-latitude. Overall, lignin concentrations spanned four orders of magnitude and revealed a strong, non-linear relationship with ag(λ. The characteristics of the relationship (shape, wavelength dependency, lignin-composition dependency and evidence from degradation indicators were all consistent with lignin being an important driver of CDOM variability in coastal oceans, and suggested physical mixing and long-term photodegradation were important in shaping the relationship. These observations were used to develop two simple empirical models for estimating lignin concentrations from ag(λ with a +/- 20% error relative to measured values. The models are expected to be applicable in most coastal oceans influenced by terrigenous inputs.

  5. Preparation and third-order nonlinear optical property of poly(urethane-imide containing dispersed red chromophore

    Directory of Open Access Journals (Sweden)

    2008-11-01

    Full Text Available A novel poly(urethane-imide (PUI containing dispersed red chromophore was synthesized. The PUI was characterized by FT-IR, UV-Vis, DSC and TGA. The results of DSC and TGA indicated that the PUI exhibited high thermal stability up to its glass-transition temperature (Tg of 196°C and 5% heat weight loss temperature of 229°C. According to UV-Vis spectrum and working curve, the maximum molar absorption coefficient and absorption wavelength were measured. They were used to calculate the third-order nonlinear optical coefficient χ(3. At the same time, the chromophore density of PUI, nonlinear refractive index coefficient and molecular hyperpolarizability of PUI were obtained. The fluorescence spectra of PUI and model compound DR-19 were determined at excitation wavelength 300 nm. The electron donor and acceptor in polymer formed the exciplex through the transfer of the electric charges. The results show that the poly(urethane-imide is a promising candidate for application in optical devices.

  6. Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine

    Energy Technology Data Exchange (ETDEWEB)

    Pletnev, Vladimir Z., E-mail: vzpletnev@gmail.com; Pletneva, Nadya V.; Lukyanov, Konstantin A.; Souslova, Ekaterina A.; Fradkov, Arkady F.; Chudakov, Dmitry M.; Chepurnykh, Tatyana; Yampolsky, Ilia V. [Russian Academy of Sciences, Moscow (Russian Federation); Wlodawer, Alexander [National Cancer Institute, Frederick, MD 21702 (United States); Dauter, Zbigniew [National Cancer Institute, Argonne, IL 60439 (United States); Pletnev, Sergei, E-mail: vzpletnev@gmail.com [National Cancer Institute, Argonne, IL 60439 (United States); SAIC-Frederick, Argonne, IL 60439 (United States); Russian Academy of Sciences, Moscow (Russian Federation)

    2013-09-01

    The crystal structure of the novel red emitting fluorescent protein from lancelet Branchiostoma lanceolatum (Chordata) revealed an unusual five residues cyclic unit comprising Gly58-Tyr59-Gly60 chromophore, the following Phe61 and Tyr62 covalently bound to chromophore Tyr59. A key property of proteins of the green fluorescent protein (GFP) family is their ability to form a chromophore group by post-translational modifications of internal amino acids, e.g. Ser65-Tyr66-Gly67 in GFP from the jellyfish Aequorea victoria (Cnidaria). Numerous structural studies have demonstrated that the green GFP-like chromophore represents the ‘core’ structure, which can be extended in red-shifted proteins owing to modifications of the protein backbone at the first chromophore-forming position. Here, the three-dimensional structures of green laGFP (λ{sub ex}/λ{sub em} = 502/511 nm) and red laRFP (λ{sub ex}/λ{sub em} ≃ 521/592 nm), which are fluorescent proteins (FPs) from the lancelet Branchiostoma lanceolatum (Chordata), were determined together with the structure of a red variant laRFP-ΔS83 (deletion of Ser83) with improved folding. Lancelet FPs are evolutionarily distant and share only ∼20% sequence identity with cnidarian FPs, which have been extensively characterized and widely used as genetically encoded probes. The structure of red-emitting laRFP revealed three exceptional features that have not been observed in wild-type fluorescent proteins from Cnidaria reported to date: (i) an unusual chromophore-forming sequence Gly58-Tyr59-Gly60, (ii) the presence of Gln211 at the position of the conserved catalytic Glu (Glu222 in Aequorea GFP), which proved to be crucial for chromophore formation, and (iii) the absence of modifications typical of known red chromophores and the presence of an extremely unusual covalent bond between the Tyr59 C{sup β} atom and the hydroxyl of the proximal Tyr62. The impact of this covalent bond on the red emission and the large Stokes shift (

  7. An effective hierarchical model for the biomolecular covalent bond: an approach integrating artificial chemistry and an actual terrestrial life system.

    Science.gov (United States)

    Oohashi, Tsutomu; Ueno, Osamu; Maekawa, Tadao; Kawai, Norie; Nishina, Emi; Honda, Manabu

    2009-01-01

    Under the AChem paradigm and the programmed self-decomposition (PSD) model, we propose a hierarchical model for the biomolecular covalent bond (HBCB model). This model assumes that terrestrial organisms arrange their biomolecules in a hierarchical structure according to the energy strength of their covalent bonds. It also assumes that they have evolutionarily selected the PSD mechanism of turning biological polymers (BPs) into biological monomers (BMs) as an efficient biomolecular recycling strategy We have examined the validity and effectiveness of the HBCB model by coordinating two complementary approaches: biological experiments using existent terrestrial life, and simulation experiments using an AChem system. Biological experiments have shown that terrestrial life possesses a PSD mechanism as an endergonic, genetically regulated process and that hydrolysis, which decomposes a BP into BMs, is one of the main processes of such a mechanism. In simulation experiments, we compared different virtual self-decomposition processes. The virtual species in which the self-decomposition process mainly involved covalent bond cleavage from a BP to BMs showed evolutionary superiority over other species in which the self-decomposition process involved cleavage from BP to classes lower than BM. These converging findings strongly support the existence of PSD and the validity and effectiveness of the HBCB model.

  8. Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.

    Science.gov (United States)

    Prinz, Jan-Hendrik; Chodera, John D; Pande, Vijay S; Swope, William C; Smith, Jeremy C; Noé, Frank

    2011-06-28

    Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.

  9. Water quality monitoring in a bathing area of Civitavecchia (Latium, Italy) using Chromophoric Dissolved Organic Matter (CDOM) as a tracer of faecal contamination

    Science.gov (United States)

    Madonia, Alice; Bonamano, Simone; Caruso, Gabriella; Stefani', Chiara; Consalvi, Natalizia; Piermattei, Viviana; Zappalà, Giuseppe; Marcelli, Marco

    2017-04-01

    Coastal urban bathing areas are often affected by events of faecal contamination, caused by the discharge of untreated wastewaters during the bathing season that can increase the risk for public health. Monitoring the quality of recreational waters is still closely linked to time-consuming seawater sampling and laboratory analysis, not allowing promptly management interventions. To face this issue, the European environmental policies strongly promote the development of coastal observing systems, above all in the Southern European Seas (SES). Chromophoric Dissolved Organic Matter (CDOM) has been increasingly used as a tracer of bacterial loads, since wastewaters are characterized by a large amount of organic compounds. The aim of this work was to study the relation between CDOM and Escherichia coli abundance, giving relevance to bacterial physiological state detected using both the standard culture method and the innovative fluorescent antibody technique. Attention has been paid also on the expression of extracellular enzymatic activity by the total microbial community to explore the role of bacteria in the decomposition processes of dissolved organic matter. Data were collected during summer 2015 and 2016 in a bathing area of Civitavecchia at increasing distances from the discharge point. The results confirm the usefulness of CDOM measurements as a proxy of faecal pollution in bathing areas. In this perspective, the low-cost stand-alone systems equipped with CDOM fluorescence sensors developed by the Laboratory of Experimental Oceanology and Marine Ecology (Tuscia University) (Marcelli et al., 2014) could allow the continous monitoring of water quality, increasing the capabilities of the Civitavecchia Coastal Environmental Monitoring System (C-CEMS) in the analysis of pollution events. Thanks to the integration of in situ fixed stations, high-resolution satellites imagery and numerical models, C-CEMS provides a management tool to support the stakeholders for timely

  10. Extension of Light-Harvesting Ability of Photosynthetic Light-Harvesting Complex 2 (LH2) through Ultrafast Energy Transfer from Covalently Attached Artificial Chromophores.

    Science.gov (United States)

    Yoneda, Yusuke; Noji, Tomoyasu; Katayama, Tetsuro; Mizutani, Naoto; Komori, Daisuke; Nango, Mamoru; Miyasaka, Hiroshi; Itoh, Shigeru; Nagasawa, Yutaka; Dewa, Takehisa

    2015-10-14

    Introducing appropriate artificial components into natural biological systems could enrich the original functionality. To expand the available wavelength range of photosynthetic bacterial light-harvesting complex 2 (LH2 from Rhodopseudomonas acidophila 10050), artificial fluorescent dye (Alexa Fluor 647: A647) was covalently attached to N- and C-terminal Lys residues in LH2 α-polypeptides with a molar ratio of A647/LH2 ≃ 9/1. Fluorescence and transient absorption spectroscopies revealed that intracomplex energy transfer from A647 to intrinsic chromophores of LH2 (B850) occurs in a multiexponential manner, with time constants varying from 440 fs to 23 ps through direct and B800-mediated indirect pathways. Kinetic analyses suggested that B800 chromophores mediate faster energy transfer, and the mechanism was interpretable in terms of Förster theory. This study demonstrates that a simple attachment of external chromophores with a flexible linkage can enhance the light harvesting activity of LH2 without affecting inherent functions of energy transfer, and can achieve energy transfer in the subpicosecond range. Addition of external chromophores, thus, represents a useful methodology for construction of advanced hybrid light-harvesting systems that afford solar energy in the broad spectrum.

  11. UV-Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 1: basic principles and properties of tyrosine chromophore.

    Science.gov (United States)

    Antosiewicz, Jan M; Shugar, David

    2016-06-01

    Spectroscopic properties of tyrosine residues may be employed in structural studies of proteins. Here we discuss several different types of UV-Vis spectroscopy, like normal, difference and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, and corresponding optical properties of the tyrosine chromophore, phenol, which are used to study protein structure.

  12. Characteristics and sources of chromophoric dissolved organic matter in lakes of the Yungui Plateau, China, differing in trophic state and altitude

    NARCIS (Netherlands)

    Zhang, Y.; Zhang, E.; Yin, Y.; Van Dijk, M.A.; Feng, L.; Shi, Z.; Liu, M.; Qina, B.

    2010-01-01

    The high-mountain lakes on the Yungui Plateau in China are exposed to high-intensity ultraviolet radiation, and contain low concentrations of chromophoric dissolved organic matter (CDOM). We determined CDOM absorption, fluorescence, composition, and source in 38 lakes on the Yungui Plateau at

  13. The crystal structure of human protein α1M reveals a chromophore-binding site and two putative protein–protein interfaces

    International Nuclear Information System (INIS)

    Zhang, Yangli; Gao, Zengqiang; Guo, Zhen; Zhang, Hongpeng; Zhang, Zhenzhen; Luo, Miao; Hou, Haifeng; Huang, Ailong; Dong, Yuhui; Wang, Deqiang

    2013-01-01

    Highlights: •We determined the first structure of human α1M with heavy electron density of the chromophore. •We proposed a new structural model of the chromophore. •We first revealed that the two conserved surface regions of α1M are proposed as putative protein–protein interface sites. -- Abstract: Lipocalin α1-microglobulin (α1M) is a conserved glycoprotein present in plasma and in the interstitial fluids of all tissues. α1M is linked to a heterogeneous yellow–brown chromophore of unknown structure, and interacts with several target proteins, including α1-inhibitor-3, fibronectin, prothrombin and albumin. To date, there is little knowledge about the interaction sites between α1M and its partners. Here, we report the crystal structure of the human α1M. Due to the crystallization occurring in a low ionic strength solution, the unidentified chromophore with heavy electron density is observed at a hydrophobic inner tube of α1M. In addition, two conserved surface regions of α1M are proposed as putative protein–protein interface sites. Further study is needed to unravel the detailed information about the interaction between α1M and its partners

  14. Ferrocene-quinoxaline Y-shaped chromophores as fascinating second-order NLO building blocks for long lasting highly active SHG polymeric films.

    Science.gov (United States)

    Senthilkumar, Kabali; Thirumoorthy, Krishnan; Dragonetti, Claudia; Marinotto, Daniele; Righetto, Stefania; Colombo, Alessia; Haukka, Matti; Palanisami, Nallasamy

    2016-07-26

    The first example of a Y-shaped ferrocene quinoxaline derivative with a surprisingly high and stable second harmonic generation (SHG) response in composite polymeric films is reported. The interesting quadratic hyperpolarizability values of different substituted Y-shaped chromophores are also investigated in solution by the EFISH technique.

  15. Phosphorescence parameters for platinum (II) organometallic chromophores: A study at the non-collinear four-component Kohn–Sham level of theory

    DEFF Research Database (Denmark)

    Norman, Patrick; Jensen, Hans Jørgen Aagaard

    2012-01-01

    A theoretical characterization of the phosphorescence decay traces of a prototypical platinum (II) organic chromophore has been conducted. The phosphorescence wavelength and radiative lifetime are predicted to equal 544 nm and 160 μs, respectively. The third triplet state is assigned as participa...

  16. Acentric 2-D ensembles of D-br-A electron-transfer chromophores via vectorial orientation within amphiphilic n-helix bundle peptides for photovoltaic device applications.

    Science.gov (United States)

    Koo, Jaseung; Park, Jaehong; Tronin, Andrey; Zhang, Ruili; Krishnan, Venkata; Strzalka, Joseph; Kuzmenko, Ivan; Fry, H Christopher; Therien, Michael J; Blasie, J Kent

    2012-02-14

    We show that simply designed amphiphilic 4-helix bundle peptides can be utilized to vectorially orient a linearly extended donor-bridge-acceptor (D-br-A) electron transfer (ET) chromophore within its core. The bundle's interior is shown to provide a unique solvation environment for the D-br-A assembly not accessible in conventional solvents and thereby control the magnitudes of both light-induced ET and thermal charge recombination rate constants. The amphiphilicity of the bundle's exterior was employed to vectorially orient the peptide-chromophore complex at a liquid-gas interface, and its ends were tailored for subsequent covalent attachment to an inorganic surface, via a "directed assembly" approach. Structural data, combined with evaluation of the excited state dynamics exhibited by these peptide-chromophore complexes, demonstrate that densely packed, acentrically ordered 2-D monolayer ensembles of such complexes at high in-plane chromophore densities approaching 1/200 Å(2) offer unique potential as active layers in binary heterojunction photovoltaic devices.

  17. iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D.

    Science.gov (United States)

    Liluashvili, Vaja; Kalayci, Selim; Fluder, Eugene; Wilson, Manda; Gabow, Aaron; Gümüs, Zeynep H

    2017-08-01

    Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment. iCAVE introduces 3D extensions of known 2D network layout, clustering, and edge-bundling algorithms, as well as new 3D network layout algorithms. Furthermore, users can simultaneously query several built-in databases within iCAVE for network generation or visualize their own networks (e.g., disease, drug, protein, metabolite). iCAVE has modular structure that allows rapid development by addition of algorithms, datasets, or features without affecting other parts of the code. Overall, iCAVE is the first freely available open source tool that enables 3D (optionally stereoscopic or immersive) visualizations of complex, dense, or multi-layered biomolecular networks. While primarily designed for researchers utilizing biomolecular networks, iCAVE can assist researchers in any field. © The Authors 2017. Published by Oxford University Press.

  18. X-ray absorption spectroscopy of ultramarine pigments: A new analytical method for the polysulfide radical anion S3- chromophore

    International Nuclear Information System (INIS)

    Fleet, Michael E.; Liu, Xi

    2010-01-01

    Blue and mauve ultramarine artists' pigments and their heat-treated products have been investigated by sulfur K-edge X-ray absorption. X-ray absorption near-edge structure spectra are dominated by features of reduced sulfur and sulfate species. There is also a pre-peak at about 2468.0 eV which reflects the presence of the unpaired electron on the polysulfide radical anion (S 3 - ). Pre-peak intensity is directly proportional to the depth of blue coloration, and provides a new, independent method for estimating the proportion of ultramarine cage sites occupied by the blue chromophore. The occupancy of the polysulfide radical anion S 3 - is estimated to be 33% in an intense ultramarine blue pigment, 22% in a dark blue ultramarine pigment, and 1% in deep royal blue lazurite from Afghanistan. The more efficient development of color in lazurite is attributed to extensive annealing of the mineral structure in the natural environment.

  19. Recent Advances in Stimuli-Responsive Photofunctional Materials Based on Accommodation of Chromophore into Layered Double Hydroxide Nanogallery

    Directory of Open Access Journals (Sweden)

    Wu Li

    2013-01-01

    Full Text Available The assembly of photofunctional molecules into host matrices has become an important strategy to achieve tunable fluorescence and to develop intelligent materials. The stimuli-responsive photofunctional materials based on chromophores-assembled layered double hydroxides (LDHs have received much attention from both academic and industry fields as a result of their advantages, such as high photo/thermal stability, easy processing, and well reversibility, which can construct new types of smart luminescent nanomaterials (e.g., ultrathin film and nanocomposite for sensor and switch applications. In this paper, external environmental stimuli have mainly involved physical (such as temperature, pressure, light, and electricity and chemical factors (such as pH and metal ion; recent progress on the LDH-based organic-inorganic stimuli-responsive materials has been summarized. Moreover, perspectives on further development of these materials are also discussed.

  20. Action spectra and chromophores for lethal photosensitization of Candida albicans by DNA monoadducts formed by 8-methoxypsoralen and monofunctional furocoumarins

    International Nuclear Information System (INIS)

    Baydoun, S.; Gibbs, N.K.; Young, A.R.

    1992-01-01

    The red-shift furocoumarin action spectra, compared with their absorption spectra, has been investigated. An action spectrum for 8-methoxypsoralen (8-Mop) monoadduct formation in the yeast Candida albicans has been determined. The yeast cells were initially exposed to sublethal doses of monochromatic UV A at different wavelengths. Monoadduct formation was monitored by growth inhibition induced, after washing out any unbound 8-Mop, by re-irradiation with a constant second (non-lethal) dose of 330 nm radiation. A comparison between this action spectrum and the absorption spectrum of the dark complex of 8-Mop and DNA was made. In addition, the action spectra of monoadduct formation of five monofunctional compounds including a coumarin derivative have been determined. These action spectra were compared with their respective DNA dark complex absorption spectra. In general, the peaks of the furocoumarin DNA dark complexes show a red-shift when compared with the free furocoumarin molecule and the action spectra show peaks which correspond with the peaks of the dark complexes. Such data indicate that the DNA dark complex is the chromophore for growth inhibition in yeast rather than the free furocoumarin. The similarity of the 8-Mop monoadduct formation spectrum and 8-Mop action spectra suggests that spectral dependence for the photobiological effects (including the red-shift) is dependent on monoadduct formation rather than, as previously suggested by several authors, crosslink formation. The action spectrum for the coumarin derivative 4-methyl N-ethylpyrrolo (3,2-g) coumarin (PCNEt) correlated well with the free molecule absorption spectrum rather than DNA dark complex indicating that the free molecule is the chromophore. This was supported by studies which showed that PCNEt photosensitization is oxygen dependent. (author). 38 refs., 3 tabs., 7 figs

  1. Cyclometalated N-heterocyclic carbene iridium(iii) complexes with naphthalimide chromophores: a novel class of phosphorescent heteroleptic compounds.

    Science.gov (United States)

    Lanoë, Pierre-Henri; Chan, Jonny; Groué, Antoine; Gontard, Geoffrey; Jutand, Anny; Rager, Marie-Noelle; Armaroli, Nicola; Monti, Filippo; Barbieri, Andrea; Amouri, Hani

    2018-03-06

    A series of cyclometalated N-heterocyclic carbene complexes of the general formula [Ir(C^N) 2 (C^C:)] has been prepared. Two sets of compounds were designed, those where (C^C:) represents a bidentate naphthalimide-substituted imidazolylidene ligand and (C^N) = ppy (3a), F2ppy (4a), bzq (5a) and those where (C^C:) represents a naphthalimide-substituted benzimidazolylidene ligand and (C^N) = ppy (3b), F2ppy (4b), bzq (5b). The naphthalimide-imidazole and naphthalimide-benzimidazole ligands 1a,b and the related imidazolium and benzimidazolium salts 2a,b were also prepared and fully characterized. The N-heterocyclic carbene Ir(iii) complexes have been characterized by NMR spectroscopy, cyclic voltammetry and elemental analysis. Moreover, the molecular structures of one imidazolium salt and four Ir(iii) complexes were determined by single-crystal X-ray diffraction. The structures provide us with valuable information, most notably the orientation of the naphthalimide chromophore with respect to the N-heterocyclic carbene moiety. All compounds are luminescent at room temperature and in a frozen solvent at 77 K, exhibiting a broad emission band that extends beyond 700 nm. The presence of the naphthalimide moiety changes the character of the lowest excited state from 3 MLCT to 3 LC, as corroborated by DFT and TD-DFT calculations. Remarkably, replacing imidazole with a benzimidazole unit improves the quantum yields of these compounds by decreasing the k nr values which is an important feature for optimized emission performance. These studies provide valuable insights about a novel class of N-heterocyclic carbene-based luminescent complexes containing organic chromophores and affording metal complexes emitting across the red-NIR range.

  2. Image analysis of skin color heterogeneity focusing on skin chromophores and the age-related changes in facial skin.

    Science.gov (United States)

    Kikuchi, Kumiko; Masuda, Yuji; Yamashita, Toyonobu; Kawai, Eriko; Hirao, Tetsuji

    2015-05-01

    Heterogeneity with respect to skin color tone is one of the key factors in visual perception of facial attractiveness and age. However, there have been few studies on quantitative analyses of the color heterogeneity of facial skin. The purpose of this study was to develop image evaluation methods for skin color heterogeneity focusing on skin chromophores and then characterize ethnic differences and age-related changes. A facial imaging system equipped with an illumination unit and a high-resolution digital camera was used to develop image evaluation methods for skin color heterogeneity. First, melanin and/or hemoglobin images were obtained using pigment-specific image-processing techniques, which involved conversion from Commission Internationale de l'Eclairage XYZ color values to melanin and/or hemoglobin indexes as measures of their contents. Second, a spatial frequency analysis with threshold settings was applied to the individual images. Cheek skin images of 194 healthy Asian and Caucasian female subjects were acquired using the imaging system. Applying this methodology, the skin color heterogeneity of Asian and Caucasian faces was characterized. The proposed pigment-specific image-processing techniques allowed visual discrimination of skin redness from skin pigmentation. In the heterogeneity analyses of cheek skin color, age-related changes in melanin were clearly detected in Asian and Caucasian skin. Furthermore, it was found that the heterogeneity indexes of hemoglobin were significantly higher in Caucasian skin than in Asian skin. We have developed evaluation methods for skin color heterogeneity by image analyses based on the major chromophores, melanin and hemoglobin, with special reference to their size. This methodology focusing on skin color heterogeneity should be useful for better understanding of aging and ethnic differences. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Proceedings of the 2nd international advisory committee on biomolecular dynamics instrument DNA in MLF at J-PARC

    International Nuclear Information System (INIS)

    Arai, Masatoshi; Aizawa, Kazuya; Nakajima, Kenji; Shibata, Kaoru; Takahashi, Nobuaki

    2009-07-01

    The 2nd International Advisory Committee on the 'Biomolecular Dynamics Backscattering Spectrometer DNA' was held on November 12th - 13th, 2008 at J-PARC Center, Japan Atomic Energy Agency. This IAC has been organized for aiming to realize an innovative neutron backscattering instrument in the Materials and Life Science Experimental Facility (MLF) at the J-PARC and therefore four leading scientists in the field of neutron backscattering instruments has been selected as the member (Dr. Dan Neumann (Chair); Prof. Ferenc Mezei; Dr. Hannu Mutka; Dr. Philip Tregenna-Piggott), and the 1st IAC had been held on February 27th - 29th, 2008. This report includes the executive summary and materials of the presentations in the 2nd IAC. (author)

  4. A model system for targeted drug release triggered by biomolecular signals logically processed through enzyme logic networks.

    Science.gov (United States)

    Mailloux, Shay; Halámek, Jan; Katz, Evgeny

    2014-03-07

    A new Sense-and-Act system was realized by the integration of a biocomputing system, performing analytical processes, with a signal-responsive electrode. A drug-mimicking release process was triggered by biomolecular signals processed by different logic networks, including three concatenated AND logic gates or a 3-input OR logic gate. Biocatalytically produced NADH, controlled by various combinations of input signals, was used to activate the electrochemical system. A biocatalytic electrode associated with signal-processing "biocomputing" systems was electrically connected to another electrode coated with a polymer film, which was dissolved upon the formation of negative potential releasing entrapped drug-mimicking species, an enzyme-antibody conjugate, operating as a model for targeted immune-delivery and consequent "prodrug" activation. The system offers great versatility for future applications in controlled drug release and personalized medicine.

  5. Uma abordagem visual para análise comparativa de redes biomoleculares com apoio de diagramas de Venn

    OpenAIRE

    Henry Heberle

    2014-01-01

    Sistemas biológicos podem ser representados por redes que armazenam não apenas informações de conectividade, mas também informações de características de seus nós. No contexto biomolecular, esses nós podem representar proteínas, metabólitos, entre outros tipos de moléculas. Cada molécula possui características anotadas e armazenadas em bases de dados como o Gene Ontology. A comparação visual dessas redes depende de ferramentas que permitam o usuário identificar diferenças e semelhanças entre ...

  6. Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems.

    Science.gov (United States)

    Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa

    2015-04-14

    We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.

  7. Single-Cell Biomolecular Analysis of Coral Algal Symbionts Reveals Opposing Metabolic Responses to Heat Stress and Expulsion

    Directory of Open Access Journals (Sweden)

    Katherina Petrou

    2018-03-01

    Full Text Available The success of corals in nutrient poor environments is largely attributed to the symbiosis between the cnidarian host and its intracellular alga. Warm water anomalies have been shown to destabilize this symbiosis, yet detailed analysis of the effect of temperature and expulsion on cell-specific carbon and nutrient allocation in the symbiont is limited. Here, we exposed colonies of the hard coral Acropora millepora to heat stress and using synchrotron-based infrared microspectroscopy measured the biomolecular profiles of individual in hospite and expelled symbiont cells at an acute state of bleaching. Our results showed symbiont metabolic profiles to be remarkably distinct with heat stress and expulsion, where the two effectors elicited opposing metabolic adjustments independent of treatment or cell type. Elevated temperature resulted in biomolecular changes reflecting cellular stress, with relative increases in free amino acids and phosphorylation of molecules and a concomitant decline in protein content, suggesting protein modification and degradation. This contrasted with the metabolic profiles of expelled symbionts, which showed relative decreases in free amino acids and phosphorylated molecules, but increases in proteins and lipids, suggesting expulsion lessens the overall effect of heat stress on the metabolic signature of the algal symbionts. Interestingly, the combined effects of expulsion and thermal stress were additive, reducing the overall shifts in all biomolecules, with the notable exception of the significant accumulation of lipids and saturated fatty acids. This first use of a single-cell metabolomics approach on the coral symbiosis provides novel insight into coral bleaching and emphasizes the importance of a single-cell approach to demark the cell-to-cell variability in the physiology of coral cellular populations.

  8. A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data.

    Science.gov (United States)

    Cho, Kwang-Hyun; Choo, Sang-Mok; Wellstead, Peter; Wolkenhauer, Olaf

    2005-08-15

    We propose a unified framework for the identification of functional interaction structures of biomolecular networks in a way that leads to a new experimental design procedure. In developing our approach, we have built upon previous work. Thus we begin by pointing out some of the restrictions associated with existing structure identification methods and point out how these restrictions may be eased. In particular, existing methods use specific forms of experimental algebraic equations with which to identify the functional interaction structure of a biomolecular network. In our work, we employ an extended form of these experimental algebraic equations which, while retaining their merits, also overcome some of their disadvantages. Experimental data are required in order to estimate the coefficients of the experimental algebraic equation set associated with the structure identification task. However, experimentalists are rarely provided with guidance on which parameters to perturb, and to what extent, to perturb them. When a model of network dynamics is required then there is also the vexed question of sample rate and sample time selection to be resolved. Supplying some answers to these questions is the main motivation of this paper. The approach is based on stationary and/or temporal data obtained from parameter perturbations, and unifies the previous approaches of Kholodenko et al. (PNAS 99 (2002) 12841-12846) and Sontag et al. (Bioinformatics 20 (2004) 1877-1886). By way of demonstration, we apply our unified approach to a network model which cannot be properly identified by existing methods. Finally, we propose an experiment design methodology, which is not limited by the amount of parameter perturbations, and illustrate its use with an in numero example.

  9. Zwitterionic Silane Copolymer for Ultra-Stable and Bright Biomolecular Probes Based on Fluorescent Quantum Dot Nanoclusters.

    Science.gov (United States)

    Dembele, Fatimata; Tasso, Mariana; Trapiella-Alfonso, Laura; Xu, Xiangzhen; Hanafi, Mohamed; Lequeux, Nicolas; Pons, Thomas

    2017-05-31

    Fluorescent semiconductor quantum dots (QDs) exhibit several unique properties that make them suitable candidates for biomolecular sensing, including high brightness, photostability, broad excitation, and narrow emission spectra. Assembling these QDs into robust and functionalizable nanosized clusters (QD-NSCs) can provide fluorescent probes that are several orders of magnitude brighter than individual QDs, thus allowing an even greater sensitivity of detection with simplified instrumentation. However, the formation of compact, antifouling, functionalizable, and stable QD-NSCs remains a challenging task, especially for a use at ultralow concentrations for single-molecule detection. Here, we describe the development of fluorescent QD-NSCs envisioned as a tool for fast and sensitive biomolecular recognition. First, QDs were assembled into very compact 100-150 nm diameter spherical aggregates; the final QD-NSCs were obtained by growing a cross-linked silica shell around these aggregates. Hydrolytic stability in several concentration and pH conditions is a key requirement for a potential and efficient single-molecule detection tool. However, the hydrolysis of Si-O-Si bonds leads to desorption of monosilane-based surface groups at very low silica concentrations or in a slightly basic medium. Thus, we designed a novel multidentate copolymer composed of multiple silane as well as zwitterionic monomers. Coating silica beads with this multidentate copolymer provided a robust surface chemistry that was demonstrated to be stable against hydrolysis, even at low concentrations. Copolymer-coated silica beads also showed low fouling properties and high colloidal stability in saline solutions. Furthermore, incorporation of additional azido-monomers enabled easy functionalization of QD-NSCs using copper-free bio-orthogonal cyclooctyne-azide click chemistry, as demonstrated by a biotin-streptavidin affinity test.

  10. A Successful Attempt to Obtain the Linear Dependence Between One-Photon and Two-Photon Spectral Properties and Hammett Parameters of Various Aromatic Substituents in New π-Extended Asymmetric Organic Chromophores.

    Science.gov (United States)

    Hu, Nvdan; Gong, Yulong; Wang, Xinchao; Lu, Yao; Peng, Guangyue; Yang, Long; Zhang, Shengtao; Luo, Ziping; Li, Hongru; Gao, Fang

    2015-11-01

    A series of new asymmetric chromophores containing aromatic substituents and possessing the excellent π-extension in space were prepared through multi-steps routes. One-photon and two-photon spectral properties of these new chromophores could be tuned by these substituents finely and simultaneously. The linear correlation of the wave numbers of the one-photon absorption and emission maxima to Hammett parameters of these substituents was presented. Near infrared two-photon absorption emission integrated areas of the target chromophores were correlated linearly to Hammett constants of these substituted groups.

  11. Rhenium complexes of chromophore-appended dipicolylamine ligands: syntheses, spectroscopic properties, DNA binding and X-ray crystal structure

    International Nuclear Information System (INIS)

    Mullice, L.A.; Buurma, N.J.; Pope, S.J.A.; Laye, R.H.; Harding, L.P.

    2008-01-01

    The syntheses of two chromophore-appended dipicolylamine-derived ligands and their reactivity with penta-carbonyl-chloro-rhenium have been studied. The resultant complexes each possess the fac-Re(CO) 3 core. The ligands L 1 1-[bis(pyridine-2-yl-methyl)amino]methyl-pyrene and L 2 2-[bis(pyridine-2-yl-methyl)amino]methyl-quinoxaline were isolated via a one-pot reductive amination in moderate yield. The corresponding rhenium complexes were isolated in good yields and characterised by 1 H NMR, MS, IR and UV-Vis studies. X-Ray crystallographic data were obtained for fac-{Re(CO) 3 (L 1 )}(BF 4 ), C 34 H 26 BF 4 N 4 O 3 Re: monoclinic, P2(1)/c, a 18.327(2) Angstroms, α = 90.00 degrees, b 14.1537(14) Angstroms, β96.263(6) degrees, c = 23.511(3) Angstroms, γ 90.00 Angstroms, 6062.4(11) (Angstroms) 3 , Z=8. The luminescence properties of the ligands and complexes were also investigated, with the emission attributed to the appended chromophore in each case. Isothermal titration calorimetry suggests that fac-{Re(CO) 3 (L 1 )}(BF 4 ) self-aggregates cooperatively in aqueous solution, probably forming micelle-like aggregates with a cmc of 0.18 mM. Investigations into the DNA-binding properties of fac-{Re(CO) 3 (L 1 )}(BF 4 ) were undertaken and revealed that fac-{Re(CO) 3 (L 1 )}(BF 4 ) binding to fish sperm DNA (binding constant 1.5 ± 0.2 * 10 5 M -1 , binding site size 3.2 ± 0.3 base pairs) is accompanied by changes in the UV-Vis spectrum as typically observed for pyrene-based intercalators while the calorimetrically determined binding enthalpy (-14 ± 2 kcal mol -1 ) also agrees favourably with values as typically found for intercalators. (authors)

  12. Linking Seasonal Variations in the Spectral Slope of Chromophoric Dissolved Organic Matter (CDOM) with Apparent Oxygen Utilization and Excess Nitrogen (DINxs) in the North Atlantic Subtropical Gyre

    Science.gov (United States)

    McDonald, N.; Barnes, R.; Nelson, N. B.

    2016-02-01

    The optically active or chromophoric fraction of dissolved organic matter (CDOM) is a topic of much interest to researchers due to its role in many biogeochemical processes in the global oceans. As CDOM effectively regulates the underwater light field, its influences on photosynthesis and primary productivity are significant. Despite recognition of its importance in biogeochemical cycles in natural waters, its chemical composition remains nebulous, due to photochemical processes, as well as spatial and temporal variations in composition. Understanding of CDOM composition and links to ocean processes is especially complex in pelagic, oligotrophic waters such as the North Atlantic Subtropical Gyre. In this region, minimum CDOM concentrations have been observed and it is decoupled from both dissolved organic carbon (DOC) and from net primary production (NPP). As CDOM absorbance has been shown to influence estimates of NPP from remote sensing models in the subtropical gyres, and as it has the potential to serve as an invaluable tracer of ocean DOM cycling, a better understanding of links between the optical properties of CDOM and biogeochemical processes in the subtropical gyres is crucial. In this study, monthly depth profiles of CDOM absorbance (between 1m and 3000m) were measured for a period of five years at the Bermuda Atlantic Timeseries Site (BATS) in the North Atlantic Subtropical Gyre to investigate seasonal variations and periodicity in CDOM optical properties. From this data, the spectral slope ratio (Sr) was calculated according to Helms et. al, 2008. Sr can be a useful tool in eliciting information about molecular weight, diagenetic state and microbial processes affecting CDOM composition, especially when coupled with other diagnostic parameters. In this study multivariate analysis techniques were utilized to examine links between Sr and ancillary parameters including apparent oxygen utilization (AOU) and excess nitrogen (DINxs) both of which can be a

  13. Combinatorial solid-phase glycopeptide libraries - Synthesis and application in biomolecular interaction studies and biosensors

    NARCIS (Netherlands)

    Maljaars, C.E.P.

    2006-01-01

    Carbohydrates play vital roles in all forms of life. Attached to proteins and lipids they serve as recognition elements in several biological interaction processes, such as intercellular communication, immune response, viral and parasitical infections, signal transduction, and development. Synthetic

  14. The Potential Applications of Real-Time Monitoring of Water Quality in a Large Shallow Lake (Lake Taihu, China) Using a Chromophoric Dissolved Organic Matter Fluorescence Sensor

    OpenAIRE

    Niu, Cheng; Zhang, Yunlin; Zhou, Yongqiang; Shi, Kun; Liu, Xiaohan; Qin, Boqiang

    2014-01-01

    This study presents results from field surveys performed over various seasons in a large, eutrophic, shallow lake (Lake Taihu, China) using an in situ chromophoric dissolved organic matter (CDOM) fluorescence sensor as a surrogate for other water quality parameters. These measurements identified highly significant empirical relationships between CDOM concentration measured using the in situ fluorescence sensor and CDOM absorption, fluorescence, dissolved organic carbon (DOC), chemical oxygen ...

  15. Effective photo-enhancement of cellular activity of fluorophore-octaarginine antisense PNA conjugates correlates with singlet oxygen formation, endosomal escape and chromophore lipophilicity

    DEFF Research Database (Denmark)

    Yarani, Reza; Shiraishi, Takehiko; Nielsen, Peter E.

    2018-01-01

    Photochemical internalization (PCI) is a cellular drug delivery method based on the generation of light-induced reactive oxygen species (ROS) causing damage to the endosomal membrane and thereby resulting in drug release to the cytoplasm. In our study a series of antisense fluorophore octaarginin...... indicate that efficient photodynamic endosomal escape is strongly dependent on the quantum yield for photochemical singlet oxygen formation, photostability as well as the lipophilicity of the chromophore....

  16. Fluorescence and absorption properties of chromophoric dissolved organic matter (CDOM) in coastal surface waters of the Northwestern Mediterranean Sea (Bay of Marseilles, France)

    OpenAIRE

    J. Para; P. G. Coble; B. Charrière; M. Tedetti; C. Fontana; R. Sempéré

    2010-01-01

    Seawater samples were collected in surface waters (2 and 5 m depths) of the Bay of Marseilles (Northwestern Mediterranean Sea; 5°17′30′′ E, 43°14′30′′ N) during one year from November 2007 to December 2008 and studied for total organic carbon (TOC) as well as chromophoric dissolved organic matter (CDOM) optical properties (absorbance and fluorescence). The annual mean value of surface CDOM absorption coefficient ...

  17. Spectroscopic analysis of the role of extractives on heat-induced discoloration of black locust (Robinia pseudoacacia)

    Science.gov (United States)

    Yao Chen; Yongming Fan; Jianmin Gao; Mandla A. Tshabalala; Nicole M. Stark

    2012-01-01

    To investigate the role of extractives on heat-induced discoloration of wood, samples of black locust (Robinia pseudoacacia) wood flour were extracted with various solvents prior to heat-treatment. Analysis of their color parameters and chromophoric structures showed that the chroma value of the unextracted sample decreased while that of the...

  18. Chromophoric dissolved organic matter and microbial enzymatic activity. A biophysical approach to understand the marine carbon cycle.

    Science.gov (United States)

    Gonnelli, Margherita; Vestri, Stefano; Santinelli, Chiara

    2013-12-01

    This study reports the first information on extracellular enzymatic activity (EEA) combined with a study of DOM dynamics at the Arno River mouth. DOM dynamics was investigated from both a quantitative (dissolved organic carbon, DOC) and a qualitative (absorption and fluorescence of chromophoric DOM, CDOM) perspective. The data here reported highlight that the Arno River was an important source of both DOC and CDOM for this coastal area. CDOM optical properties suggested that terrestrial DOM did not undergo simple dilution at the river mouth but, other physical-chemical and biological processes were probably at work to change its molecular characteristics. This observation was further supported by the "potential" enzymatic activity of β-glucosidase (BG) and leucine aminopeptidase (LAP). Their Vmax values were markedly higher in the river water than in the seawater and their ratio suggested that most of the DOM used by microbes in the Arno River was polysaccharide-like, while in the seawater it was mainly protein-like. © 2013. Published by Elsevier B.V. All rights reserved.

  19. Influence of environmental factors on spectral characteristic of chromophoric dissolved organic matter (CDOM) in Inner Mongolia Plateau, China

    Science.gov (United States)

    Wen, Z. D.; Song, K. S.; Zhao, Y.; Du, J.; Ma, J. H.

    2015-06-01

    Spectral characteristics of chromophoric dissolved organic matter (CDOM) were examined in conjunction with environmental factors in the waters of 22 rivers and 26 terminal waters in Hulun Buir plateau, northeast China. Dissolved organic carbon (DOC), total nitrogen (TN), and total phosphorous (TP) were significantly higher in terminal waters than rivers waters (p CDOM absorption in river waters was significantly lower than terminal waters (p CDOM in river waters had higher aromaticity, molecular weight, and vascular plant contribution than in terminal waters. Furthermore, results showed that DOC concentration, CDOM light absorption, and the proportion of autochthonous sources of CDOM in plateau waters were all higher than in other freshwater rivers reported in the literature. The strong evapoconcentration, intense ultraviolet irradiance and landscape features of Hulun Buir plateau may be responsible for the above phenomenon. Redundancy analysis (RDA) indicated that the environmental variables TSM, TN, and EC had a strong correlation with light absorption characteristics, followed by TDS and chlorophyll a. In most sampling locations, CDOM was the dominant non-water light-absorbing substance. Light absorption by non-algal particles often exceeded that by phytoplankton in the plateau waters. Study of these optical-physicochemical correlations is helpful in the evaluation of the potential influence of water quality factors on non-water light absorption in cold plateau water environments. And the study on organic carbon in plateau lakes had a vital contribution to global carbon balance estimation.

  20. Alteration of chromophoric dissolved organic matter by solar UV radiation causes rapid changes in bacterial community composition†

    Science.gov (United States)

    Piccini, Claudia; Conde, Daniel; Pernthaler, Jakob; Sommaruga, Ruben

    2010-01-01

    We evaluated the effect of photochemical alterations of chromophoric dissolved organic matter (CDOM) on bacterial abundance, activity and community composition in a coastal lagoon of the Atlantic Ocean with high dissolved organic carbon concentration. On two occasions during the austral summer, bacteria-free water of the lagoon was exposed to different regions of the solar spectrum (full solar radiation, UV-A + PAR, PAR) or kept in the dark. Subsequently, dilution cultures were established with bacterioplankton from the lagoon that were incubated in the pre-exposed water for 5 h in the dark. Cell abundance, activity, and community composition of bacterioplankton were assessed before and after incubation in the different treatments. Changes in absorption, fluorescence, and DOC concentration were used as proxies for CDOM photoalteration. We found a significant CDOM photobleaching signal, DOC loss, as well as a stimulation of bacterial activity in the treatments pre-exposed to UV radiation, suggesting increased bioavailability of DOM. Bacterial community analysis by fluorescence in situ hybridization revealed that this stimulation was mainly accompanied by the specific enrichment of Alpha- and Betaproteobacteria. Thus, our results suggest that CDOM photoalteration not only stimulates bacterioplankton growth, but also induces rapid changes in bacterioplankton composition, which can be of relevance for ecosystem functioning, particularly considering present and future changes in the input of terrestrial CDOM to aquatic systems. PMID:19707620

  1. Alteration of chromophoric dissolved organic matter by solar UV radiation causes rapid changes in bacterial community composition.

    Science.gov (United States)

    Piccini, Claudia; Conde, Daniel; Pernthaler, Jakob; Sommaruga, Ruben

    2009-09-01

    We evaluated the effect of photochemical alterations of chromophoric dissolved organic matter (CDOM) on bacterial abundance, activity and community composition in a coastal lagoon of the Atlantic Ocean with high dissolved organic carbon concentration. On two occasions during the austral summer, bacteria-free water of the lagoon was exposed to different regions of the solar spectrum (full solar radiation, UV-A+PAR, PAR) or kept in the dark. Subsequently, dilution cultures were established with bacterioplankton from the lagoon that were incubated in the pre-exposed water for 5 h in the dark. Cell abundance, activity, and community composition of bacterioplankton were assessed before and after incubation in the different treatments. Changes in absorption, fluorescence, and DOC concentration were used as proxies for CDOM photoalteration. We found a significant CDOM photobleaching signal, DOC loss, as well as a stimulation of bacterial activity in the treatments pre-exposed to UV radiation, suggesting increased bioavailability of DOM. Bacterial community analysis by fluorescence in situ hybridization revealed that this stimulation was mainly accompanied by the specific enrichment of Alpha- and Betaproteobacteria. Thus, our results suggest that CDOM photoalteration not only stimulates bacterioplankton growth, but also induces rapid changes in bacterioplankton composition, which can be of relevance for ecosystem functioning, particularly considering present and future changes in the input of terrestrial CDOM to aquatic systems.

  2. Molecular characterization of brown carbon (BrC) chromophores in secondary organic aerosol generated from photo-oxidation of toluene.

    Science.gov (United States)

    Lin, Peng; Liu, Jiumeng; Shilling, John E; Kathmann, Shawn M; Laskin, Julia; Laskin, Alexander

    2015-09-28

    Atmospheric brown carbon (BrC) is a significant contributor to light absorption and climate forcing. However, little is known about a fundamental relationship between the chemical composition of BrC and its optical properties. In this work, light-absorbing secondary organic aerosol (SOA) was generated in the PNNL chamber from toluene photo-oxidation in the presence of NOx (Tol-SOA). Molecular structures of BrC components were examined using nanospray desorption electrospray ionization (nano-DESI) and liquid chromatography (LC) combined with UV/Vis spectroscopy and electrospray ionization (ESI) high-resolution mass spectrometry (HRMS). The chemical composition of BrC chromophores and the light absorption properties of toluene SOA (Tol-SOA) depend strongly on the initial NOx concentration. Specifically, Tol-SOA generated under high-NOx conditions (defined here as initial NOx/toluene of 5/1) appears yellow and mass absorption coefficient of the bulk sample (MACbulk@365 nm = 0.78 m(2) g(-1)) is nearly 80 fold higher than that measured for the Tol-SOA sample generated under low-NOx conditions (NOx/toluene atmosphere.

  3. Light-harvesting dendrimer zinc-phthalocyanines chromophores labeled single-wall carbon nanotube nanoensembles: Synthesis and photoinduced electron transfer

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Hongqin [Key Laboratory of Optoelectronic Science and Technology for Medicine, Ministry of Education and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350007 (China); Pan, Sujuan; Ma, Dongdong; He, Dandan; Wang, Yuhua [College of Chemistry & Engineering, Fujian Provincial Key Laboratory of Polymer Materials, Fujian Normal University, Fuzhou 350007 (China); Xie, Shusen [Key Laboratory of Optoelectronic Science and Technology for Medicine, Ministry of Education and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350007 (China); Peng, Yiru, E-mail: yirupeng@fjnu.edu.cn [College of Chemistry & Engineering, Fujian Provincial Key Laboratory of Polymer Materials, Fujian Normal University, Fuzhou 350007 (China)

    2016-11-15

    A novel series of light-harvesting dendrimer zinc-phthalocyanines chromophores labeled-single-wall carbon nanotubes (SWNTs) nanoparticles, in which 0–2 generations dendrimer zinc phthalocyanines covalently linked with SWNTs using either ethylenediamine or hexamethylenediamine as the space linkers were prepared. The structures and morphologies of these nanoconjugates were comprehensively characterized by Raman spectroscopy, transmission electron microscopy and thermal gravimetric analysis methods. Their photophysical properties were investigated by fluorescence and time-resolved spectroscopic methods. The photoinduced intramolecular electron transfer occurred from phthalocyanines (donors) to SWNTs (acceptors). Besides, the electron transfer exchange rates and exchange efficacies between the dendritic phthalocyanines and single-wall carbon nanotubes increased as the length of spacer linker decreased, or as the dendritic generation increased. Cyclic voltammetry (CV) method further confirmed thermodynamics possibility of the electron transfer from phthalocyanines to single-wall carbon nanotubes. These new nanoconjugates are fundamentally important due to the synergy effects of both carbon nanotubes and dendrimer phthalocyanines, which may find potential applications in the fields of drug delivery, biological labeling, or others.

  4. Design and synthesis of bipyridine platinum(II) bisalkynyl fullerene donor-chromophore-acceptor triads with ultrafast charge separation.

    Science.gov (United States)

    Lee, Sai-Ho; Chan, Chris Tsz-Leung; Wong, Keith Man-Chung; Lam, Wai Han; Kwok, Wai-Ming; Yam, Vivian Wing-Wah

    2014-07-16

    Donor-chromophore-acceptor triads, (PTZ)2-Pt(bpy)-C60 and ((t)BuPTZ)2-Pt(bpy)-C60, along with their model compound, (Ph)2-Pt(bpy)-C60, have been synthesized and characterized; their photophysical and electrochemical properties have been studied, and the origin of the absorption and emission properties has been supported by computational studies. The photoinduced electron transfer reactions have been investigated using the femtosecond and nanosecond transient absorption spectroscopy. In dichloromethane, (Ph)2-Pt(bpy)-C60 shows ultrafast triplet-triplet energy transfer from the (3)MLCT/LLCT excited state within 4 ps to give the (3)C60* state, while in (PTZ)2-Pt(bpy)-C60 and ((t)BuPTZ)2-Pt(bpy)-C60, charge-separated state forms within 400 fs from the (3)MLCT/LLCT excited state with efficiency of over 0.90, and the total efficiency with the contribution of (3)C60* is estimated to be 0.99. Although the forward electron transfer reactions are very rapid, the charge-separated state recombines to the singlet ground state at a time of hundreds of nanoseconds because of the difference in spin multiplicity between the charge-separated state and the ground state.

  5. Spatial and seasonal changes in optical properties of autochthonous and allochthonous chromophoric dissolved organic matter in a stratified mountain lake.

    Science.gov (United States)

    Bracchini, Luca; Dattilo, Arduino Massimo; Hull, Vincent; Loiselle, Steven Arthur; Nannicini, Luciano; Picchi, Maria Pia; Ricci, Maso; Santinelli, Chiara; Seritti, Alfredo; Tognazzi, Antonio; Rossi, Claudio

    2010-03-01

    In this study, we present results on seasonal and spatial changes in CDOM absorption and fluorescence (fCDOM) in a deep mountain lake (Salto Lake, Italy). A novel approach was used to describe the shape of CDOM absorption between 250-700 nm (distribution of the spectral slope, S(lambda)) and a new fluorescence ratio is used to distinguish between humic and amino acid-like components. Solar ultraviolet irradiance, dissolved organic carbon (DOC), DOM fluorescence and absorption measurements were analysed and compared to other physicochemical parameters. We show that in the UV-exposed mixed layer: (i) fluorescence by autochthonous amino acid-like CDOM, (ii) values of S(lambda) across UV-C and UV-B wavebands increased during the summer months, whereas (i) average molar absorption coefficient and (ii) fluorescence by allochthonous humic CDOM decreased. In the unexposed deep layer of the water column (and in the entire water column in winter), humic-like CDOM presented high values of molar absorption coefficients and low values of S(lambda). UV attenuation coefficients correlated with both chlorophyll a concentrations and CDOM absorption. In agreement with changes in CDOM, minimal values in UV attenuation were found in summer. The S(lambda) curve was used as a signature of the mixture between photobleached and algal-derived CDOM with respect to the unexposed chromophoric dissolved compounds in this thermal stratified lake. Furthermore, S(lambda) curves were useful to distinguish between low and high molecular weight CDOM.

  6. Selective elimination of chromophoric and fluorescent dissolved organic matter in a full-scale municipal wastewater treatment plant.

    Science.gov (United States)

    Yang, Xiaofang; Zhou, Zhongbo; Raju, Maddela Naga; Cai, Xiaoxuan; Meng, Fangang

    2017-07-01

    Effluent organic matter (EfOM) from municipal wastewater treatment plants potentially has a detrimental effect on both aquatic organisms and humans. This study evaluated the removal and transformation of chromophoric dissolved organic matter (CDOM) and fluorescent dissolved organic matter (FDOM) in a full-scale wastewater treatment plant under different seasons. The results showed that bio-treatment was found to be more efficient in removing bulk DOM (in term of dissolved organic carbon, DOC) than CDOM and FDOM, which was contrary to the disinfection process. CDOM and FDOM were selectively removed at various stages during the treatment. Typically, the low molecular weight fractions of CDOM and protein-like FDOM were more efficiently removed during bio-treatment process, whereas the humic-like FDOM exhibited comparable decreases in both bio-treatment and disinfection processes. Overall, the performance of the WWTP was weak in terms of CDOM and FDOM removal, resulting in enrichment of CDOM and FDOM in effluent. Moreover, the total removal of the bulk DOM (PCDOM and the humic-like FDOM showed little differences between summer and winter. In all, the results provide useful information for understanding the fate and transformation of DOM, illustrating that sub-fractions of DOM could be selectively removed depending on treatment processes and seasonality. Copyright © 2016. Published by Elsevier B.V.

  7. [Near ultraviolet absorption spectral properties of chromophoric dissolved organic matter in the north area of Yellow Sea].

    Science.gov (United States)

    Wang, Lin; Zhao, Dong-Zhi; Yang, Jian-Hong; Chen, Yan-Long

    2010-12-01

    Chromophoric dissolved organic matter (CDOM) near ultraviolet absorption spectra contains CDOM molecular structure, composition and other important physical and chemical information. Based on the measured data of CDOM absorption coefficient in March 2009 in the north area of Yellow Sea, the present paper analyzed near ultraviolet absorption spectral properties of CDOM. The results showed that due to the impact of near-shore terrigenous input, the composition of CDOM is quite different in the north area of Yellow Sea, and this area is a typical case II water; fitted slope with specific range of spectral band and absorption coefficient at specific band can indicate the relative size of CDOM molecular weight, correlation between spectral slope of the Sg,275-300), Sg,300-350, Sg,350-400 and Sg,250-275 and the relative size of CDOM molecular weight indicative parameter M increases in turn and the highest is up to 0.95. Correlation between a(g)(lambda) and M value increases gradually with the increase in wavelength, and the highest is up to 0.92 at 400 nm; being correlated or not between spectral slope and absorption coefficient is decided by the fitting-band wavelength range for the spectra slope and the wavelength for absorption coefficient. Correlation between Sg,275-300 and a(g)(400) is the largest, up to 0.87.

  8. Chromophoric dissolved organic matter of black waters in a highly eutrophic Chinese lake: Freshly produced from algal scums?

    Science.gov (United States)

    Zhou, Yongqiang; Jeppesen, Erik; Zhang, Yunlin; Niu, Cheng; Shi, Kun; Liu, Xiaohan; Zhu, Guangwei; Qin, Boqiang

    2015-12-15

    Field campaigns and an incubation experiment were conducted to evaluate the sources of chromophoric dissolved organic matter (CDOM) in black water spots in highly polluted regions of the Chinese Lake Taihu. A significant positive correlation (pCDOM absorption coefficient a(350), indicating that algae degradation was likely the primary source of CDOM in black waters. This is supported by our field results that Chl-a, a(350) and the spectral slope ratio (SR) were significantly higher in the black water samples than in the regular samples (pCDOM source where a(350) increased with decreasing Chl-a concentrations. After seven days' incubation, a 72.2% decrease and a 74.9% increase were recorded for Chl-a and a(350), respectively, relative to the initial values. Parallel factor analysis identified five fluorescent components. The maximal fluorescence intensity (Fmax) of tryptophan-like C1 and microbial humic-like C3 of black water samples was significantly higher than in the regular water samples (pCDOM source in black water spots. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Characterization of chromophoric dissolved organic matter and relationships among PARAFAC components and water quality parameters in Heilongjiang, China.

    Science.gov (United States)

    Cui, Hongyang; Shi, Jianhong; Qiu, Linlin; Zhao, Yue; Wei, Zimin; Wang, Xinglei; Jia, Liming; Li, Jiming

    2016-05-01

    Chromophoric dissolved organic matter (CDOM) is an important optically active substance that can transports nutrients and pollutants from terrestrial to aquatic systems. Additionally, it is used as a measure of water quality. To investigate the source and composition of CDOM, we used chemical and fluorescent analyses to characterize CDOM in Heilongjiang. The composition of CDOM can be investigated by excitation-emission matrix (EEM) fluorescence and parallel factor analysis (PARAFAC). PARAFAC identified four individual components that were attributed to microbial humic-like (C1) and terrestrial humic-like (C2-4) in water samples collected from the Heilongjiang River. The relationships between the maximum fluorescence intensities of the four PARAFAC components and the water quality parameters indicate that the dynamic of the four components is related to nutrients in the Heilongjiang River. The relationships between the fluorescence component C3 and the biochemical oxygen demand (BOD5) indicates that component C3 makes a great contribution to BOD5 and it can be used as a carbon source for microbes in the Heilongjiang River. Furthermore, the relationships between component C3, the particulate organic carbon (POC), and the chemical oxygen demand (CODMn) show that component C3 and POC make great contributions to BOD5 and CODMn. The use of these indexes along with PARAFAC results would be of help to characterize the co-variation between the CDOM and water quality parameters in the Heilongjiang River.

  10. The relationship of chromophoric dissolved organic matter parallel factor analysis fluorescence and polycyclic aromatic hydrocarbons in natural surface waters.

    Science.gov (United States)

    Li, Sijia; Chen, Ya'nan; Zhang, Jiquan; Song, Kaishan; Mu, Guangyi; Sun, Caiyun; Ju, Hanyu; Ji, Meichen

    2018-01-01

    Polycyclic aromatic hydrocarbons (PAHs), a large group of persistent organic pollutants (POPs), have caused wide environmental pollution and ecological effects. Chromophoric dissolved organic matter (CDOM), which consists of complex compounds, was seen as a proxy of water quality. An attempt was made to understand the relationships of CDOM absorption parameters and parallel factor analysis (PARAFAC) components with PAHs under seasonal variation in the riverine, reservoir, and urban waters of the Yinma River watershed in 2016. These different types of water bodies provided wide CDOM and PAHs concentration ranges with CDOM absorption coefficients at a wavelength of 350 nm (a CDOM (350)) of 1.17-20.74 m -1 and total PAHs of 0-1829 ng/L. CDOM excitation-emission matrix (EEM) presented two fluorescent components, e.g., terrestrial humic-like (C1) and tryptophan-like (C2) were identified using PARAFAC. Tryptophan-like associated protein-like fluorescence often dominates the EEM signatures of sewage samples. Our finding is that seasonal CDOM EEM-PARAFAC and PAHs concentration showed consistent tendency indicated that PAHs were un-ignorable pollutants. However, the disparities in seasonal CDOM-PAH relationships relate to the similar sources of CDOM and PAHs, and the proportion of PAHs in CDOM. Overlooked and poorly appreciated, quantifying the relationship between CDOM and PAHs has important implications, because these results simplify ecological and health-based risk assessment of pollutants compared to the traditional chemical measurements.

  11. Absorption properties of chromophoric dissolved organic matter (CDOM) in the East China Sea and the waters off eastern Taiwan

    Science.gov (United States)

    Zhou, Fengxia; Gao, Xuelu; Song, Jinming; Chen, Chen-Tung Arthur; Yuan, Huamao; Xing, Qianguo

    2018-05-01

    The absorption properties of chromophoric dissolved organic matter (CDOM) in the East China Sea (ECS) and the waters off eastern Taiwan (WET) were studied during May 2014. CDOM absorption coefficient (a280) and spectral slope (S275-295) revealed considerable spatial variations. In the ECS, the values of a280 and S275-295 presented a reverse distribution pattern. In the WET, a280 values were generally low while S275-295 values were generally high. Vertical distributions of a280 and S275-295 also varied in different regions. Terrestrial input, phytoplankton production, sediment release or photobleaching may be responsible for the dynamics of CDOM. Relationships among CDOM related parameters could partly support this conclusion. a280 were also used to trace different water masses and the result showed that the influence of Changjiang Diluted Water could reach the outer shelf of the northern ECS, and that the Kuroshio Current had a strong influence on the middle shelf of the southern ECS.

  12. Dynamics and ecological risk assessment of chromophoric dissolved organic matter in the Yinma River Watershed: Rivers, reservoirs, and urban waters.

    Science.gov (United States)

    Li, Sijia; Zhang, Jiquan; Guo, Enliang; Zhang, Feng; Ma, Qiyun; Mu, Guangyi

    2017-10-01

    The extensive use of a geographic information system (GIS) and remote sensing in ecological risk assessment from a spatiotemporal perspective complements ecological environment management. Chromophoric dissolved organic matter (CDOM), which is a complex mixture of organic matter that can be estimated via remote sensing, carries and produces carcinogenic disinfection by-products and organic pollutants in various aquatic environments. This paper reports the first ecological risk assessment, which was conducted in 2016, of CDOM in the Yinma River watershed including riverine waters, reservoir waters, and urban waters. Referring to the risk formation theory of natural disaster, the entropy evaluation method and DPSIR (driving force-pressure-state-impact-response) framework were coupled to establish a hazard and vulnerability index with multisource data, i.e., meteorological, remote sensing, experimental, and socioeconomic data, of this watershed. This ecological vulnerability assessment indicator system contains 23 indicators with respect to ecological sensitivity, ecological pressure, and self-resilience. The characteristics of CDOM absorption parameters from different waters showed higher aromatic content and molecular weights in May because of increased terrestrial inputs. The assessment results indicated that the overall ecosystem risk in the study area was focused in the extremely, heavily, and moderately vulnerable regions. The ecological risk assessment results objectively reflect the regional ecological environment and demonstrate the potential of ecological risk assessment of pollutants over traditional chemical measurements. Copyright © 2017. Published by Elsevier Inc.

  13. Seasonal dynamics of light absorption by chromophoric dissolved organic matter (CDOM) in the NW Mediterranean Sea (BOUSSOLE site)

    Science.gov (United States)

    Organelli, Emanuele; Bricaud, Annick; Antoine, David; Matsuoka, Atsushi

    2014-09-01

    We analyze a two-year time-series of chromophoric dissolved organic matter (CDOM) light absorption measurements in the upper 400 m of the water column at the BOUSSOLE site in the NW Mediterranean Sea. The seasonal dynamics of the CDOM light absorption coefficients at 440 nm (acdom(440)) is essentially characterized by (i) subsurface maxima forming in spring and progressively reinforcing throughout summer, (ii) impoverishment in the surface layer throughout summer and (iii) vertical homogeneity in winter. Seasonal variations of the spectral dependence of CDOM absorption, as described by the exponential slope value (Scdom), are characterized by highest values in summer and autumn at the surface and low values at the depths of acdom(440) subsurface maxima or just below them. Variations of acdom(440) are likely controlled by microbial digestion of phytoplankton cells, which leads to CDOM production, and by photochemical destruction (photobleaching), which leads to CDOM degradation. Photobleaching is also the main driver of Scdom variations. Consistently with previous observations, acdom(440) for a given chlorophyll a concentration is higher than expected from Case I waters bio-optical models. The total non-water light absorption budget shows that surface waters at the BOUSSOLE site are largely dominated by CDOM during all seasons but the algal bloom in March and April. These results improve the knowledge of CDOM absorption dynamics in the Mediterranean Sea, which is scarcely documented. In addition, they open the way to improved algorithms for the retrieval of CDOM absorption from field or satellite radiometric measurements.

  14. Insight into the effects of modifying chromophores on the performance of quinoline-based dye-sensitized solar cells

    Science.gov (United States)

    Mao, Mao; Wang, Jian-Bo; Liu, Xiu-Lin; Wu, Guo-Hua; Fang, Xia-Qin; Song, Qin-Hua

    2018-02-01

    A series of organic dyes based on quinoline as an electron-deficient π-linker, were designed and synthesized for dye sensitized solar cells (DSSC) application. These push-pull conjugated dyes, sharing same anchoring group with distinctive electron-rich donating groups such as N,N-diethyl (DEA-Q), 3,6-dimethoxy carbazole (CBZ-Q), bis(4-butoxyphenyl)amine (BPA-Q), were synthesized by Riley oxidation of sbnd CH3 followed by Knoevenagel condensation of the corresponding aldehyde precursors 2a-c with cyanoacrylic acid. The optical, electrochemical, theoretical calculation and photovoltaic properties with these three dyes were systematically investigated. Compared to DEA-Q and CBZ-Q, BPA-Q possesses better light harvesting properties with regard to extended conjugate length, red-shifted intramolecular charge transfer band absorption and broaden light-responsive IPCE spectrum, resulting in a greater short circuit photocurrent density output. BPA-Q also has improved open-circuit voltage due to the apparent large charge recombination resistance. Consequently, assembled with iodine redox electrolytes, the device with BPA-Q achieved the best overall conversion efficiency value of 3.07% among three dyes under AM 1.5G standard conditions. This present investigation demonstrates the importance of various N-substituent chromophores in the prevalent D-π-A type organic sensitizers for tuning the photovoltaic performance of their DSSCs.

  15. Thirty years of European biotechnology programmes: from biomolecular engineering to the bioeconomy.

    Science.gov (United States)

    Aguilar, Alfredo; Magnien, Etienne; Thomas, Daniel

    2013-06-25

    This article traces back thirty years of biotechnology research sponsored by the European Union (EU). It outlines the crucial role played by De Nettancourt, Goffeau and Van Hoeck to promote and prepare the first European programme on biotechnology (1982-1986) run by the European Commission. Following this first biotechnology programme, others followed until the current one, part of the seventh Framework Programme for Research, Technological Development and Demonstration (2007-2013) (FP7). Particular attention is given to the statutory role of the European institutions in the design and orientation of the successive biotechnology programmes, compared to the more informal-yet visionary-role of key individuals upstream to any legislative decision. Examples of success stories and of the role of the biotechnology programmes in addressing societal issues and industrial competitiveness are also presented. Finally, an outline of Horizon 2020, the successor of FP7, is described, together with the role of biotechnology in building the bioeconomy. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Photo-initiated dynamics and spectroscopy of the deprotonated Green Fluorescent Protein chromophore

    DEFF Research Database (Denmark)

    Bochenkova, Anastasia; Andersen, Lars Henrik

    2013-01-01

    . Knowledge of intrinsic properties of the GFP photoabsorbing molecular unit is a prerequisite in understanding the atomic-scale interactions that play a key role for the diverse functioning of these proteins. Here, we show how recent developments in action and photoelectron spectroscopy combined with state...... efficiently compete with each other in spite of their inherently different intrinsic timescales. The reason behind this is an efficient coupling between the nuclear and electronic motion in the photo-initiated dynamics, where the energy may be transferred from nuclei to electrons and from electrons to nuclei...

  17. FY 2000 report on the results of the R and D of the fusion domain. Volume 3. Biomolecular mechanism and design; 2000 nendo yugo ryoiki kenkyu kaihatsu. 3. Biomolecular mechanism and design

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-03-01

    For the purpose of creating cells/tissue assemblies and the molecular machine that substitute for self-organizing and self-repairing functions of a living body outside the body, the basic technology research was conducted, and the FY 2000 results were reported. In the study of 3D cell and tissue module engineering, the following were conducted: study of the surface modification and functional expression of biomaterials, study of the mechanical stress to cartilaginous cells and the response, development of the production method of biodegradable synthetic polymer porous materials, study of organism hard tissue materials/bone remodeling and cultured bone transportation, development of zinc-releasing calcium phosphate ceramics. In the study of biomolecular mechanism and design, 1D unidirectional movement of microtubules by applying microlithography technology, structural study of kinesin-family molecular motor by low temperature microscope, ribozyme and the application to leukemia, basic study on assessment of chemical substances by human cultured cells, study of a low molecule detection system using nucleic acid and peptide. (NEDO)

  18. Hydrogen exchange mass spectrometry of bacteriorhodopsin reveals light-induced changes in the structural dynamics of a biomolecular machine.

    Science.gov (United States)

    Pan, Yan; Brown, Leonid; Konermann, Lars

    2011-12-21

    Many proteins act as molecular machines that are fuelled by a nonthermal energy source. Examples include transmembrane pumps and stator-rotor complexes. These systems undergo cyclic motions (CMs) that are being driven along a well-defined conformational trajectory. Superimposed on these CMs are thermal fluctuations (TFs) that are coupled to stochastic motions of the solvent. Here we explore whether the TFs of a molecular machine are affected by the occurrence of CMs. Bacteriorhodopsin (BR) is a light-driven proton pump that serves as a model system in this study. The function of BR is based on a photocycle that involves trans/cis isomerization of a retinal chromophore, as well as motions of transmembrane helices. Hydrogen/deuterium exchange (HDX) mass spectrometry was used to monitor the TFs of BR, focusing on the monomeric form of the protein. Comparative HDX studies were conducted under illumination and in the dark. The HDX kinetics of BR are dramatically accelerated in the presence of light. The isotope exchange rates and the number of backbone amides involved in EX2 opening transitions increase roughly 2-fold upon illumination. In contrast, light/dark control experiments on retinal-free protein produced no discernible differences. It can be concluded that the extent of TFs in BR strongly depends on photon-driven CMs. The light-induced differences in HDX behavior are ascribed to protein destabilization. Specifically, the thermodynamic stability of the dark-adapted protein is estimated to be 5.5 kJ mol(-1) under the conditions of our work. This value represents the free energy difference between the folded state F and a significantly unfolded conformer U. Illumination reduces the stability of F by 2.2 kJ mol(-1). Mechanical agitation caused by isomerization of the chromophore is transferred to the surrounding protein scaffold, and subsequently, the energy dissipates into the solvent. Light-induced retinal motions therefore act analogously to an internal heat

  19. AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems.

    Science.gov (United States)

    LeVine, Michael V; Weinstein, Harel

    2015-05-01

    In performing their biological functions, molecular machines must process and transmit information with high fidelity. Information transmission requires dynamic coupling between the conformations of discrete structural components within the protein positioned far from one another on the molecular scale. This type of biomolecular "action at a distance" is termed allostery . Although allostery is ubiquitous in biological regulation and signal transduction, its treatment in theoretical models has mostly eschewed quantitative descriptions involving the system's underlying structural components and their interactions. Here, we show how Ising models can be used to formulate an approach to allostery in a structural context of interactions between the constitutive components by building simple allosteric constructs we termed Allosteric Ising Models (AIMs). We introduce the use of AIMs in analytical and numerical calculations that relate thermodynamic descriptions of allostery to the structural context, and then show that many fundamental properties of allostery, such as the multiplicative property of parallel allosteric channels, are revealed from the analysis of such models. The power of exploring mechanistic structural models of allosteric function in more complex systems by using AIMs is demonstrated by building a model of allosteric signaling for an experimentally well-characterized asymmetric homodimer of the dopamine D2 receptor.

  20. SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation.

    Science.gov (United States)

    Xie, Yang; Ying, Jinyong; Xie, Dexuan

    2017-03-30

    SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  1. Environmental Light and Its Relationship with Electromagnetic Resonances of Biomolecular Interactions, as Predicted by the Resonant Recognition Model

    Directory of Open Access Journals (Sweden)

    Irena Cosic

    2016-06-01

    Full Text Available The meaning and influence of light to biomolecular interactions, and consequently to health, has been analyzed using the Resonant Recognition Model (RRM. The RRM proposes that biological processes/interactions are based on electromagnetic resonances between interacting biomolecules at specific electromagnetic frequencies within the infra-red, visible and ultra-violet frequency ranges, where each interaction can be identified by the certain frequency critical for resonant activation of specific biological activities of proteins and DNA. We found that: (1 the various biological interactions could be grouped according to their resonant frequency into super families of these functions, enabling simpler analyses of these interactions and consequently analyses of influence of electromagnetic frequencies to health; (2 the RRM spectrum of all analyzed biological functions/interactions is the same as the spectrum of the sun light on the Earth, which is in accordance with fact that life is sustained by the sun light; (3 the water is transparent to RRM frequencies, enabling proteins and DNA to interact without loss of energy; (4 the spectrum of some artificial sources of light, as opposed to the sun light, do not cover the whole RRM spectrum, causing concerns for disturbance to some biological functions and consequently we speculate that it can influence health.

  2. Biomolecular bases of the senescence process and cancer. A new approach to oncological treatment linked to ageing.

    Science.gov (United States)

    Badiola, Iker; Santaolalla, Francisco; Garcia-Gallastegui, Patricia; Ana, Sánchez-Del Rey; Unda, Fernando; Ibarretxe, Gaskon

    2015-09-01

    Human ageing is associated with a gradual decline in the physiological functions of the body at multiple levels and it is a key risk factor for many diseases, including cancer. Ageing process is intimately related to widespread cellular senescence, characterised by an irreversible loss of proliferative capacity and altered functioning associated with telomere attrition, accumulation of DNA damage and compromised mitochondrial and metabolic function. Tumour and senescent cells may be generated in response to the same stimuli, where either cellular senescence or transformation would constitute two opposite outcomes of the same degenerative process. This paper aims to review the state of knowledge on the biomolecular relationship between cellular senescence, ageing and cancer. Importantly, many of the cell signalling pathways that are found to be altered during both cellular senescence and tumourigenesis are regulated through shared epigenetic mechanisms and, therefore, they are potentially reversible. MicroRNAs are emerging as pivotal players linking ageing and cancer. These small RNA molecules have generated great interest from the point of view of future clinical therapy for cancer because successful experimental results have been obtained in animal models. Micro-RNA therapies for cancer are already being tested in clinical phase trials. These findings have potential importance in cancer treatment in aged people although further research-based knowledge is needed to convert them into an effective molecular therapies for cancer linked to ageing. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

    Science.gov (United States)

    2017-01-01

    Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the geometric and biological complexity. To address this problem we introduce the element-specific persistent homology (ESPH) method. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains important biological information via a multichannel image-like representation. This representation reveals hidden structure-function relationships in biomolecules. We further integrate ESPH and deep convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability changes upon mutation. To overcome the deep learning limitations from small and noisy training sets, we propose a multi-task multichannel topological convolutional neural network (MM-TCNN). We demonstrate that TopologyNet outperforms the latest methods in the prediction of protein-ligand binding affinities, mutation induced globular protein folding free energy changes, and mutation induced membrane protein folding free energy changes. Availability: weilab.math.msu.edu/TDL/ PMID:28749969

  4. Protein-Ligand Informatics Force Field (PLIff): Toward a Fully Knowledge Driven "Force Field" for Biomolecular Interactions.

    Science.gov (United States)

    Verdonk, Marcel L; Ludlow, R Frederick; Giangreco, Ilenia; Rathi, Prakash Chandra

    2016-07-28

    The Protein Data Bank (PDB) contains a wealth of data on nonbonded biomolecular interactions. If this information could be distilled down to nonbonded interaction potentials, these would have some key advantages over standard force fields. However, there are some important outstanding issues to address in order to do this successfully. This paper introduces the protein-ligand informatics "force field", PLIff, which begins to address these key challenges ( https://bitbucket.org/AstexUK/pli ). As a result of their knowledge-based nature, the next-generation nonbonded potentials that make up PLIff automatically capture a wide range of interaction types, including special interactions that are often poorly described by standard force fields. We illustrate how PLIff may be used in structure-based design applications, including interaction fields, fragment mapping, and protein-ligand docking. PLIff performs at least as well as state-of-the art scoring functions in terms of pose predictions and ranking compounds in a virtual screening context.

  5. Single-molecule pull-down (SiMPull) for new-age biochemistry: methodology and biochemical applications of single-molecule pull-down (SiMPull) for probing biomolecular interactions in crude cell extracts.

    Science.gov (United States)

    Aggarwal, Vasudha; Ha, Taekjip

    2014-11-01

    Macromolecular interactions play a central role in many biological processes. Protein-protein interactions have mostly been studied by co-immunoprecipitation, which cannot provide quantitative information on all possible molecular connections present in the complex. We will review a new approach that allows cellular proteins and biomolecular complexes to be studied in real-time at the single-molecule level. This technique is called single-molecule pull-down (SiMPull), because it integrates principles of conventional immunoprecipitation with the powerful single-molecule fluorescence microscopy. SiMPull is used to count how many of each protein is present in the physiological complexes found in cytosol and membranes. Concurrently, it serves as a single-molecule biochemical tool to perform functional studies on the pulled-down proteins. In this review, we will focus on the detailed methodology of SiMPull, its salient features and a wide range of biological applications in comparison with other biosensing tools. © 2014 WILEY Periodicals, Inc.

  6. Brightening and locking a weak and floppy N-H chromophore: the case of pyrrolidine.

    Science.gov (United States)

    Hesse, Susanne; Wassermann, Tobias N; Suhm, Martin A

    2010-10-07

    The N-H stretching signature of the puckering equilibrium between equatorial and axial pyrrolidine is analyzed via FTIR and Raman spectroscopy in supersonic jets as a function of aggregation. Vibrational temperatures along the expansion axis can be extracted from the Raman spectra and allow for a localization of the compression shock waves. While the equatorial conformation is more stable in the ground state monomer, this preference is probably switched in the excited state with one N-H stretching quantum. Furthermore, the dominant dimer involves an axial donor and the trimer and tetramer structures seem to prefer uniform axial conformations. The IR intensity is boosted by up to 3 orders of magnitude upon aggregation, whereas the Raman scattering intensity shows only moderate hydrogen bond effects. B3LYP and MP2 calculations provide a reasonable description of the N-H vibrational dynamics under the influence of self-aggregation. In mixed dimers with pyrrole, pyrrolidine assumes the role of a hydrogen bond acceptor.

  7. Spatio-seasonal variability of chromophoric dissolved organic matter absorption and responses to photobleaching in a large shallow temperate lake

    Science.gov (United States)

    Encina Aulló-Maestro, María; Hunter, Peter; Spyrakos, Evangelos; Mercatoris, Pierre; Kovács, Attila; Horváth, Hajnalka; Preston, Tom; Présing, Mátyás; Torres Palenzuela, Jesús; Tyler, Andrew

    2017-03-01

    The development and validation of remote-sensing-based approaches for the retrieval of chromophoric dissolved organic matter (CDOM) concentrations requires a comprehensive understanding of the sources and magnitude of variability in the optical properties of dissolved material within lakes. In this study, spatial and seasonal variability in concentration and composition of CDOM and the origin of its variation was studied in Lake Balaton (Hungary), a large temperate shallow lake in central Europe. In addition, we investigated the effect of photobleaching on the optical properties of CDOM through in-lake incubation experiments. There was marked variability throughout the year in CDOM absorption in Lake Balaton (aCDOM(440) = 0. 06-9.01 m-1). The highest values were consistently observed at the mouth of the main inflow (Zala River), which drains humic-rich material from the adjoining Kis-Balaton wetland, but CDOM absorption decreased rapidly towards the east where it was consistently lower and less variable than in the westernmost lake basins. The spectral slope parameter for the interval of 350-500 nm (SCDOM(350-500)) was more variable with increasing distance from the inflow (observed range 0.0161-0.0181 nm-1 for the mouth of the main inflow and 0.0158-0.0300 nm-1 for waters closer to the outflow). However, spatial variation in SCDOM was more constant exhibiting a negative correlation with aCDOM(440). Dissolved organic carbon (DOC) was strongly positively correlated with aCDOM(440) and followed a similar seasonal trend but it demonstrated more variability than either aCDOM or SCDOM with distance through the system. Photobleaching resulting from a 7-day exposure to natural solar UV radiation resulted in a marked decrease in allochthonous CDOM absorption (7.04 to 3.36 m-1, 42 % decrease). Photodegradation also resulted in an increase in the spectral slope coefficient of dissolved material.

  8. Influence of environmental factors on spectral characteristics of chromophoric dissolved organic matter (CDOM) in Inner Mongolia Plateau, China

    Science.gov (United States)

    Wen, Z. D.; Song, K. S.; Zhao, Y.; Du, J.; Ma, J. H.

    2016-02-01

    Spectral characteristics of chromophoric dissolved organic matter (CDOM) were examined in conjunction with environmental factors in the waters of rivers and terminal lakes within the Hulun Buir plateau, northeast China. Dissolved organic carbon (DOC), total nitrogen (TN), and total phosphorous (TP) were significantly higher in terminal lakes than rivers waters (p CDOM absorption in river waters was significantly lower than terminal lakes. Analysis of the ratio of absorption at 250 to 365 nm (E250 : 365), specific ultraviolet (UV) absorbance (SUVA254), and the spectral slope ratio (Sr) indicated that CDOM in river waters had higher aromaticity, molecular weight, and vascular plant contribution than in terminal lakes. Furthermore, results showed that DOC concentration, CDOM light absorption, and the proportion of autochthonous sources of CDOM in plateau waters were all higher than in other freshwater rivers reported in the literature. The strong evapoconcentration, intense ultraviolet irradiance, and landscape features of the Hulun Buir plateau may be responsible for the above phenomenon. Redundancy analysis (RDA) indicated that the environmental variables total suspended matter (TSM), TN, and electrical conductivity (EC) had a strong correlation with light absorption characteristics, followed by total dissolved solid (TDS) and chlorophyll a. In most sampling locations, CDOM was the dominant non-water light-absorbing substance. Light absorption by non-algal particles often exceeded that by phytoplankton in the plateau waters. Study of these optical-physicochemical correlations is helpful in the evaluation of the potential influence of water quality factors on non-water light absorption in cold plateau water environments. The construction of a correlation between DOC concentration and water quality factors may help contribute to regional estimates of carbon sources and fate for catchment carbon budget assessments.

  9. Characterization of light absorption by chromophoric dissolved organic matter (CDOM) in the upper layer of the Red Sea

    Science.gov (United States)

    Kheireddine, Malika; Ouhssain, Mustapha; Calleja, Maria Ll.; Morán, Xosé Anxelu G.; Sarma, Y. V. B.; Tiwari, Surya P.; Jones, Burton H.

    2018-03-01

    The absorption coefficient of chromophoric dissolved organic matter (CDOM) is a major variable used in developing robust bio-optical models and understanding biogeochemical processes. Over the last decade, the optical properties of CDOM in the open sea have been intensely studied. However, their variations in clear water are poorly documented, particularly in the Red Sea, owing to the absence of in situ measurements. We performed several cruises in the Red Sea to investigate the spatial distribution of the absorption coefficient of CDOM. The spectral absorption coefficients were determined from 400 nm to 740 nm using a WETLabs ac-s hyper-spectral spectrophotometer. In general, we found a latitudinal gradient in the CDOM absorption coefficient at 443 nm (aCDOM(443)) from south to north that is likely influenced by the exchange of water through the strait of Bab-el-Mandeb and the thermohaline circulation of the Red Sea. However, high aCDOM(443) values were observed in the northern Red Sea due to the existence of a sub-mesoscale feature that may induce an increase in phytoplankton production and lead to CDOM production. The aCDOM(443) covaried with the chlorophyll a concentration ([Chl a],) despite a high scatter. Furthermore, the aCDOM(443) for a given [Chl a] concentration was higher than those predicted by global ocean bio-optical models. This study advances our understanding of CDOM concentration in the Red Sea and may help improve the accuracy of the algorithms used to obtain CDOM absorption from ocean color.

  10. Constructing polyatomic potential energy surfaces by interpolating diabatic Hamiltonian matrices with demonstration on green fluorescent protein chromophore

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jae Woo; Rhee, Young Min, E-mail: ymrhee@postech.ac.kr [Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 790-784 (Korea, Republic of); Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784 (Korea, Republic of)

    2014-04-28

    Simulating molecular dynamics directly on quantum chemically obtained potential energy surfaces is generally time consuming. The cost becomes overwhelming especially when excited state dynamics is aimed with multiple electronic states. The interpolated potential has been suggested as a remedy for the cost issue in various simulation settings ranging from fast gas phase reactions of small molecules to relatively slow condensed phase dynamics with complex surrounding. Here, we present a scheme for interpolating multiple electronic surfaces of a relatively large molecule, with an intention of applying it to studying nonadiabatic behaviors. The scheme starts with adiabatic potential information and its diabatic transformation, both of which can be readily obtained, in principle, with quantum chemical calculations. The adiabatic energies and their derivatives on each interpolation center are combined with the derivative coupling vectors to generate the corresponding diabatic Hamiltonian and its derivatives, and they are subsequently adopted in producing a globally defined diabatic Hamiltonian function. As a demonstration, we employ the scheme to build an interpolated Hamiltonian of a relatively large chromophore, para-hydroxybenzylidene imidazolinone, in reference to its all-atom analytical surface model. We show that the interpolation is indeed reliable enough to reproduce important features of the reference surface model, such as its adiabatic energies and derivative couplings. In addition, nonadiabatic surface hopping simulations with interpolation yield population transfer dynamics that is well in accord with the result generated with the reference analytic surface. With these, we conclude by suggesting that the interpolation of diabatic Hamiltonians will be applicable for studying nonadiabatic behaviors of sizeable molecules.

  11. Study of influencing factors to chromophoric dissolved organic matter absorption properties from fluorescence features in Taihu lake in autumn

    Directory of Open Access Journals (Sweden)

    Chuang-Chun Huang

    2013-04-01

    Full Text Available In order to identify the components of chromophoric dissolved organic matter (CDOM, confirm the influence of components to the absorption coefficient of CDOM (aCDOM, and estimate aCDOM from fluorescence spectra, fluorescence and optical measurements of CDOM were carried out in November 2008. The results indicate that, the primary component of CDOM is humic-like. The secondary component is tryptophan-like, which is the product of phytoplankton and aquatic debris rather than the wastewater treatment drainaged from city. In this study, six fluorophores with multiple excitation-emission matrices (EEMs peaks (A, B, C, N, M, T were identified according to the parallel factor analysis (PARAFAC. The average contribution of each component to the CDOM is 19.93, 18.82, 16.88, 16.39, 12.26, and 15.72%, respectively. Red Shifted phenomenon will happen with the increase of fluorescence intensity for ultraviolet and terrestrially humic-like. Conversely, marine humic-like will appear Reverse Red Shifted with the increase of fluorescence intensity. The primary contributor to the shoulder value of CDOM’s absorption coefficient at 275 nm is phytoplankton productivity, followed by marine humic-like. The main contributors to the shoulder shape are UV humic-like and phytoplankton productivity, followed by marine humic-like and tryptophan-like. A strong correlation between CDOM absorption and fluorescence intensity at emission wavelength of 424 nm and excitation wavelength ranging from 280 to 360 nm was found. The absorption coefficient can be retrieved successfully from the same excitation wavelength’s fluorescence intensity by an exponential model.

  12. Variations in Spectral Absorption Properties of Phytoplankton, Non-algal Particles and Chromophoric Dissolved Organic Matter in Lake Qiandaohu

    Directory of Open Access Journals (Sweden)

    Liangliang Shi

    2017-05-01

    Full Text Available Light absorption by phytoplankton, non-algal particles (NAP and chromophoric dissolved organic matter (CDOM was investigated at 90 sites of a clear, deep artificial lake (Lake Qiandaohu to study natural variability of absorption coefficients. Our study shows that CDOM absorption is a major contributor to the total absorption signal in Lake Qiandaohu during all seasons, except autumn when it has an equivalent contribution as total particle absorption. The exponential slope of CDOM absorption varies within a narrow range around a mean value of 0.0164 nm−1 ( s d = 0.00176 nm−1. Our study finds some evidence for thIS autochthonous production of CDOM in winter and spring. Absorption by phytoplankton, and therefore its contribution to total absorption, is generally greatest in spring, suggesting that phytoplankton growth in Lake Qiandaohu occurs predominantly in the spring. Phytoplankton absorption in freshwater lakes generally has a direct relationship with chlorophyll-a concentration, similar to the one established for open ocean waters. The NAP absorption, whose relative contribution to total absorption is highest in summer, has a spectral shape that can be well fitted by an exponential function with an average slope of 0.0065 nm−1 ( s d = 0.00076 nm−1. There is significant spatial variability present in the summer of Lake Qiandaohu, especially in the northwestern and southwestern extremes where the optical properties of the water column are strongly affected by the presence of allochthonous matter. Variations in the properties of the particle absorption spectra with depths provides evidence that the water column was vertically inhomogeneous and can be monitored with an optical measurement program. Moreover, the optical inhomogeneity in winter is less obvious. Our study will support the parameterization of the Bio-optical model for Lake Qiandaohu from in situ or remotely sensing aquatic color signals.

  13. Characterizing spatiotemporal variations of chromophoric dissolved organic matter in headwater catchment of a key drinking water source in China.

    Science.gov (United States)

    Chen, Yihan; Yu, Kaifeng; Zhou, Yongqiang; Ren, Longfei; Kirumba, George; Zhang, Bo; He, Yiliang

    2017-12-01

    Natural surface drinking water sources with the increasing chromophoric dissolved organic matter (CDOM) have profound influences on the aquatic environment and drinking water safety. Here, this study investigated the spatiotemporal variations of CDOM in Fengshuba Reservoir and its catchments in China. Twenty-four surface water samples, 45 water samples (including surface water, middle water, and bottom water), and 15 pore water samples were collected from rivers, reservoir, and sediment of the reservoir, respectively. Then, three fluorescent components, namely two humic-like components (C1 and C2) and a tryptophan-like component (C3), were identified from the excitation-emission matrix coupled with parallel factor analysis (EEM-PARAFAC) for all samples. For spatial distributions, the levels of CDOM and two humic-like components in the reservoir were significantly lower than those in the upstream rivers (p CDOM and humic-like matters from the surrounding catchment. For temporal variations, the mean levels of CDOM and three fluorescent components did not significantly change in rivers, suggesting that perennial anthropic activity maybe an important factor impacting the concentration and composition of river CDOM but not the precipitation and runoff. However, these mean values of CDOM for the bulk waters of the reservoir changed markedly along with seasonal variations, indicating that the hydrological processes in the reservoir could control the quality and quantity of CDOM. The different correlations between the fluorescent components and primary water parameters in the river, reservoir, and pore water samples further suggest that the reservoir is an important factor regulating the migration and transformation of FDOM along with the variations of different environmental gradients.

  14. Characterization of light absorption by chromophoric dissolved organic matter (CDOM) in the upper layer of the Red Sea

    KAUST Repository

    Kheireddine, Malika

    2018-02-07

    The absorption coefficient of chromophoric dissolved organic matter (CDOM) is a major variable used in developing robust bio‐optical models and understanding biogeochemical processes. Over the last decade, the optical properties of CDOM in the open sea have been intensely studied. However, their variations in clear water are poorly documented, particularly in the Red Sea, owing to the absence of in situ measurements. We performed several cruises in the Red Sea to investigate the spatial distribution of the absorption coefficient of CDOM. The spectral absorption coefficients were determined from 400nm to 740nm using a WETLabs ac-s hyper-spectral spectrophotometer. In general, we found a latitudinal gradient in the CDOM absorption coefficient at 443nm (aCDOM(443)) from south to north that is likely influenced by the exchange of water through the strait of Bab-el-Mandeb and the thermohaline circulation of the Red Sea. However, high aCDOM(443) values were observed in the northern Red Sea due to the existence of a sub-mesoscale feature that may induce an increase in phytoplankton production and lead to CDOM production. The aCDOM(443) covaried with the chlorophyll a concentration ([Chl a],) despite a high scatter. Furthermore, the aCDOM(443) for a given [Chl a] concentration was higher than those predicted by global ocean bio-optical models. This study advances our understanding of CDOM concentration in the Red Sea and may help improve the accuracy of the algorithms used to obtain CDOM absorption from ocean color.

  15. Imaging and chemical surface analysis of biomolecular functionalization of monolithically integrated on silicon Mach-Zehnder interferometric immunosensors

    International Nuclear Information System (INIS)

    Gajos, Katarzyna; Angelopoulou, Michailia; Petrou, Panagiota; Awsiuk, Kamil; Kakabakos, Sotirios; Haasnoot, Willem; Bernasik, Andrzej; Rysz, Jakub; Marzec, Mateusz M.; Misiakos, Konstantinos; Raptis, Ioannis; Budkowski, Andrzej

    2016-01-01

    Highlights: • Optimization of probe immobilization with robotic spotter printing overlapping spots. • In-situ inspection of microstructured surfaces of biosensors integrated on silicon. • Imaging and chemical analysis of immobilization, surface blocking and immunoreaction. • Insight with molecular discrimination into step-by-step sensor surface modifications. • Optimized biofunctionalization improves sensor sensitivity and response repeatability. - Abstract: Time-of-flight secondary ion mass spectrometry (imaging, micro-analysis) has been employed to evaluate biofunctionalization of the sensing arm areas of Mach-Zehnder interferometers monolithically integrated on silicon chips for the immunochemical (competitive) detection of bovine κ-casein in goat milk. Biosensor surfaces are examined after: modification with (3-aminopropyl)triethoxysilane, application of multiple overlapping spots of κ-casein solutions, blocking with 100-times diluted goat milk, and reaction with monoclonal mouse anti-κ-casein antibodies in blocking solution. The areas spotted with κ-casein solutions of different concentrations are examined and optimum concentration providing homogeneous coverage is determined. Coverage of biosensor surfaces with biomolecules after each of the sequential steps employed in immunodetection is also evaluated with TOF-SIMS, supplemented by Atomic force microscopy and X-ray photoelectron spectroscopy. Uniform molecular distributions are observed on the sensing arm areas after spotting with optimum κ-casein concentration, blocking and immunoreaction. The corresponding biomolecular compositions are determined with a Principal Component Analysis that distinguished between protein amino acids and milk glycerides, as well as between amino acids characteristic for Mabs and κ-casein, respectively. Use of the optimum conditions (κ-casein concentration) for functionalization of chips with arrays of ten Mach-Zehnder interferometers provided on-chips assays

  16. Imaging and chemical surface analysis of biomolecular functionalization of monolithically integrated on silicon Mach-Zehnder interferometric immunosensors

    Energy Technology Data Exchange (ETDEWEB)

    Gajos, Katarzyna, E-mail: kasia.fornal@uj.edu.pl [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Angelopoulou, Michailia; Petrou, Panagiota [Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Awsiuk, Kamil [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Kakabakos, Sotirios [Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Haasnoot, Willem [RIKILT Wageningen UR, Akkermaalsbos 2, 6708 WB Wageningen (Netherlands); Bernasik, Andrzej [Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Rysz, Jakub [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Marzec, Mateusz M. [Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Misiakos, Konstantinos; Raptis, Ioannis [Department of Microelectronics, Institute of Nanoscience and Nanotechnology, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Budkowski, Andrzej [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland)

    2016-11-01

    Highlights: • Optimization of probe immobilization with robotic spotter printing overlapping spots. • In-situ inspection of microstructured surfaces of biosensors integrated on silicon. • Imaging and chemical analysis of immobilization, surface blocking and immunoreaction. • Insight with molecular discrimination into step-by-step sensor surface modifications. • Optimized biofunctionalization improves sensor sensitivity and response repeatability. - Abstract: Time-of-flight secondary ion mass spectrometry (imaging, micro-analysis) has been employed to evaluate biofunctionalization of the sensing arm areas of Mach-Zehnder interferometers monolithically integrated on silicon chips for the immunochemical (competitive) detection of bovine κ-casein in goat milk. Biosensor surfaces are examined after: modification with (3-aminopropyl)triethoxysilane, application of multiple overlapping spots of κ-casein solutions, blocking with 100-times diluted goat milk, and reaction with monoclonal mouse anti-κ-casein antibodies in blocking solution. The areas spotted with κ-casein solutions of different concentrations are examined and optimum concentration providing homogeneous coverage is determined. Coverage of biosensor surfaces with biomolecules after each of the sequential steps employed in immunodetection is also evaluated with TOF-SIMS, supplemented by Atomic force microscopy and X-ray photoelectron spectroscopy. Uniform molecular distributions are observed on the sensing arm areas after spotting with optimum κ-casein concentration, blocking and immunoreaction. The corresponding biomolecular compositions are determined with a Principal Component Analysis that distinguished between protein amino acids and milk glycerides, as well as between amino acids characteristic for Mabs and κ-casein, respectively. Use of the optimum conditions (κ-casein concentration) for functionalization of chips with arrays of ten Mach-Zehnder interferometers provided on-chips assays

  17. ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach.

    Directory of Open Access Journals (Sweden)

    Yoshiyuki Ogata

    Full Text Available Ecosystems can be conceptually thought of as interconnected environmental and metabolic systems, in which small molecules to macro-molecules interact through diverse networks. State-of-the-art technologies in post-genomic science offer ways to inspect and analyze this biomolecular web using omics-based approaches. Exploring useful genes and enzymes, as well as biomass resources responsible for anabolism and catabolism within ecosystems will contribute to a better understanding of environmental functions and their application to biotechnology. Here we present ECOMICS, a suite of web-based tools for ECosystem trans-OMICS investigation that target metagenomic, metatranscriptomic, and meta-metabolomic systems, including biomacromolecular mixtures derived from biomass. ECOMICS is made of four integrated webtools. E-class allows for the sequence-based taxonomic classification of eukaryotic and prokaryotic ribosomal data and the functional classification of selected enzymes. FT2B allows for the digital processing of NMR spectra for downstream metabolic or chemical phenotyping. Bm-Char allows for statistical assignment of specific compounds found in lignocellulose-based biomass, and HetMap is a data matrix generator and correlation calculator that can be applied to trans-omics datasets as analyzed by these and other web tools. This web suite is unique in that it allows for the monitoring of biomass metabolism in a particular environment, i.e., from macromolecular complexes (FT2DB and Bm-Char to microbial composition and degradation (E-class, and makes possible the understanding of relationships between molecular and microbial elements (HetMap. This website is available to the public domain at: https://database.riken.jp/ecomics/.

  18. "Peak tracking chip" for label-free optical detection of bio-molecular interaction and bulk sensing.

    Science.gov (United States)

    Bougot-Robin, Kristelle; Li, Shunbo; Zhang, Yinghua; Hsing, I-Ming; Benisty, Henri; Wen, Weijia

    2012-10-21

    A novel imaging method for bulk refractive index sensing or label-free bio-molecular interaction sensing is presented. This method is based on specially designed "Peak tracking chip" (PTC) involving "tracks" of adjacent resonant waveguide gratings (RWG) "micropads" with slowly evolving resonance position. Using a simple camera the spatial information robustly retrieves the diffraction efficiency, which in turn transduces either the refractive index of the liquids on the tracks or the effective thickness of an immobilized biological layer. Our intrinsically multiplex chip combines tunability and versatility advantages of dielectric guided wave biochips without the need of costly hyperspectral instrumentation. The current success of surface plasmon imaging techniques suggests that our chip proposal could leverage an untapped potential to routinely extend such techniques in a convenient and sturdy optical configuration toward, for instance for large analytes detection. PTC design and fabrication are discussed with challenging process to control micropads properties by varying their period (step of 2 nm) or their duty cycle through the groove width (steps of 4 nm). Through monochromatic imaging of our PTC, we present experimental demonstration of bulk index sensing on the range [1.33-1.47] and of surface biomolecule detection of molecular weight 30 kDa in aqueous solution using different surface densities. A sensitivity of the order of 10(-5) RIU for bulk detection and a sensitivity of the order of ∼10 pg mm(-2) for label-free surface detection are expected, therefore opening a large range of application of our chip based imaging technique. Exploiting and chip design, we expect as well our chip to open new direction for multispectral studies through imaging.

  19. Mapping the Excited State Potential Energy Surface of a Retinal Chromophore Model with Multireference and Equation-of-Motion Coupled-Cluster Methods.

    Science.gov (United States)

    Gozem, Samer; Melaccio, Federico; Lindh, Roland; Krylov, Anna I; Granovsky, Alexander A; Angeli, Celestino; Olivucci, Massimo

    2013-10-08

    The photoisomerization of the retinal chromophore of visual pigments proceeds along a complex reaction coordinate on a multidimensional surface that comprises a hydrogen-out-of-plane (HOOP) coordinate, a bond length alternation (BLA) coordinate, a single bond torsion and, finally, the reactive double bond torsion. These degrees of freedom are coupled with changes in the electronic structure of the chromophore and, therefore, the computational investigation of the photochemistry of such systems requires the use of a methodology capable of describing electronic structure changes along all those coordinates. Here, we employ the penta-2,4-dieniminium (PSB3) cation as a minimal model of the retinal chromophore of visual pigments and compare its excited state isomerization paths at the CASSCF and CASPT2 levels of theory. These paths connect the cis isomer and the trans isomer of PSB3 with two structurally and energetically distinct conical intersections (CIs) that belong to the same intersection space. MRCISD+Q energy profiles along these paths provide benchmark values against which other ab initio methods are validated. Accordingly, we compare the energy profiles of MRPT2 methods (CASPT2, QD-NEVPT2, and XMCQDPT2) and EOM-SF-CC methods (EOM-SF-CCSD and EOM-SF-CCSD(dT)) to the MRCISD+Q reference profiles. We find that the paths produced with CASSCF and CASPT2 are topologically and energetically different, partially due to the existence of a "locally excited" region on the CASPT2 excited state near the Franck-Condon point that is absent in CASSCF and that involves a single bond, rather than double bond, torsion. We also find that MRPT2 methods as well as EOM-SF-CCSD(dT) are capable of quantitatively describing the processes involved in the photoisomerization of systems like PSB3.

  20. Fluorescence and absorption properties of chromophoric dissolved organic matter (CDOM) in coastal surface waters of the northwestern Mediterranean Sea, influence of the Rhône River

    OpenAIRE

    J. Para; P. G. Coble; B. Charrière; M. Tedetti; C. Fontana; R. Sempéré

    2010-01-01

    Seawater samples were collected monthly in surface waters (2 and 5 m depths) of the Bay of Marseilles (northwestern Mediterranean Sea; 5°17'30" E, 43°14'30" N) during one year from November 2007 to December 2008 and studied for total organic carbon (TOC) as well as chromophoric dissolved organic matter (CDOM) optical properties (absorbance and fluorescence). The annual mean value of surface CDOM absorption coefficient at 350 nm [aCDOM(350)] was very l...

  1. Quantitative spatially resolved measurement of tissue chromophore concentrations using photoacoustic spectroscopy: application to the measurement of blood oxygenation and haemoglobin concentration

    Science.gov (United States)

    Laufer, Jan; Delpy, Dave; Elwell, Clare; Beard, Paul

    2007-01-01

    A new approach based on pulsed photoacoustic spectroscopy for non-invasively quantifying tissue chromophore concentrations with high spatial resolution has been developed. The technique is applicable to the quantification of tissue chromophores such as oxyhaemoglobin (HbO2) and deoxyhaemoglobin (HHb) for the measurement of physiological parameters such as blood oxygen saturation (SO2) and total haemoglobin concentration. It can also be used to quantify the local accumulation of targeted contrast agents used in photoacoustic molecular imaging. The technique employs a model-based inversion scheme to recover the chromophore concentrations from photoacoustic measurements. This comprises a numerical forward model of the detected time-dependent photoacoustic signal that incorporates a multiwavelength diffusion-based finite element light propagation model to describe the light transport and a time-domain acoustic model to describe the generation, propagation and detection of the photoacoustic wave. The forward model is then inverted by iteratively fitting it to measurements of photoacoustic signals acquired at different wavelengths to recover the chromophore concentrations. To validate this approach, photoacoustic signals were generated in a tissue phantom using nanosecond laser pulses between 740 nm and 1040 nm. The tissue phantom comprised a suspension of intralipid, blood and a near-infrared dye in which three tubes were immersed. Blood at physiological haemoglobin concentrations and oxygen saturation levels ranging from 2% to 100% was circulated through the tubes. The signal amplitude from different temporal sections of the detected photoacoustic waveforms was plotted as a function of wavelength and the forward model fitted to these data to recover the concentrations of HbO2 and HHb, total haemoglobin concentration and SO2. The performance was found to compare favourably to that of a laboratory CO-oximeter with measurement resolutions of ±3.8 g l-1 (±58 µM) and ±4

  2. Quantitative spatially resolved measurement of tissue chromophore concentrations using photoacoustic spectroscopy: application to the measurement of blood oxygenation and haemoglobin concentration

    Energy Technology Data Exchange (ETDEWEB)

    Laufer, Jan; Delpy, Dave; Elwell, Clare; Beard, Paul [Department of Medical Physics and Bioengineering, University College London, Malet Place Engineering Building, London WC1E 6BT (United Kingdom)

    2007-01-07

    A new approach based on pulsed photoacoustic spectroscopy for non-invasively quantifying tissue chromophore concentrations with high spatial resolution has been developed. The technique is applicable to the quantification of tissue chromophores such as oxyhaemoglobin (HbO{sub 2}) and deoxyhaemoglobin (HHb) for the measurement of physiological parameters such as blood oxygen saturation (SO{sub 2}) and total haemoglobin concentration. It can also be used to quantify the local accumulation of targeted contrast agents used in photoacoustic molecular imaging. The technique employs a model-based inversion scheme to recover the chromophore concentrations from photoacoustic measurements. This comprises a numerical forward model of the detected time-dependent photoacoustic signal that incorporates a multiwavelength diffusion-based finite element light propagation model to describe the light transport and a time-domain acoustic model to describe the generation, propagation and detection of the photoacoustic wave. The forward model is then inverted by iteratively fitting it to measurements of photoacoustic signals acquired at different wavelengths to recover the chromophore concentrations. To validate this approach, photoacoustic signals were generated in a tissue phantom using nanosecond laser pulses between 740 nm and 1040 nm. The tissue phantom comprised a suspension of intralipid, blood and a near-infrared dye in which three tubes were immersed. Blood at physiological haemoglobin concentrations and oxygen saturation levels ranging from 2% to 100% was circulated through the tubes. The signal amplitude from different temporal sections of the detected photoacoustic waveforms was plotted as a function of wavelength and the forward model fitted to these data to recover the concentrations of HbO{sub 2} and HHb, total haemoglobin concentration and SO{sub 2}. The performance was found to compare favourably to that of a laboratory CO-oximeter with measurement resolutions of {+-}3

  3. Quantitative spatially resolved measurement of tissue chromophore concentrations using photoacoustic spectroscopy: application to the measurement of blood oxygenation and haemoglobin concentration

    International Nuclear Information System (INIS)

    Laufer, Jan; Delpy, Dave; Elwell, Clare; Beard, Paul

    2007-01-01

    A new approach based on pulsed photoacoustic spectroscopy for non-invasively quantifying tissue chromophore concentrations with high spatial resolution has been developed. The technique is applicable to the quantification of tissue chromophores such as oxyhaemoglobin (HbO 2 ) and deoxyhaemoglobin (HHb) for the measurement of physiological parameters such as blood oxygen saturation (SO 2 ) and total haemoglobin concentration. It can also be used to quantify the local accumulation of targeted contrast agents used in photoacoustic molecular imaging. The technique employs a model-based inversion scheme to recover the chromophore concentrations from photoacoustic measurements. This comprises a numerical forward model of the detected time-dependent photoacoustic signal that incorporates a multiwavelength diffusion-based finite element light propagation model to describe the light transport and a time-domain acoustic model to describe the generation, propagation and detection of the photoacoustic wave. The forward model is then inverted by iteratively fitting it to measurements of photoacoustic signals acquired at different wavelengths to recover the chromophore concentrations. To validate this approach, photoacoustic signals were generated in a tissue phantom using nanosecond laser pulses between 740 nm and 1040 nm. The tissue phantom comprised a suspension of intralipid, blood and a near-infrared dye in which three tubes were immersed. Blood at physiological haemoglobin concentrations and oxygen saturation levels ranging from 2% to 100% was circulated through the tubes. The signal amplitude from different temporal sections of the detected photoacoustic waveforms was plotted as a function of wavelength and the forward model fitted to these data to recover the concentrations of HbO 2 and HHb, total haemoglobin concentration and SO 2 . The performance was found to compare favourably to that of a laboratory CO-oximeter with measurement resolutions of ±3.8 g l -1 (±58

  4. An Unprecedented Blue Chromophore Found in Nature using a "Chemistry First" and Molecular Networking Approach: Discovery of Dactylocyanines A-H.

    Science.gov (United States)

    Bonneau, Natacha; Chen, Guanming; Lachkar, David; Boufridi, Asmaa; Gallard, Jean-François; Retailleau, Pascal; Petek, Sylvain; Debitus, Cécile; Evanno, Laurent; Beniddir, Mehdi A; Poupon, Erwan

    2017-10-17

    Guided by a "chemistry first" approach using molecular networking, eight new bright-blue colored natural compounds, namely dactylocyanines A-H (3-10), were isolated from the Polynesian marine sponge Dactylospongia metachromia. Starting from ilimaquinone (1), an hemisynthetic phishing probe (2) was prepared for annotating and matching structurally related natural substances in D. metachromia crude extract network. This strategy allowed characterizing for the first time in Nature the blue zwitterionic quinonoid chromophore. The solvatochromic properties of the latter are reported. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Biomolecular Mechanisms of Mercury Transfers and Transformations by Proteins of the Mer Operon

    Science.gov (United States)

    Miller, S. M.; Hong, B.; Nauss, R.; Momany, C.; Summers, A. O.; Feng, X.; Harwood, I.; Stroud, R.

    2008-12-01

    Aerobic bacteria exhibiting resistance to the toxic effects of Hg(II) and organomercurials [RHg(I), e.g. MeHg(I)] and are widely found in both pristine and mercury contaminated environments. Resistance, afforded by a plasmid- or transposon-associated mer operon, involves an unusual pathway where Hg(II) and organomercurials [RHg(I)] undergo facilitated entry into the bacterial cytoplasm via an integral membrane transport protein (MerT) and are then "detoxified" by the concerted effort of two enzymes, organomercurial lyase (MerB), which catalyzes dealkylation (i.e., demethylation) of RHg(I) to Hg(II) and a hydrocarbon, and mercuric ion reductase (MerA), which catalyzes reduction of Hg(II) to Hg(0) as the ultimate detoxification for the organism. With a widespread distribution, these bacterial transformations play a significant role in the fate of mercury in the environment. Our focus is on elucidation of the molecular mechanisms for the transport and catalytic transformations of RHg(I) and Hg(II) by these proteins and the factors that influence the overall efficiency of the process. Current efforts are focused primarily on elucidating details of RHg(I) binding and dealkylation by MerB as well as the mechanism for transfer of the Hg(II) product to MerA. Key findings include the demonstration of a non-cysteine residue as essential for the catalytic activity and demonstration that direct transfer of Hg(II) to MerA proceeds more rapidly and more completely than transfer to small MW thiols such as cysteines or glutathione. Reuslts of these studies as well as an overview of our current understanding of the whole system will be presented.

  6. Absorption and fluorescence properties of chromophoric dissolved organic matter of the eastern Bering Sea in the summer with special reference to the influence of a cold pool

    Science.gov (United States)

    D'Sa, E. J.; Goes, J. I.; Gomes, H.; Mouw, C.

    2014-06-01

    The absorption and fluorescence properties of chromophoric dissolved organic matter (CDOM) are reported for the inner shelf, slope waters and outer shelf regions of the eastern Bering Sea during the summer of 2008, when a warm, thermally stratified surface mixed layer lay over a cold pool (CDOM absorption at 355 nm (ag355) and its spectral slope (S) in conjunction with excitation-emission matrix (EEM) fluorescence and parallel factor analysis (PARAFAC) revealed large variability in the characteristics of CDOM in different regions of the Bering Sea. PARAFAC analysis aided in the identification of three humic-like (components one, two and five) and two protein-like (a tyrosine-like component three, and a tryptophan-like component four) components. In the extensive shelf region, average absorption coefficients at 355 nm (ag355, m-1) and DOC concentrations (μM) were highest in the inner shelf (0.342 ± 0.11 m-1, 92.67 ± 14.60 μM) and lower in the middle (0.226 ± 0.05 m-1, 78.38 ± 10.64 μM) and outer (0.185 ± 0.05 m-1, 79.24 ± 18.01 μM) shelves, respectively. DOC concentrations, however were not significantly different, suggesting CDOM sources and sinks to be uncoupled from DOC. Mean spectral slopes S were elevated in the middle shelf (24.38 ± 2.25 μm-1) especially in the surface waters (26.87 ± 2.39 μm-1) indicating high rates of photodegradation in the highly stratified surface mixed layer, which intensified northwards in the northern middle shelf likely contributing to greater light penetration and to phytoplankton blooms at deeper depths. The fluorescent humic-like components one, two, and five were most elevated in the inner shelf most likely from riverine inputs. Along the productive "green belt" in the outer shelf/slope region, absorption and fluorescence properties indicated the presence of fresh and degraded autochthonous DOM. Near the Unimak Pass region of the Aleutian Islands, low DOC and ag355 (mean 66.99 ± 7.94 μM; 0.182 ± 0.05 m-1) and a

  7. [Characterization of Chromophoric dissolved organic matter (CDOM) in Zhoushan fishery using excitation-emission matrix spectroscopy (EEMs) and parallel factor analysis (PARAFAC)].

    Science.gov (United States)

    Zhou, Qian-qian; Su, Rong-guo; Bai, Ying; Zhang, Chuan-song; Shi, Xiao-yong

    2015-01-01

    The composition, distribution characteristics and sources of chromophoric dissolved organic matter(CDOM) in Zhoushan Fishery in spring were evaluated by fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (EEMs-PARAFAC). Three humic-like components [C1 (330/420 nm)], C2 [(290) 365/440 nm] and C3 [(260) 370/490 nm)] and two protein-like components [C4(285/340 nm) and C5 (270/310 nm)] were identified by EEMs-PARAFAC. The horizontal distribution patterns of the five components were almost the same with only slight differences, showing decreasing trends with increasing distance from shore. In the surface and middle layers, the high value areas were located in the north of Hangzhou Bay estuary and the outlet of Xiazhimen channel, and the former's was higher in the surface layer while the latter's was higher in the middle layer. In the bottom layer, CDOM decreased gradiently from the inshore to offshore, with higher CDOM near Zhoushan Island. The distributions of fluorescence components showed an opposite trend with salinity, and no significant linear relationship with Chl-a concentration was found, which indicated that CDOM in the surface and middle layers were dominated by terrestrial input and human activities of Zhoushan Island and that of the bottom layer was attribute to human activities of Zhoushan Island. The vertical distribution of five fluorescent components along 30.5 degrees N transect showed a decreasing trend from the surface and middle layers to bottom layer with high values in inshore and offshore areas, which were correlated with the lower salinity and higher Chl-a concentration, respectively. On this transect, CDOM was mainly affected by Yangtze River input in coastal area but by bioactivities in offshore waters. Along the 30 degrees N transect, the vertical distribution patterns of CDOM were similar to those of 30.5 degrees N transect but there was a high value area in the bottom layer near the shore, attributing to

  8. Enhanced Measurements of Chromophoric Dissolved Organic Matter (CDOM) for Water Quality Analysis using a New Simultaneous Absorbance and Fluorescence Instrument

    Science.gov (United States)

    Gilmore, A. M.

    2009-12-01

    Water quality, with respect to suspended particles and dissolved organic and inorganic compounds, is now recognized as one of the top global environmental concerns. Contemporary research indicates fluorescence spectral analyses coupled with UV-VIS absorbance assays have the potential, especially when combined and coordinated, to facilitate rapid, robust quantification of a wide range of compounds, including interactions among them. Fluorescence excitation-emission matrices (EEMs) collected over the UV-VIS region provide a wealth of information on chromophoric dissolved organic matter (CDOM). CDOM includes humic and fulvic acid, chlorophyll, petroleum, protein, amino acid, quinone, fertilizer, pesticide, sewage and numerous other compound classes. Analysis of the EEMs using conventional and multivariate techniques, including primarily parallel factor analysis (PARAFAC), provides information about many types of CDOM relevant to carbon cycling and pollution of fresh, marine and drinking water sources. Of critical concern also are the CDOM interactions with, and optical activities of, dissolved inorganic compounds. Many of the inorganic compounds and oxygen demand parameters can be analyzed with a wide range of UV-VIS absorbance assays. The instrument is designed and optimized for high UV throughput and low stray light performance. The sampling optics are optimized for both fluorescence and absorbance detection with the same sample. Both EEM and absorbance measurements implement NIST traceable instrument correction and calibration routines. The fluorescence detection utilizes a high dynamic range CCD coupled to a high-resolution spectrograph while absorbance utilizes diode based detection with a high dynamic range and extremely low-stray light specifications. The CDOM analysis is facilitated by a transfer of the data and model information with the PARAFAC routine. The EEM analysis software package facilitates coordinated correction of and correlation with the

  9. Dynamics of chromophoric dissolved organic matter influenced by hydrological conditions in a large, shallow, and eutrophic lake in China.

    Science.gov (United States)

    Zhou, Yongqiang; Zhang, Yunlin; Shi, Kun; Liu, Xiaohan; Niu, Cheng

    2015-09-01

    High concentrations of chromophoric dissolved organic matter (CDOM) are terrestrially derived from upstream tributaries to Lake Taihu, China, and are influenced by hydrological conditions of the upstream watershed. To investigate how the dynamics of CDOM in Lake Taihu are influenced by upstream inflow runoff, four sampling cruises, differing in hydrological conditions, were undertaken in the lake and its three major tributaries, rivers Yincun, Dapu, and Changdou. CDOM absorption, fluorescence spectroscopy, chemical oxygen demand (COD), and stable isotope δ(13)C and δ(15)N measurements were conducted to characterize the dynamics of CDOM. The mean absorption coefficient a(350) collected from the three river profiles (5.15 ± 1.92 m(-1)) was significantly higher than that of the lake (2.95 ± 1.88 m(-1)), indicating that the upstream rivers carried a substantial load of CDOM to the lake. This finding was substantiated by the exclusively terrestrial signal exhibited by the level of δ(13)C (-26.23 ± 0.49‰) of CDOM samples collected from the rivers. Mean a(350) and COD in Lake Taihu were significantly higher in the wet season than in the dry season (t test, p CDOM in the lake is strongly influenced by hydrological conditions of the watershed. Four components were identified by parallel factor analysis, including two protein-like components (C1 and C2), a terrestrial humic-like component (C3), and a microbial humic-like (C4) component. The contribution percentage of the two humic-like components relative to the summed fluorescence intensity of the four components (C humic) increased significantly from the dry to the wet season. This seasonal difference in contribution further substantiated that an enhanced rainfall followed by an elevated inflow runoff in the lake watershed in the wet season may result in an increase in humic-like substances being discharged into the lake compared to that in the dry season. This finding was further supported by an

  10. Foreword [IJEGMBE 2015: India-Japan expert group meeting on biomolecular electronics and organic nanotechnology for environment preservation, Fukuoka (Japan), 23-26 December 2015

    International Nuclear Information System (INIS)

    2016-01-01

    There is increased interest in organic nanotechnology and biomolecular electronics for environmental preservation, and in their anticipated impact on the economics of both the developing and the developed world. Keeping this in mind, the Department of Biological Functions, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology (KIT), Kitakyushu, Japan, and the Department of Science and Technology Centre on Biomolecular Electronics (DSTCBE), National Physical Laboratory (NPL) jointly organized the India-Japan Workshop on Biomolecular Electronics and Organic Nanotechnology for Environmental Preservation (IJWBME 2009) at NPL, New Delhi from 17 th - 19 th December 2009, IJWBME 2011 at EGRET Himeji, Himeji, from 7 th - 10 th December, Japan, and IJWBME 2013 at Delhi Technological University, New Delhi, from 13 th - 15 th December. The India-Japan Expert Group Meeting on Biomolecular Electronics and Organic Nanotechnology for Environment Preservation (IJEGMBE) will be held from 22 th – 25 th , December, 2015, at Nakamura Centenary Memorial Hall, Kyushu Institute of Technology, Kitakyushu, Japan in association with Delhi Technological University, Delhi, India. Recent years have seen rapid growth in the area of Biomolecular Electronics involving the association and expertise of physicists, biologists, chemists, electronics engineers and information technologists. There is increasing interest in the development of nanotechnology and biomolecular electronic devices for the preservation of our precious environment. In this context, the world of the electronics, which developed on Si semiconductors, is going to change drastically. A paradigm shift towards organic or printed electronics is more likely in the future. The field of organic electronics promises exciting new technologies based on inexpensive and mechanically flexible electronic devices, and is now starting to see commercial success. On the sidelines of this increasingly well

  11. Identification of Biomolecular Building Blocks by Recognition Tunneling: Stride towards Nanopore Sequencing of Biomolecules

    Science.gov (United States)

    Sen, Suman

    DNA, RNA and Protein are three pivotal biomolecules in human and other organisms, playing decisive roles in functionality, appearance, diseases development and other physiological phenomena. Hence, sequencing of these biomolecules acquires the prime interest in the scientific community. Single molecular identification of their building blocks can be done by a technique called Recognition Tunneling (RT) based on Scanning Tunneling Microscope (STM). A single layer of specially designed recognition molecule is attached to the STM electrodes, which trap the targeted molecules (DNA nucleoside monophosphates, RNA nucleoside monophosphates or amino acids) inside the STM nanogap. Depending on their different binding interactions with the recognition molecules, the analyte molecules generate stochastic signal trains accommodating their "electronic fingerprints". Signal features are used to detect the molecules using a machine learning algorithm and different molecules can be identified with significantly high accuracy. This, in turn, paves the way for rapid, economical nanopore sequencing platform, overcoming the drawbacks of Next Generation Sequencing (NGS) techniques. To read DNA nucleotides with high accuracy in an STM tunnel junction a series of nitrogen-based heterocycles were designed and examined to check their capabilities to interact with naturally occurring DNA nucleotides by hydrogen bonding in the tunnel junction. These recognition molecules are Benzimidazole, Imidazole, Triazole and Pyrrole. Benzimidazole proved to be best among them showing DNA nucleotide classification accuracy close to 99%. Also, Imidazole reader can read an abasic monophosphate (AP), a product from depurination or depyrimidination that occurs 10,000 times per human cell per day. In another study, I have investigated a new universal reader, 1-(2-mercaptoethyl)pyrene (Pyrene reader) based on stacking interactions, which should be more specific to the canonical DNA nucleosides. In addition

  12. A estória biomolecular do pólipo adenomatoso

    Directory of Open Access Journals (Sweden)

    Mauro de Souza Leite Pinho

    2006-06-01

    Full Text Available Um dos principais objetivos do estudo da biologia molecular é compreender os mecanismos bioquímicos capazes de determinar o comportamento biológico das células em seus respectivos tecidos conforme observado à microscopia e macroscopia. A análise histológica da mucosa colonica normal nos mostra que esta é uma estrutura essencialmente dinâmica, com uma grande rotatividade em suas células, a qual é determinada pela concentração nestas células das proteínas que atuam sobre o controle do ciclo celular. Dentre estas, a proteína APC é aparentemente um elemento chave, promovendo a inibição da ação estimulante sobre as divisões celulares exercida por outras proteínas de grande relevância, como a beta-catenina e a survivina. Além de representar a marca genotípica da polipose adenomatosa familiar, a mutação da proteína APC parece desempenhar uma função de gatilho nos processos de desequilíbrio proliferativo observado no processo neoplásico colorretal, o qual pode variar desde a formação de um pequeno adenoma (ou carcinoma intramucoso até o desenvolvimento de neoplasias invasivas avançadas. A utilização da imunoistoquímica nos permite demonstrar esta relação entre as concentrações de proteínas e o aspecto histológico, representando uma importante ferramenta para um conhecimento cada vez melhor do processo de carcinogênese colorretal.One of the main objectives of molecular biology studies is the understanding of biochemical mechanisms which will ultimately contribute to biological behavior of tissues as observed by macroscopic or microscopic analysis. Hystological examination of normal colonic mucosa shows a relevant cellular turnover, determined by local concentration of proteins related to circle cell control. Among these proteins, APC seems to be a key element, promoting inhibition of other important circle cell stimulating proteins as beta-catenin and survivin. Thus, besides its role as genotypic landmark in

  13. The Icebreaker Life Mission to Mars: A Search for Biomolecular Evidence for Life

    Science.gov (United States)

    Mckay, Christopher P.; Stoker, Carol R.; Glass, Brian J.; Dave, Arwen I.; Davila, Alfonso F.; Heldmann, Jennifer L.; Marinova, Margarita M.; Fairen, Alberto G; Quinn, Richard C; Zacny, Kris A.; hide

    2012-01-01

    The search for evidence of life on Mars is the primary motivation for the exploration of that planet. The results from previous missions, and the Phoenix mission in particular, indicate that the ice-cemented ground in the north polar plains is likely to be the most recently habitable place that is currently known on Mars. The near-surface ice likely provided adequate water activity during periods of high obliquity, 5 Myr ago. Carbon dioxide and nitrogen is present in the atmosphere, and nitrates may be present in the soil. Perchlorate in the soil together with iron in basaltic rock provides a possible energy source for life. Furthermore, the presence of organics must once again be considered, as the results of the Viking GCMS are now suspect given the discovery of the thermally reactive perchlorate. Ground-ice may provide a way to preserve organic molecules for extended periods of time, especially organic biomarkers. The Mars Icebreaker Life mission focuses on the following science goals: 1. Search for specific biomolecules that would be conclusive evidence of life. 2. A general search for organic molecules in the ground ice. 3. Determine the processes of ground ice formation and the role of liquid water. 4. Understand the mechanical properties of the Mars polar ice-cemented soil. 5. Assess the recent habitability of the environment with respect to required elements to support life, energy sources, and possible toxic elements. And 6. Compare the elemental composition of the northern plains with mid-latitude sites. The Icebreaker Life payload has been designed around the Phoenix spacecraft and is targeted to a site near the Phoenix landing site. However, the Icebreaker payload could be supported on other Mars landing systems. Preliminary studies of the SpaceX Dragon lander show that it could support the Icebreaker payload for a landing either at the Phoenix site or at mid-latitudes. Duplicate samples could be cached as a target for possible return by a Mars Sample

  14. The Icebreaker Life Mission to Mars: a search for biomolecular evidence for life.

    Science.gov (United States)

    McKay, Christopher P; Stoker, Carol R; Glass, Brian J; Davé, Arwen I; Davila, Alfonso F; Heldmann, Jennifer L; Marinova, Margarita M; Fairen, Alberto G; Quinn, Richard C; Zacny, Kris A; Paulsen, Gale; Smith, Peter H; Parro, Victor; Andersen, Dale T; Hecht, Michael H; Lacelle, Denis; Pollard, Wayne H

    2013-04-01

    The search for evidence of life on Mars is the primary motivation for the exploration of that planet. The results from previous missions, and the Phoenix mission in particular, indicate that the ice-cemented ground in the north polar plains is likely to be the most recently habitable place that is currently known on Mars. The near-surface ice likely provided adequate water activity during periods of high obliquity, ≈ 5 Myr ago. Carbon dioxide and nitrogen are present in the atmosphere, and nitrates may be present in the soil. Perchlorate in the soil together with iron in basaltic rock provides a possible energy source for life. Furthermore, the presence of organics must once again be considered, as the results of the Viking GCMS are now suspect given the discovery of the thermally reactive perchlorate. Ground ice may provide a way to preserve organic molecules for extended periods of time, especially organic biomarkers. The Mars Icebreaker Life mission focuses on the following science goals: (1) Search for specific biomolecules that would be conclusive evidence of life. (2) Perform a general search for organic molecules in the ground ice. (3) Determine the processes of ground ice formation and the role of liquid water. (4) Understand the mechanical properties of the martian polar ice-cemented soil. (5) Assess the recent habitability of the environment with respect to required elements to support life, energy sources, and possible toxic elements. (6) Compare the elemental composition of the northern plains with midlatitude sites. The Icebreaker Life payload has been designed around the Phoenix spacecraft and is targeted to a site near the Phoenix landing site. However, the Icebreaker payload could be supported on other Mars landing systems. Preliminary studies of the SpaceX Dragon lander show that it could support the Icebreaker payload for a landing either at the Phoenix site or at midlatitudes. Duplicate samples could be cached as a target for possible return by

  15. Evaluation of light scattering properties and chromophore concentrations in skin tissue based on diffuse reflectance signals at isosbestic wavelengths of hemoglobin

    Science.gov (United States)

    Yokokawa, Takumi; Nishidate, Izumi

    2016-04-01

    We investigate a method to evaluate light-scattering properties and chromophore concentrations in human skin tissue through diffuse reflectance spectroscopy using the reflectance signals acquired at isosbestic wavelengths of hemoglobin (420, 450, 500, and 585 nm). In the proposed method, Monte Carlo simulation-based empirical formulas are used to specify the scattering parameters of skin tissue, such as the scattering amplitude a and the scattering power b, as well as the concentration of melanin C m and the total blood concentration C tb. The use of isosbestic wavelengths of hemoglobin enables the values of C m, C tb, a, and b to be estimated independently of the oxygenation of hemoglobin. The spectrum of the reduced scattering coefficient is reconstructed from the scattering parameters. Experiments using in vivo human skin tissues were performed to confirm the feasibility of the proposed method for evaluating the changes in scattering properties and chromophore concentrations in skin tissue. The experimental results revealed that light scattering is significantly reduced by the application of a glycerol solution, which indicates an optical clearing effect due to osmotic dehydration and the matching of the refractive indices of scatterers in the epidermis.

  16. The Role of the Innate Immune System in Alzheimer’s Disease and Frontotemporal Lobar Degeneration: An Eye on Microglia

    Directory of Open Access Journals (Sweden)

    Elisa Ridolfi

    2013-01-01

    Full Text Available In the last few years, genetic and biomolecular mechanisms at the basis of Alzheimer’s disease (AD and frontotemporal lobar degeneration (FTLD have been unraveled. A key role is played by microglia, which represent the immune effector cells in the central nervous system (CNS. They are extremely sensitive to the environmental changes in the brain and are activated in response to several pathologic events within the CNS, including altered neuronal function, infection, injury, and inflammation. While short-term microglial activity has generally a neuroprotective role, chronic activation has been implicated in the pathogenesis of neurodegenerative disorders, including AD and FTLD. In this framework, the purpose of this review is to give an overview of clinical features, genetics, and novel discoveries on biomolecular pathogenic mechanisms at the basis of these two neurodegenerative diseases and to outline current evidence regarding the role played by activated microglia in their pathogenesis.

  17. The role of the innate immune system in Alzheimer's disease and frontotemporal lobar degeneration: an eye on microglia.

    Science.gov (United States)

    Ridolfi, Elisa; Barone, Cinzia; Scarpini, Elio; Galimberti, Daniela

    2013-01-01

    In the last few years, genetic and biomolecular mechanisms at the basis of Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) have been unraveled. A key role is played by microglia, which represent the immune effector cells in the central nervous system (CNS). They are extremely sensitive to the environmental changes in the brain and are activated in response to several pathologic events within the CNS, including altered neuronal function, infection, injury, and inflammation. While short-term microglial activity has generally a neuroprotective role, chronic activation has been implicated in the pathogenesis of neurodegenerative disorders, including AD and FTLD. In this framework, the purpose of this review is to give an overview of clinical features, genetics, and novel discoveries on biomolecular pathogenic mechanisms at the basis of these two neurodegenerative diseases and to outline current evidence regarding the role played by activated microglia in their pathogenesis.

  18. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

    Science.gov (United States)

    Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

    2012-07-01

    The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

  19. [Chromophoric dissolved organic matter absorption characteristics with relation to fluorescence in typical macrophyte, algae lake zones of Lake Taihu].

    Science.gov (United States)

    Zhang, Yun-lin; Qin, Bo-qiang; Ma, Rong-hua; Zhu, Guang-wei; Zhang, Lu; Chen, Wei-min

    2005-03-01

    Chromophoric dissolved organic matter (CDOM) represents one of the primary light-absorbing species in natural waters and plays a critical in determining the aquatic light field. CDOM shows a featureless absorption spectrum that increases exponentially with decreasing wavelength, which limits the penetration of biologically damaging UV-B radiation (wavelength from 280 to 320 nm) in the water column, thus shielding aquatic organisms. CDOM absorption measurements and their relationship with dissolved organic carbon (DOC), and fluorescence are presented in typical macrophyte and algae lake zone of Lake Taihu based on a field investigation in April in 2004 and lab analysis. Absorption spectral of CDOM was measured from 240 to 800 nm using a Shimadzu UV-2401PC UV-Vis recording spectrophotometer. Fluorescence with an excitation wavelength of 355 nm, an emission wavelength of 450 nm is measured using a Shimadzu 5301 spectrofluorometer. Concentrations of DOC ranged from 6.3 to 17.2 mg/L with an average of 9.08 +/- 2.66 mg/L. CDOM absorption coefficients at 280 nm and 355 nm were in the range of 11.2 - 32.6 m(-1) (average 17.46m(-1) +/- 5.75 m(-1) and 2.4 - 8.3 m(-1) (average 4.17m(-1) +/- 1.47 m(-l)), respectively. The values of the DOC-specific absorption coefficient at 355 nm ranged from 0.31 to 0.64 L x (mg x m)-1. Fluorescence emission at 450 nm, excited at 355 nm, had a mean value of 1.32nm(-1) +/- 0.84 nm(-1). A significant lake zone difference is found in DOC concentration, CDOM absorption coefficient and fluorescence, but not in DOC-specific absorption coefficient and spectral slope coefficient. This regional distribution pattern is in agreement with the location of sources of yellow substance: highest concentrations close to river mouth under the influence of river inflow, lower values in East Lake Taihu. The values of algae lake zone are obvious larger than those of macrophyte lake zone. In Meiliang Bay, CDOM absorption, DOC concentration and fluorescence tend to

  20. Sources and fate of chromophoric dissolved organic matter and water mass ventilation in the upper Arctic Ocean

    Science.gov (United States)

    Walker, S. A.; Amon, R. M.; Stedmon, C. A.

    2011-12-01

    The majority of high latitude soil organic carbon is stored within vast permafrost regions surrounding the Arctic, which are highly susceptible to climate change. As global warming persists increased river discharge combined with permafrost erosion and extended ice free periods will increase the supply of soil organic carbon to the Arctic Ocean. Increased river discharge to the Arctic will also have a significant impact its hydrological cycle and could potentially be critical to sea ice formation. This impact is due to freshwater discharge to the Arctic which has been shown to help sustain halocline formation, a critical water mass that acts as an insulator trapping heat from inflowing Atlantic waters from ice at the surface. As the climate warms it is therefore important to identify halocline source waters and to determine fluctuations in their contribution to this critical water mass. To better understand dissolved organic matter (DOM) quality and its fate within the Arctic as well as runoff distributions across the basin the optical properties of chromophoric dissolved organic carbon (CDOM) were evaluated during a trans-Arctic expedition, AOS 2005. This cruise is unique because it is the first time fluorescence data have been obtained from all basins in the Arctic. Excitation/Emission Matrix Spectroscopy (EEM's) coupled to Parallel Factor Analysis (PARAFAC) was used to decompose the combined CDOM fluorescence signal into six independent components that can be traced to a source. Three humic-like CDOM components were isolated and linked to runoff waters using Principal Component Analysis (PCA). Inherent differences were observed between Eurasian (EB) and Canadian (CB) basin surface waters in terms of DOM quality and freshwater distributions. In EB surface waters (0-50m) the humic-like CDOM components explained roughly half of the variance in the DOC pool and were strongly related to lignin phenol concentrations. These results indicate CDOM in Trans-Polar Drift