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Sample records for biomolecular solvent accessible

  1. 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

  2. Bridge- and Solvent-Mediated Intramolecular Electronic Communications in Ubiquinone-Based Biomolecular Wires

    OpenAIRE

    Liu, Xiao-Yuan; Ma, Wei; Zhou, Hao; Cao, Xiao-Ming; Long, Yi-Tao

    2015-01-01

    Intramolecular electronic communications of molecular wires play a crucial role for developing molecular devices. In the present work, we describe different degrees of intramolecular electronic communications in the redox processes of three ubiquinone-based biomolecular wires (Bis-CoQ0s) evaluated by electrochemistry and Density Functional Theory (DFT) methods in different solvents. We found that the bridges linkers have a significant effect on the electronic communications between the two pe...

  3. Bridge- and Solvent-Mediated Intramolecular Electronic Communications in Ubiquinone-Based Biomolecular Wires

    Science.gov (United States)

    Liu, Xiao-Yuan; Ma, Wei; Zhou, Hao; Cao, Xiao-Ming; Long, Yi-Tao

    2015-05-01

    Intramolecular electronic communications of molecular wires play a crucial role for developing molecular devices. In the present work, we describe different degrees of intramolecular electronic communications in the redox processes of three ubiquinone-based biomolecular wires (Bis-CoQ0s) evaluated by electrochemistry and Density Functional Theory (DFT) methods in different solvents. We found that the bridges linkers have a significant effect on the electronic communications between the two peripheral ubiquinone moieties and solvents effects are limited and mostly depend on the nature of solvents. The DFT calculations for the first time indicate the intensity of the electronic communications during the redox processes rely on the molecular orbital elements VL for electron transfer (half of the energy splitting of the LUMO and LUMO+1), which is could be affected by the bridges linkers. The DFT calculations also demonstrates the effect of solvents on the latter two-electron transfer of Bis-CoQ0s is more significant than the former two electrons transfer as the observed electrochemical behaviors of three Bis-CoQ0s. In addition, the electrochemistry and theoretical calculations reveal the intramolecular electronic communications vary in the four-electron redox processes of three Bis-CoQ0s.

  4. Quantum dynamics of electronic excitations in biomolecular chromophores: role of the protein environment and solvent

    CERN Document Server

    Gilmore, J; Gilmore, Joel; Kenzie, Ross H. Mc

    2006-01-01

    We consider continuum dielectric models as minimal models to understand the effect of the surrounding protein and solvent on the quantum dynamics of electronic excitations in a biological chromophore. For these models we describe expressions for the frequency dependent spectral density which describes the coupling of the electronic levels in the chromophore to its environment. We find the contributions to the spectral density from each component of the chromophore environment: the bulk solvent, protein, and water bound to the protein. The relative importance of each component is determined by the time scale on which one is considering the quantum dynamics of the chromophore. Our results provide a natural explanation and model for the different time scales observed in the spectral density extracted from the solvation dynamics probed by ultra-fast laser spectroscopy techniques such as the dynamic Stokes shift and three pulse photon echo spectroscopy. Our results can be used to define under what conditions the d...

  5. Solvent accessible surface area (ASA) of simulated phospholipid membranes

    DEFF Research Database (Denmark)

    Tuchsen, E.; Jensen, Morten Østergaard; Westh, P.

    2003-01-01

    The membrane-solvent interface has been investigated through calculations of the solvent accessible surface area (ASA) for simulated membranes of DPPC and POPE. For DPPC at 52 degreesC we found an ASA of 126 +/- 8 Angstrom(2) per lipid molecule, equivalent to twice the projected lateral area...... compensated by increased exposure of the ethylene and phosphate moieties. The ASA of the polar moieties Of (PO4, NH3 and COO) constitutes 65% of the total accessible area for POPE, making this interface more polar than that of DPPC. It is suggested that ASA information can be valuable in attempts...

  6. Models of the solvent-accessible surface of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Smith, R.E.

    1996-09-01

    Many biopolymers such as proteins, DNA, and RNA have been studied because they have important biomedical roles and may be good targets for therapeutic action in treating diseases. This report describes how plastic models of the solvent-accessible surface of biopolymers were made. Computer files containing sets of triangles were calculated, then used on a stereolithography machine to make the models. Small (2 in.) models were made to test whether the computer calculations were done correctly. Also, files of the type (.stl) required by any ISO 9001 rapid prototyping machine were written onto a CD-ROM for distribution to American companies.

  7. FLOSYS--a web-accessible workflow system for protocol-driven biomolecular sequence analysis.

    Science.gov (United States)

    Badidi, E; Lang, B F; Burger, G

    2004-11-01

    FLOSYS is an interactive web-accessible bioinformatics workflow system designed to assist biologists in multi-step data analyses. FLOSYS allows the user to create complex analysis pathways (protocols) graphically, similar to drawing a flowchart: icons representing particular bioinformatics tools are dragged and dropped onto a canvas and lines connecting those icons are drawn to specify the relationships between the tools. In addition, FLOSYS permits to select input-data, execute the protocol and store the results in a personal workspace. The three-tier architecture of FLOSYS has been implemented in Java and uses a relational database system together with new technologies for distributed and web computing such as CORBA, RMI, JSP and JDBC. The prototype of FLOSYS, which is part of the bioinformatics workbench AnaBench, is accessible on-line at http://malawimonas.bcm.umontreal.ca: 8091/anabench. The entire package is available on request to academic groups who wish to have a customized local analysis environment for research or teaching.

  8. A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

    CERN Document Server

    Cooper, Christopher D; Barba, L A

    2013-01-01

    The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known APBS finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2%, then the simpler, single-surface model can be used. When calculating b...

  9. Variational Methods for Biomolecular Modeling

    CERN Document Server

    Wei, Guo-Wei

    2016-01-01

    Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrosta...

  10. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica.

    Science.gov (United States)

    Bustamante, C D; Townsend, J P; Hartl, D L

    2000-02-01

    The neutral theory of molecular evolution predicts that variation within species is inversely related to the strength of purifying selection, but the strength of purifying selection itself must be related to physical constraints imposed by protein folding and function. In this paper, we analyzed five enzymes for which polymorphic sequence variation within Escherichia coli and/or Salmonella enterica was available, along with a protein structure. Single and multivariate logistic regression models are presented that evaluate amino acid size, physicochemical properties, solvent accessibility, and secondary structure as predictors of polymorphism. A model that contains a positive coefficient of association between polymorphism and solvent accessibility and separate intercepts for each secondary-structure element is sufficient to explain the observed variation in polymorphism between sites. The model predicts an increase in the probability of amino acid polymorphism with increasing solvent accessibility for each protein regardless of physicochemical properties, secondary-structure element, or size of the amino acid. This result, when compared with the distribution of synonymous polymorphism, which shows no association with solvent accessibility, suggests a strong decrease in purifying selection with increasing solvent accessibility. PMID:10677853

  11. octanol/water partition coefficient using solvation free energy and solvent-accessible surface area

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The regression model for octanol/water partition coefficients (Kow ), is founded with only two molecular descriptors available through quantum chemical calculations: solvation free energy (△ Gs ), and solvent-accessible surface area (SASA). For the properties of 47 organic compounds from 17 types, the model gives a oonection coefficient (adjusted for degrees of freedom) of 0.959 and a standard error of 0.277 log unit. It is a suitable way to predict the partition properties that are related to solute-solvent interactions in the water phase.

  12. Modeling coding-sequence evolution within the context of residue solvent accessibility

    Directory of Open Access Journals (Sweden)

    Scherrer Michael P

    2012-09-01

    Full Text Available Abstract Background Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues. Results Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94 model in which all model parameters can be functions of the relative solvent accessibility (RSA of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94 model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Conclusions Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω.

  13. RSARF: Prediction of residue solvent accessibility from protein sequence using random forest method

    KAUST Repository

    Ganesan, Pugalenthi

    2012-01-01

    Prediction of protein structure from its amino acid sequence is still a challenging problem. The complete physicochemical understanding of protein folding is essential for the accurate structure prediction. Knowledge of residue solvent accessibility gives useful insights into protein structure prediction and function prediction. In this work, we propose a random forest method, RSARF, to predict residue accessible surface area from protein sequence information. The training and testing was performed using 120 proteins containing 22006 residues. For each residue, buried and exposed state was computed using five thresholds (0%, 5%, 10%, 25%, and 50%). The prediction accuracy for 0%, 5%, 10%, 25%, and 50% thresholds are 72.9%, 78.25%, 78.12%, 77.57% and 72.07% respectively. Further, comparison of RSARF with other methods using a benchmark dataset containing 20 proteins shows that our approach is useful for prediction of residue solvent accessibility from protein sequence without using structural information. The RSARF program, datasets and supplementary data are available at http://caps.ncbs.res.in/download/pugal/RSARF/. - See more at: http://www.eurekaselect.com/89216/article#sthash.pwVGFUjq.dpuf

  14. 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.

  15. FreeSASA: An open source C library for solvent accessible surface area calculations.

    Science.gov (United States)

    Mitternacht, Simon

    2016-01-01

    Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy tool-chain integration. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. The library implements both Lee and Richards' and Shrake and Rupley's approximations, and is highly configurable to allow the user to control molecular parameters, accuracy and output granularity. It only depends on standard C libraries and should therefore be easy to compile and install on any platform. The library is well-documented, stable and efficient. The command-line interface can easily replace closed source legacy programs, with comparable or better accuracy and speed, and with some added functionality.

  16. Stereolithographic models of the solvent-accessible surface of biopolymers. Topical report

    Energy Technology Data Exchange (ETDEWEB)

    Bradford, J. [Olathe South High School, KS (United States); Noel, P. [Center High School, Kansas City, MO (United States); Emery, J.D. [and others

    1996-11-01

    The solvent-accessible surfaces of several biopolymers were calculated. As part of the DOE education outreach activity, two high school students participated in this project. Computer files containing sets of triangles were produced. These files are called stl files and are the ISO 9001 standard. They have been written onto CD-ROMs for distribution to American companies. Stereolithographic models were made of some of them to ensure that the computer calculations were done correctly. Stereolithographic models were made of interleukin 1{beta} (IL-1{beta}), three antibodies (an anti-p-azobenzene arsonate, an anti-Brucella A cell wall polysaccharide, and an HIV neutralizing antibody), a triple stranded coiled coil, and an engrailed homeodomain. Also, the biopolymers and their files are described.

  17. Develop and test a solvent accessible surface area-based model in conformational entropy calculations.

    Science.gov (United States)

    Wang, Junmei; Hou, Tingjun

    2012-05-25

    It is of great interest in modern drug design to accurately calculate the free energies of protein-ligand or nucleic acid-ligand binding. MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) and MM-GBSA (molecular mechanics generalized Born surface area) have gained popularity in this field. For both methods, the conformational entropy, which is usually calculated through normal-mode analysis (NMA), is needed to calculate the absolute binding free energies. Unfortunately, NMA is computationally demanding and becomes a bottleneck of the MM-PB/GBSA-NMA methods. In this work, we have developed a fast approach to estimate the conformational entropy based upon solvent accessible surface area calculations. In our approach, the conformational entropy of a molecule, S, can be obtained by summing up the contributions of all atoms, no matter they are buried or exposed. Each atom has two types of surface areas, solvent accessible surface area (SAS) and buried SAS (BSAS). The two types of surface areas are weighted to estimate the contribution of an atom to S. Atoms having the same atom type share the same weight and a general parameter k is applied to balance the contributions of the two types of surface areas. This entropy model was parametrized using a large set of small molecules for which their conformational entropies were calculated at the B3LYP/6-31G* level taking the solvent effect into account. The weighted solvent accessible surface area (WSAS) model was extensively evaluated in three tests. For convenience, TS values, the product of temperature T and conformational entropy S, were calculated in those tests. T was always set to 298.15 K through the text. First of all, good correlations were achieved between WSAS TS and NMA TS for 44 protein or nucleic acid systems sampled with molecular dynamics simulations (10 snapshots were collected for postentropy calculations): the mean correlation coefficient squares (R²) was 0.56. As to the 20 complexes, the TS

  18. Integrative NMR for biomolecular research.

    Science.gov (United States)

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

    2016-04-01

    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 ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html ). PMID:27023095

  19. Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

    OpenAIRE

    Wei, Guo Wei; Baker, Nathan A.

    2014-01-01

    This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, el...

  20. Programming in Biomolecular Computation:

    DEFF Research Database (Denmark)

    Hartmann, Lars; 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...

  1. 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...

  2. Solvent-driven electron trapping and mass transport in reduced graphites to access perfect graphene

    Science.gov (United States)

    Vecera, Philipp; Holzwarth, Johannes; Edelthalhammer, Konstantin F.; Mundloch, Udo; Peterlik, Herwig; Hauke, Frank; Hirsch, Andreas

    2016-08-01

    Herein, we report on a significant discovery, namely, the quantitative discharging of reduced graphite forms, such as graphite intercalation compounds, graphenide dispersions and graphenides deposited on surfaces with the simple solvent benzonitrile. Because of its comparatively low reduction potential, benzonitrile is reduced during this process to the radical anion, which exhibits a red colour and serves as a reporter molecule for the quantitative determination of negative charges on the carbon sheets. Moreover, this discovery reveals a very fundamental physical-chemical phenomenon, namely a quantitative solvent reduction induced and electrostatically driven mass transport of K+ ions from the graphite intercalation compounds into the liquid. The simple treatment of dispersed graphenides suspended on silica substrates with benzonitrile leads to the clean conversion to graphene. This unprecedented procedure represents a rather mild, scalable and inexpensive method for graphene production surpassing previous wet-chemical approaches.

  3. Programming in Biomolecular Computation

    DEFF Research Database (Denmark)

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

    2010-01-01

    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 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...... in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient. A prototype model has been implemented (for now in silico on a conventional computer). This work opens new perspectives on just how computation may be specified at the biological level....

  4. Restricted access supramolecular solvents for sample treatment in enzyme-linked immuno-sorbent assay of mycotoxins in food.

    Science.gov (United States)

    García-Fonseca, Sergio; Ballesteros-Gómez, Ana; Rubio, Soledad

    2016-09-01

    A restricted access supramolecular solvent (SUPRAS-RAM) made up of tetradecanoic acid reverse micelles is proposed as a wide-scope and low-cost strategy for the treatment of agrifood samples prior to enzyme-linked immunosorbent assays (ELISA). The approach was assessed for the determination of ochratoxin A (OTA) in wines and spices and aflatoxin B1 (AFB1) in cereals, two ubiquitous mycotoxins that were selected as representative contaminants for this study. The samples were selected to cover a variety of matrices in terms diverse composition and high complexity. Macromolecules such as proteins and carbohydrates were not-co-extracted due to the restricted access properties of the SUPRAS that are provided by chemical and physical mechanisms. In this sense, analyte extraction and clean-up were carried out in a single step. Parameters determining the extraction efficiency were studied and optimized. Certified reference materials were used for method validation. Recoveries of OTA ranged between 83% and 96% in wines (with relative standard deviation, RSD, of about 10%) and between 81% and 93% in spices (RSD 7%). Recoveries for AFB1 in wheat ranged from 75% to 85% (RSD 8%). The detection limits were all below the maximum levels established for OTA and for AFB1 by EU directives. This method offers a green and low-cost alternative to the organic solvent-based extraction and/or immunoaffinity columns-based cleanup of complex samples prior to ELISA. PMID:27543022

  5. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

    Science.gov (United States)

    Heffernan, Rhys; Paliwal, Kuldip; Lyons, James; Dehzangi, Abdollah; Sharma, Alok; Wang, Jihua; Sattar, Abdul; Yang, Yuedong; Zhou, Yaoqi

    2015-01-01

    Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary structure and torsion angle prediction. In this study, we expand the iterative features to include solvent accessible surface area and backbone angles and dihedrals based on Cα atoms. By using a deep learning neural network in three iterations, we achieved 82% accuracy for secondary structure prediction, 0.76 for the correlation coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute errors of backbone φ and ψ angles, respectively, and 8° and 32° for mean absolute errors of Cα-based θ and τ angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking.

  6. Gd(3+) Spin Labels Report the Conformation and Solvent Accessibility of Solution and Vesicle-Bound Melittin.

    Science.gov (United States)

    Manukovsky, Nurit; Frydman, Veronica; Goldfarb, Daniella

    2015-10-29

    Although Gd(3+)-based spin labels have been shown to be an alternative to nitroxides for double electron-electron resonance (DEER) distance measurements at high fields, their ability to provide solvent accessibility information, as nitroxides do, has not been explored. In addition, the effect of the label type on the measured distance distribution has not been sufficiently characterized. In this work, we extended the applicability of Gd(3+) spin labels to solvent accessibility measurements on a peptide in model membranes, namely, large unilamellar vesicles (LUVs) using W-band (2)H Mims electron-nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) techniques and Gd(3+)-ADO3A-labeled melittin. In addition, we carried out Gd(3+)-Gd(3+) DEER distance measurements to probe the peptide conformation in solution and when bound to LUVs. A comparison with earlier results reported for the same system with nitroxide labels shows that, although in both cases the peptide binds parallel to the membrane surface, the Gd(3+)-ADO3A label tends to protrude from the membrane into the solvent, whereas the nitroxide does the opposite. This can be explained on the basis of the hydrophilicity of the Gd(3+)-ADO3A labels in contrast with the hydrophobicity of nitroxides. The distance distributions obtained from different labels are accordingly different, with the Gd(3+)-ADO3A yielding consistently broader distributions. These discrepancies are most pronounced when the peptide termini are labeled, which implies that such labeling positions may be inadvisible. PMID:26001213

  7. FreeSASA: An open source C library for solvent accessible surface area calculations [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Simon Mitternacht

    2016-02-01

    Full Text Available Calculating solvent accessible surface areas (SASA is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy tool-chain integration. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. The library implements both Lee and Richards’ and Shrake and Rupley’s approximations, and is highly configurable to allow the user to control molecular parameters, accuracy and output granularity. It only depends on standard C libraries and should therefore be easy to compile and install on any platform. The library is well-documented, stable and efficient. The command-line interface can easily replace closed source legacy programs, with comparable or better accuracy and speed, and with some added functionality.

  8. Enhancing cellulose accessibility of corn stover by deep eutectic solvent pretreatment for butanol fermentation.

    Science.gov (United States)

    Xu, Guo-Chao; Ding, Ji-Cai; Han, Rui-Zhi; Dong, Jin-Jun; Ni, Ye

    2016-03-01

    In this study, an effective corn stover (CS) pretreatment method was developed for biobutanol fermentation. Deep eutectic solvents (DESs), consisted of quaternary ammonium salts and hydrogen donors, display similar properties to room temperature ionic liquid. Seven DESs with different hydrogen donors were facilely synthesized. Choline chloride:formic acid (ChCl:formic acid), an acidic DES, displayed excellent performance in the pretreatment of corn stover by removal of hemicellulose and lignin as confirmed by SEM, FTIR and XRD analysis. After optimization, glucose released from pretreated CS reached 17.0 g L(-1) and yield of 99%. The CS hydrolysate was successfully utilized in butanol fermentation by Clostridium saccharobutylicum DSM 13864, achieving butanol titer of 5.63 g L(-1) with a yield of 0.17 g g(-1) total sugar and productivity of 0.12 g L(-1)h(-1). This study demonstrates DES could be used as a promising and biocompatible pretreatment method for the conversion of lignocellulosic biomass into biofuel. PMID:26597485

  9. Grid computing and biomolecular simulation.

    Science.gov (United States)

    Woods, Christopher J; Ng, Muan Hong; Johnston, Steven; Murdock, Stuart E; Wu, Bing; Tai, Kaihsu; Fangohr, Hans; Jeffreys, Paul; Cox, Simon; Frey, Jeremy G; Sansom, Mark S P; Essex, Jonathan W

    2005-08-15

    Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design. In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology. In the second, the rationale and design of a database of biomolecular simulation trajectories is described. Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.

  10. A generic method for assignment of reliability scores applied to solvent accessibility predictions

    Directory of Open Access Journals (Sweden)

    Nielsen Morten

    2009-07-01

    Full Text Available Abstract Background Estimation of the reliability of specific real value predictions is nontrivial and the efficacy of this is often questionable. It is important to know if you can trust a given prediction and therefore the best methods associate a prediction with a reliability score or index. For discrete qualitative predictions, the reliability is conventionally estimated as the difference between output scores of selected classes. Such an approach is not feasible for methods that predict a biological feature as a single real value rather than a classification. As a solution to this challenge, we have implemented a method that predicts the relative surface accessibility of an amino acid and simultaneously predicts the reliability for each prediction, in the form of a Z-score. Results An ensemble of artificial neural networks has been trained on a set of experimentally solved protein structures to predict the relative exposure of the amino acids. The method assigns a reliability score to each surface accessibility prediction as an inherent part of the training process. This is in contrast to the most commonly used procedures where reliabilities are obtained by post-processing the output. Conclusion The performance of the neural networks was evaluated on a commonly used set of sequences known as the CB513 set. An overall Pearson's correlation coefficient of 0.72 was obtained, which is comparable to the performance of the currently best public available method, Real-SPINE. Both methods associate a reliability score with the individual predictions. However, our implementation of reliability scores in the form of a Z-score is shown to be the more informative measure for discriminating good predictions from bad ones in the entire range from completely buried to fully exposed amino acids. This is evident when comparing the Pearson's correlation coefficient for the upper 20% of predictions sorted according to reliability. For this subset, values of 0

  11. Accurate single-sequence prediction of solvent accessible surface area using local and global features.

    Science.gov (United States)

    Faraggi, Eshel; Zhou, Yaoqi; Kloczkowski, Andrzej

    2014-11-01

    We present a new approach for predicting the Accessible Surface Area (ASA) using a General Neural Network (GENN). The novelty of the new approach lies in not using residue mutation profiles generated by multiple sequence alignments as descriptive inputs. Instead we use solely sequential window information and global features such as single-residue and two-residue compositions of the chain. The resulting predictor is both highly more efficient than sequence alignment-based predictors and of comparable accuracy to them. Introduction of the global inputs significantly helps achieve this comparable accuracy. The predictor, termed ASAquick, is tested on predicting the ASA of globular proteins and found to perform similarly well for so-called easy and hard cases indicating generalizability and possible usability for de-novo protein structure prediction. The source code and a Linux executables for GENN and ASAquick are available from Research and Information Systems at http://mamiris.com, from the SPARKS Lab at http://sparks-lab.org, and from the Battelle Center for Mathematical Medicine at http://mathmed.org. PMID:25204636

  12. Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network.

    Science.gov (United States)

    Faraggi, Eshel; Xue, Bin; Zhou, Yaoqi

    2009-03-01

    This article attempts to increase the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins through improved learning. Most methods developed for improving the backpropagation algorithm of artificial neural networks are limited to small neural networks. Here, we introduce a guided-learning method suitable for networks of any size. The method employs a part of the weights for guiding and the other part for training and optimization. We demonstrate this technique by predicting residue solvent accessibility and real-value backbone torsion angles of proteins. In this application, the guiding factor is designed to satisfy the intuitive condition that for most residues, the contribution of a residue to the structural properties of another residue is smaller for greater separation in the protein-sequence distance between the two residues. We show that the guided-learning method makes a 2-4% reduction in 10-fold cross-validated mean absolute errors (MAE) for predicting residue solvent accessibility and backbone torsion angles, regardless of the size of database, the number of hidden layers and the size of input windows. This together with introduction of two-layer neural network with a bipolar activation function leads to a new method that has a MAE of 0.11 for residue solvent accessibility, 36 degrees for psi, and 22 degrees for phi. The method is available as a Real-SPINE 3.0 server in http://sparks.informatics.iupui.edu.

  13. AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multitask Learning Framework under the Conditional Neural Fields Model

    Directory of Open Access Journals (Sweden)

    Jianzhu Ma

    2015-01-01

    Full Text Available Motivation. The solvent accessibility of protein residues is one of the driving forces of protein folding, while the contact number of protein residues limits the possibilities of protein conformations. The de novo prediction of these properties from protein sequence is important for the study of protein structure and function. Although these two properties are certainly related with each other, it is challenging to exploit this dependency for the prediction. Method. We present a method AcconPred for predicting solvent accessibility and contact number simultaneously, which is based on a shared weight multitask learning framework under the CNF (conditional neural fields model. The multitask learning framework on a collection of related tasks provides more accurate prediction than the framework trained only on a single task. The CNF method not only models the complex relationship between the input features and the predicted labels, but also exploits the interdependency among adjacent labels. Results. Trained on 5729 monomeric soluble globular protein datasets, AcconPred could reach 0.68 three-state accuracy for solvent accessibility and 0.75 correlation for contact number. Tested on the 105 CASP11 domain datasets for solvent accessibility, AcconPred could reach 0.64 accuracy, which outperforms existing methods.

  14. Dynamic Presentation of Immobilized Ligands Regulated through Biomolecular Recognition

    OpenAIRE

    Liu, Bo; Liu, Yang; Riesberg, Jeremiah J.; Shen, Wei

    2010-01-01

    To mimic the dynamic regulation of signaling ligands immobilized on extracellular matrices or on the surfaces of neighboring cells for guidance of cell behavior and fate selection, we have harnessed biomolecular recognition in combination with polymer engineering to create dynamic surfaces on which the accessibility of immobilized ligands to cell surface receptors can be reversibly interconverted under physiological conditions. The cell-adhesive RGD peptide is chosen as a model ligand. RGD is...

  15. HMM-based prediction for protein structural motifs' two local properties: solvent accessibility and backbone torsion angles.

    Science.gov (United States)

    Yu, Jianyong; Xiang, Leijun; Hong, Jiang; Zhang, Weidong

    2013-02-01

    Protein structure prediction is often assisted by predicting one-dimensional structural properties including relative solvent accessibility (RSA) surface and backbone torsion angles (BTA) of residues, and these two properties are continuously varying variables because proteins can move freely in a three-dimensional space. Instead of subdividing them into a few arbitrarily defined states that many popular approaches used, this paper proposes an integrated system for realvalue prediction of protein structural motifs' two local properties, based on the modified Hidden Markov Model that we previously presented. The model was used to capture the relevance of RSA and the dependency of BTA between adjacent residues along the local protein chain in motifs with definite probabilities. These two properties were predicted according to their own probability distribution. The method was applied to a protein fragment library. For nine different classes of motifs, real values of RSA were predicted with mean absolute error (MAE) of 0.122-0.175 and Pearson's correlation coefficient (PCC) of 0.623-0.714 between predicted and actual RSA. Meanwhile, real values of BTA were obtained with MAE of 8.5⁰-29.4⁰ for Φ angles, 11.2⁰-38.5⁰ for ψ angles and PCC of 0.601-0.716 for Φ, 0.597-0.713 for ψ. The results were compared with well-known Real-SPINE Server, and indicate the proposed method may at least serve as the foundation to obtain better local properties from structural motifs for protein structure prediction. PMID:22894152

  16. Easy Access to Coumarin Derivatives Using Alumina Sulfuric Acid as an Efficient and Reusable Catalyst under Solvent-Free Conditions

    Directory of Open Access Journals (Sweden)

    Ali Amoozadeh

    2013-01-01

    Full Text Available A new and efficient condition for the use of alumina sulfuric acid (ASA as a heterogeneous catalyst in the Pechmann condensation reaction in solvent-free condition for the formation of coumarins has been reported.

  17. The solvent component of macromolecular crystals

    Energy Technology Data Exchange (ETDEWEB)

    Weichenberger, Christian X. [European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, Bozen/Bolzano, I-39100 Südtirol/Alto Adige (Italy); Afonine, Pavel V. [Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mail Stop 64R0121, Berkeley, CA 94720 (United States); Kantardjieff, Katherine [California State University, San Marcos, CA 92078 (United States); Rupp, Bernhard, E-mail: br@hofkristallamt.org [k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084 (United States); Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck (Austria)

    2015-04-30

    On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity. The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.

  18. [Advances in biomolecular machine: methane monooxygenases].

    Science.gov (United States)

    Lu, Jixue; Wang, Shizhen; Fang, Baishan

    2015-07-01

    Methane monooxygenases (MMO), regarded as "an amazing biomolecular machine", catalyze the oxidation of methane to methanol under aerobic conditions. MMO catalyze the oxidation of methane elaborately, which is a novel way to catalyze methane to methanol. Furthermore, MMO can inspire the biomolecular machine design. In this review, we introduced MMO including structure, gene and catalytic mechanism. The history and the taxonomy of MMO were also introduced. PMID:26647577

  19. Comparative study of corn stover pretreated by dilute acid and cellulose solvent-based lignocellulose fractionation: Enzymatic hydrolysis, supramolecular structure, and substrate accessibility.

    Science.gov (United States)

    Zhu, Zhiguang; Sathitsuksanoh, Noppadon; Vinzant, Todd; Schell, Daniel J; McMillan, James D; Zhang, Y-H Percival

    2009-07-01

    Liberation of fermentable sugars from recalcitrant biomass is among the most costly steps for emerging cellulosic ethanol production. Here we compared two pretreatment methods (dilute acid, DA, and cellulose solvent and organic solvent lignocellulose fractionation, COSLIF) for corn stover. At a high cellulase loading [15 filter paper units (FPUs) or 12.3 mg cellulase per gram of glucan], glucan digestibilities of the corn stover pretreated by DA and COSLIF were 84% at hour 72 and 97% at hour 24, respectively. At a low cellulase loading (5 FPUs per gram of glucan), digestibility remained as high as 93% at hour 24 for the COSLIF-pretreated corn stover but reached only approximately 60% for the DA-pretreated biomass. Quantitative determinations of total substrate accessibility to cellulase (TSAC), cellulose accessibility to cellulase (CAC), and non-cellulose accessibility to cellulase (NCAC) based on adsorption of a non-hydrolytic recombinant protein TGC were measured for the first time. The COSLIF-pretreated corn stover had a CAC of 11.57 m(2)/g, nearly twice that of the DA-pretreated biomass (5.89 m(2)/g). These results, along with scanning electron microscopy images showing dramatic structural differences between the DA- and COSLIF-pretreated samples, suggest that COSLIF treatment disrupts microfibrillar structures within biomass while DA treatment mainly removes hemicellulose. Under the tested conditions COSLIF treatment breaks down lignocellulose structure more extensively than DA treatment, producing a more enzymatically reactive material with a higher CAC accompanied by faster hydrolysis rates and higher enzymatic digestibility.

  20. Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area.

    Science.gov (United States)

    Cao, Chen; Xu, Shutan

    2016-01-01

    Protein ligand-binding site prediction is highly important for protein function determination and structure-based drug design. Over the past twenty years, dozens of computational methods have been developed to address this problem. Soga et al. identified ligand cavities based on the preferences of amino acids for the ligand-binding site (RA) and proposed the propensity for ligand binding (PLB) index to rank the cavities on the protein surface. However, we found that residues exhibit different RAs in response to changes in solvent exposure. Furthermore, previous studies have suggested that some dihedral angles of amino acids in specific regions of the Ramachandran plot are preferred at the functional sites of proteins. Based on these discoveries, the amino acid solvent-accessible surface area and dihedral angles were combined with the RA and PLB to obtain two new indexes, multi-factor RA (MF-RA) and multi-factor PLB (MF-PLB). MF-PLB, PLB and other methods were tested using two benchmark databases and two particular ligand-binding sites. The results show that MF-PLB can improve the success rate of PLB for both ligand-bound and ligand-unbound structures, particularly for top choice prediction. PMID:27619067

  1. Biomolecular solvation study of proteins in liquid water by a wide range gigahertz-to-terahertz spectroscopy

    Science.gov (United States)

    Charkhesht, Ali; George, Deepu; Nguyen, Vinh

    Solvent dynamics within biomolecular solvation layers play a major role in enzyme activity, but obtaining an accurate and quantitative picture of solvent activity around proteins is challenging. Due to the strong absorption of water in the gigahertz-to-terahertz frequencies, it is challenging to study properties of the solvent dynamics as well as conformational changes protein in water. We have developed a highly sensitive dielectric gigahertz-to-terahertz frequency-domain spectroscopy system for probing the collective dynamics of proteins and solvent. Using this technique, we investigate the complex dielectric response of bovine serum albumin and lysozyme proteins in aqueous environment on a wide frequency range from 0.1 GHz up to 2 THz. We explore the conformation flexibility of proteins and compare the hydration dynamics around proteins to understand the effects of surface-mediated solvent dynamics, relationships among different measures of interfacial solvent dynamics, and protein-mediated solvent dynamics.

  2. Scanning probe and optical tweezer investigations of biomolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Rigby-Singleton, Shellie

    2002-07-01

    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 {approx}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

  3. Conducting polymer based biomolecular electronic devices

    Indian Academy of Sciences (India)

    B D Malhotra; Rahul Singhal

    2003-08-01

    Biomolecular electronics is rapidly evolving from physics, chemistry, biology, electronics and information technology. Organic materials such as proteins, pigments and conducting polymers have been considered as alternatives for carrying out the functions that are presently being performed by semiconductor silicon. Conducting polymers such as polypyrroles, polythiophenes and polyanilines have been projected for applications for a wide range of biomolecular electronic devices such as optical, electronic, drug-delivery, memory and biosensing devices. Our group has been actively working towards the application of conducting polymers to Schottky diodes, metal–insulator–semiconductor (MIS) devices and biosensors for the past 10 years. This paper is a review of some of the results obtained at our laboratory in the area of conducting polymer biomolecular electronics.

  4. Flourescence from Gas-Phase Biomolecular Ions

    DEFF Research Database (Denmark)

    Nielsen, Steen Brøndsted

    2013-01-01

    from experiments on dye-derivatised biomolecular ions that provide important information on folding/unfolding processes and local structural changes are presented. Examples included here are a model DNA duplex, the Trp-cage protein, polyproline peptides, and the cytochrome c heme protein. The chapter......This chapter deals with measurements of fluorescence from electronically excited biomolecular ions where there are no interactions with an external environment. Biomolecules with no natural fluorophores are labelled with a dye for such experiments. First, some of the advantages, but also...

  5. Advances in integrative modeling of biomolecular complexes

    NARCIS (Netherlands)

    Karaca, E.; Bonvin, A.M.J.J.

    2013-01-01

    High-resolution structural information is needed in order to unveil the underlying mechanistic of biomolecular function. Due to the technical limitations or the nature of the underlying complexes, acquiring atomic resolution information is difficult for many challenging systems, while, often, low-re

  6. Restricted access supramolecular solvents for removal of matrix-induced ionization effects in mass spectrometry: Application to the determination of Fusarium toxins in cereals.

    Science.gov (United States)

    García-Fonseca, Sergio; Rubio, Soledad

    2016-02-01

    Ion suppression/enhancement caused by matrix effects continues being a major concern in liquid chromatography-mass spectrometry (LC-MS). This research explores the ability of a supramolecular solvent (SUPRAS) made up of inverted hexagonal aggregates of oleic acid to behave as a liquid with restricted access properties (SUPRAS-RAM). Fusarium toxins in cereals were extracted with the oleic acid-based SUPRAS-RAM prior to their quantification by LC-electrospray ionization (ESI)-ion trap-MS (LC-ESI-IT-MS) in order to investigate the capability of this solvent to remove or reduce ionization suppression and/or enhancement in the analysis of complex samples by MS. The method involved the vortex-shaking of 300 mg of cereal with 600 μL of the SUPRAS-RAM for 15 min, centrifugation for separation of the supernatant and quantitation by LC-ESI-IT-MS. Macromolecules such as proteins and carbohydrates were excluded from extraction by chemical and physical mechanisms. Extraction of analytes and sample clean-up were thus carried out in a single step. No evaporation of the extracts was needed. Method detection limits for the legislated Fusarium toxins [i.e. deoxynivalenol (DON), zearalenone (ZEA) and fumonisins B1 (FB1) and B2 (FB2)] were 15 μg kg(-1) for DON and ZEA and 8 μg kg(-1) for fumonisins. These values were far below the maximum levels set by the European Commission for these toxins in foodstuffs. The method was successfully applied to the determination of these toxins in wheat and maize harvested in the South of Spain. No contamination of Fusarium toxins was found in samples at detectable levels. Recoveries in spiked samples were in the range 87-105%, with relative standard deviations between 1 and 7%. The use of the oleic acid-based SUPRAS-RAM effectively removed matrix interferences and allowed reliable quantitation of Fusarium toxins in cereals using solvent-based calibration.

  7. Systematic evaluation of bundled SPC water for biomolecular simulations.

    Science.gov (United States)

    Gopal, Srinivasa M; Kuhn, Alexander B; Schäfer, Lars V

    2015-04-01

    In bundled SPC water models, the relative motion of groups of four water molecules is restrained by distance-dependent potentials. Bundled SPC models have been used in hybrid all-atom/coarse-grained (AA/CG) multiscale simulations, since they enable to couple atomistic SPC water with supra-molecular CG water models that effectively represent more than a single water molecule. In the present work, we systematically validated and critically tested bundled SPC water models as solvent for biomolecular simulations. To that aim, we investigated both thermodynamic and structural properties of various biomolecular systems through molecular dynamics (MD) simulations. Potentials of mean force of dimerization of pairs of amino acid side chains as well as hydration free energies of single side chains obtained with bundled SPC and standard (unrestrained) SPC water agree closely with each other and with experimental data. Decomposition of the hydration free energies into enthalpic and entropic contributions reveals that in bundled SPC, this favorable agreement of the free energies is due to a larger degree of error compensation between hydration enthalpy and entropy. The Ramachandran maps of Ala3, Ala5, and Ala7 peptides are similar in bundled and unrestrained SPC, whereas for the (GS)2 peptide, bundled water leads to a slight overpopulation of extended conformations. Analysis of the end-to-end distance autocorrelation times of the Ala5 and (GS)2 peptides shows that sampling in more viscous bundled SPC water is about two times slower. Pronounced differences between the water models were found for the structure of a coiled-coil dimer, which is instable in bundled SPC but not in standard SPC. In addition, the hydration of the active site of the serine protease α-chymotrypsin depends on the water model. Bundled SPC leads to an increased hydration of the active site region, more hydrogen bonds between water and catalytic triad residues, and a significantly slower exchange of water

  8. Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the influence of conformational uncertainty in biomolecular solvation

    Energy Technology Data Exchange (ETDEWEB)

    Lei, Huan; Yang, Xiu; Zheng, Bin; Baker, Nathan A.

    2015-11-05

    Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method to quantify the uncertainty of target properties induced by conformational fluctuations. Using a generalized polynomial chaos (gPC) expansion, we construct a surrogate model of the target property with respect to varying conformational states. We also propose a method to increase the sparsity of the gPC expansion by defining a set of conformational “active space” random variables. With the increased sparsity, we employ the compressive sensing method to accurately construct the surrogate model. We demonstrate the performance of the surrogate model by evaluating fluctuation-induced uncertainty in solvent-accessible surface area for the bovine trypsin inhibitor protein system and show that the new approach offers more accurate statistical information than standard Monte Carlo approaches. Further more, the constructed surrogate model also enables us to directly evaluate the target property under various conformational states, yielding a more accurate response surface than standard sparse grid collocation methods. In particular, the new method provides higher accuracy in high-dimensional systems, such as biomolecules, where sparse grid performance is limited by the accuracy of the computed quantity of interest. Our new framework is generalizable and can be used to investigate the uncertainty of a wide variety of target properties in biomolecular systems.

  9. Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the Influence of Conformational Uncertainty in Biomolecular Solvation

    Energy Technology Data Exchange (ETDEWEB)

    Lei, Huan; Yang, Xiu; Zheng, Bin; Lin, Guang; Baker, Nathan A.

    2015-12-31

    Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method to quantify the uncertainty of target properties induced by conformational fluctuations. Using a generalized polynomial chaos (gPC) expansion, we construct a surrogate model of the target property with respect to varying conformational states. We also propose a method to increase the sparsity of the gPC expansion by defining a set of conformational “active space” random variables. With the increased sparsity, we employ the compressive sensing method to accurately construct the surrogate model. We demonstrate the performance of the surrogate model by evaluating fluctuation-induced uncertainty in solvent-accessible surface area for the bovine trypsin inhibitor protein system and show that the new approach offers more accurate statistical information than standard Monte Carlo approaches. Further more, the constructed surrogate model also enables us to directly evaluate the target property under various conformational states, yielding a more accurate response surface than standard sparse grid collocation methods. In particular, the new method provides higher accuracy in high-dimensional systems, such as biomolecules, where sparse grid performance is limited by the accuracy of the computed quantity of interest. Our new framework is generalizable and can be used to investigate the uncertainty of a wide variety of target properties in biomolecular systems.

  10. Advances in biomolecular surface meshing and its applications to mathematical modeling

    Institute of Scientific and Technical Information of China (English)

    CHEN MinXin; LU BenZhuo

    2013-01-01

    In the field of molecular modeling and simulation,molecular surface meshes are necessary for many problems,such as molecular structure visualization and analysis,docking problem and implicit solvent modeling and simulation.Recently,with the developments of advanced mathematical modeling in the field of implicit solvent modeling and simulation,providing surface meshes with good qualities efficiently for large real biomolecular systems becomes an urgent issue beyond its traditional purposes for visualization and geometry analyses for molecular structure.In this review,we summarize recent works on this issue.First,various definitions of molecular surfaces and corresponding meshing methods are introduced.Second,our recent meshing tool,TMSmesh,and its performances are presented.Finally,we show the applications of the molecular surface mesh in implicit solvent modeling and simulations using boundary element method (BEM) and finite element method (FEM).

  11. 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.

  12. Improvements in continuum modeling for biomolecular systems

    CERN Document Server

    Qiao, Yu

    2015-01-01

    Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulation. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and PNP equations, the coupling of polar and nonpolar interactions, and numerical progress.

  13. A statistical mechanical description of biomolecular hydration

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-02-01

    We present an efficient and accurate theoretical description of the structural hydration of biological macromolecules. The hydration of molecules of almost arbitrary size (tRNA, antibody-antigen complexes, photosynthetic reaction centre) can be studied in solution and in the crystal environment. The biomolecular structure obtained from x-ray crystallography, NMR, or modeling is required as input information. The structural arrangement of water molecules near a biomolecular surface is represented by the local water density analogous to the corresponding electron density in an x-ray diffraction experiment. The water-density distribution is approximated in terms of two- and three-particle correlation functions of solute atoms with water using a potentials-of-mean-force expansion.

  14. Visualization of confocal microscopic biomolecular data

    Science.gov (United States)

    Liu, Zhanping; Moorhead, Robert J., II

    2005-04-01

    Biomolecular visualization facilitates insightful interpretation of molecular structures and complex mechanisms underlying bio-chemical processes. Effective visualization techniques are required to deal with confocal microscopic biomolecular data in which intricate structures, fine features, and obscure patterns might be overlooked without sophisticated data processing and image synthesis. This paper presents major challenges in visualizing confocal microscopic biomolecular data, followed by a survey of related work. We then introduce a case study conducted to investigate the interaction between two proteins contained in a budding yeast saccharomyces cerevisiae by embedding custom modules in Amira. The multi-channel confocal microscopic volume data was first processed using an exponential operator to correct z-drop artifacts introduced during data acquisition. Channel correlation was then exploited to extract the overlap between the proteins as a new channel to represent the interaction while a statistical method was employed to compute the intensity of interaction to locate hot spots. To take advantage of crisp surface representation of region boundaries by iso-surfaces and visually pleasing translucent delineation of dense volumes by volume rendering, we adopted hybrid rendering that incorporates these two methods to display clear-cut protein boundaries, amorphous interior materials, and the scattered interaction in the same view volume with suppressed and highlighted parts selected by the user. The highlighted overlap helped biologists learn where the interaction happens and how it spreads, particularly when the volume was investigated in an immersive Cave Automatic Virtual Environment (CAVE) for intuitive comprehension of the data.

  15. Function of Amphiphilic Biomolecular Machines: Elastic Protein-based Polymers

    Science.gov (United States)

    Urry, Dan W.

    2000-03-01

    Elastic protein-based polymers function as biomolecular machines due to inverse temperature transitions of hydrophobic folding and assembly. The transitions occur either on raising the temperature from below to above the transition temperature, Tt, or on isothermally lowering Tt from above to below an operating temperature. The inverse temperature transition involves a decrease in entropy of the polymer component of the system on raising the temperature and a larger increase in solvent entropy on hydrophobic association. Tt depends on the quantity of hydrophobic hydration that undergoes transition to bulk water. Designed amphiphilic polymers perform free energy transductions involving the intensive variables of mechanical force, pressure, temperature, chemical potential, electrochemical potential and electromagnetic radiation and define a set of five axioms for their function as machines. The physical basis for these diverse energy conversions is competition for hydration between apolar (hydrophobic) and polar (e.g., charged) moieties. The effectiveness of these Tt-type entropic elastic protein-based machines is due to repeating peptide sequences that form regular, dynamic repeating structures and exhibit damping of backbone torsional oscillations on extension.

  16. Nanotube-Based Chemical and Biomolecular Sensors

    Institute of Scientific and Technical Information of China (English)

    J.Koh; B.Kim; S.Hong; H.Lim; H.C.Choi

    2008-01-01

    We present a brief review about recent results regarding carbon nanotube (CNT)-based chemical and biomolecular sensors. For the fabrication of CNT-based sensors, devices containing CNT channels between two metal electrodes are first fabricated usually via chemical vapor deposition (CVD) process or "surface programmed assembly" method. Then, the CNT surfaces are often functionalized to enhance the selectivity of the sensors. Using this process, highly-sensitive CNT-based sensors can be fabricated for the selective detection of various chemical and biological molecules such as hydrogen, ammonia, carbon monoxide, chlorine gas, DNA, glucose, alcohol, and proteins.

  17. Azurin for Biomolecular Electronics: a Reliability Study

    Science.gov (United States)

    Bramanti, Alessandro; Pompa, Pier Paolo; Maruccio, Giuseppe; Calabi, Franco; Arima, Valentina; Cingolani, Roberto; Corni, Stefano; Di Felice, Rosa; De Rienzo, Francesca; Rinaldi, Ross

    2005-09-01

    The metalloprotein azurin, used in biomolecular electronics, is investigated with respect to its resilience to high electric fields and ambient conditions, which are crucial reliability issues. Concerning the effect of electric fields, two models of different complexity agree indicating an unexpectedly high robustness. Experiments in device-like conditions confirm that no structural modifications occur, according to fluorescence spectra, even after a 40-min exposure to tens of MV/m. Ageing is then investigated experimentally, at ambient conditions and without field, over several days. Only a small conformational rearrangement is observed in the first tens of hours, followed by an equilibrium state.

  18. 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.

  19. 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.

  20. Bio-molecular sensors based on guided mode resonance filters

    Science.gov (United States)

    Saleem, M. R.; Ali, R.; Honkanen, S.; Turunen, J.

    2016-08-01

    In this work a low surface roughness and homogenous, high refractive index, and amorphous TiO2 layer on corrugated structures of diffractive optical element is coated by Atomic Layer Deposition (ALD) for biosensors. The design of Guided Mode Resonance Filters (GMRFs) is based on refractive indices and thicknesses of the waveguide biomolecular layers. The designed spectral shifts are calculated by Fourier Modal Method (FMM) and depend on the magnitude of the variations in refractive index of the biomolecular layer on waveguide structures. Furthermore, the sensitivity of the biomolecular sensors depends on the thickness of biomolecular layer and periodicity of the structures. The waveguide structures designed for larger periods show an enhancement in the sensitivity (nm/RIU) of the biomolecular sensor at longer wavelengths. The periodicities of nanophotonic structures are varied from 300 to 500 nm in design calculations with predominance of increase in effective index of the structure to support leaky waveguide modes.

  1. Coassembly of aromatic dipeptides into biomolecular necklaces.

    Science.gov (United States)

    Yuran, Sivan; Razvag, Yair; Reches, Meital

    2012-11-27

    This paper describes the formation of complex peptide-based structures by the coassembly of two simple peptides, the diphenylalanine peptide and its tert-butyl dicarbonate (Boc) protected analogue. Each of these peptides can self-assemble into a distinct architecture: the diphenylalanine peptide into tubular structures and its analogue into spheres. Integrated together, these peptides coassemble into a construction of beaded strings, where spherical assemblies are connected by elongated elements. Electron and scanning force microscopy demonstrated the morphology of these structures, which we termed "biomolecular necklaces". Additional experiments indicated the reversibility of the coassembly process and the stability of the structures. Furthermore, we suggest a possible mechanism of formation for the biomolecular necklaces. Our suggestion is based on the necklace model for polyelectrolyte chains, which proposes that a necklace structure appears as a result of counterion condensation on the backbone of a polyelectrolyte. Overall, the approach of coassembly, demonstrated using aromatic peptides, can be adapted to any peptides and may lead to the development and discovery of new self-assembled architectures formed by peptides and other biomolecules. PMID:23061818

  2. Improvements in continuum modeling for biomolecular systems

    Science.gov (United States)

    Yu, Qiao; Ben-Zhuo, Lu

    2016-01-01

    Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson- Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of the biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress. Project supported by the National Natural Science Foundation of China (Grant No. 91230106) and the Chinese Academy of Sciences Program for Cross & Cooperative Team of the Science & Technology Innovation.

  3. Biomolecular detection with a thin membrane transducer.

    Science.gov (United States)

    Cha, Misun; Shin, Jaeha; Kim, June-Hyung; Kim, Ilchaek; Choi, Junbo; Lee, Nahum; Kim, Byung-Gee; Lee, Junghoon

    2008-06-01

    We present a thin membrane transducer (TMT) that can detect nucleic acid based biomolecular reactions including DNA hybridization and protein recognition by aptamers. Specific molecular interactions on an extremely thin and flexible membrane surface cause the deflection of the membrane due to surface stress change which can be measured by a compact capacitive circuit. A gold-coated thin PDMS membrane assembled with metal patterned glass substrate is used to realize the capacitive detection. It is demonstrated that perfect match and mismatch hybridizations can be sharply discriminated with a 16-mer DNA oligonucleotide immobilized on the gold-coated surface. While the mismatched sample caused little capacitance change, the perfectly matched sample caused a well-defined capacitance decrease vs. time due to an upward deformation of the membrane by a compressive surface stress. Additionally, the TMT demonstrated the single nucleotide polymorphism (SNP) capabilities which enabled a detection of mismatching base pairs in the middle of the sequence. It is intriguing that the increase of capacitance, therefore a downward deflection due to tensile stress, was observed with the internal double mismatch hybridization. We further present the detection of thrombin protein through ligand-receptor type recognition with 15-mer thrombin aptamer as a receptor. Key aspects of this detection such as the effect of concentration variation are investigated. This capacitive thin membrane transducer presents a completely new approach for detecting biomolecular reactions with high sensitivity and specificity without molecular labelling and optical measurement. PMID:18497914

  4. Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

    Science.gov (United States)

    Zhou, Shenggao; Sun, Hui; Cheng, Li-Tien; Dzubiella, Joachim; Li, Bo; McCammon, J. Andrew

    2016-08-01

    Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the "normal velocity" that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of

  5. Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations.

    Science.gov (United States)

    Zhou, Shenggao; Sun, Hui; Cheng, Li-Tien; Dzubiella, Joachim; Li, Bo; McCammon, J Andrew

    2016-08-01

    Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the "normal velocity" that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of

  6. Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations.

    Science.gov (United States)

    Zhou, Shenggao; Sun, Hui; Cheng, Li-Tien; Dzubiella, Joachim; Li, Bo; McCammon, J Andrew

    2016-08-01

    Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the "normal velocity" that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of

  7. Biomolecular Structure Determination with Divide and Concur

    Science.gov (United States)

    Kallus, Yoav; Elser, Veit

    2009-03-01

    Divide and concur (D-C) is a general computational approach, designed for the solution of highly frustrated problems. Recently applied to the problems of disk packing, the kissing number problem, and 3-SAT, it was competitive or outperformed special-purpose methods.ootnotetextS. Gravel and V. Elser, Phys. Rev. E 78, 036706 (2008) We present a method for applying the D-C framework to the problem of biomolecular structure determination. From a list of geometric constraints on groups of atoms in the molecule, we construct a deterministic iterative map that efficiently searches for structures simultaneously satisfying all constraints. As our method eschews an energy function and its minimization to focus on geometric constraints, it can very naturally integrate with the geometric constraints due to chemistry and physics, experimental constraints due to NMR data or many other experimental or biological hints. We present some results of our method.

  8. 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.

  9. Nonequilibrium phase transitions in biomolecular signal transduction

    Science.gov (United States)

    Smith, Eric; Krishnamurthy, Supriya; Fontana, Walter; Krakauer, David

    2011-11-01

    We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state transitions of any molecule, by means of which the switch is implemented, are highly stochastic. The emergence of switching is a nonequilibrium phase transition in an energetically driven, dissipative system described by a master equation. We use operator and functional integral methods from reaction-diffusion theory to solve for the phase structure, noise spectrum, and escape trajectories and first-passage times of a class of minimal models of switches, showing how all critical properties for switch behavior can be computed within a unified framework.

  10. Micro- and nanodevices integrated with biomolecular probes

    Science.gov (United States)

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

    2016-01-01

    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. PMID:26363089

  11. [Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). Implications for pathology].

    Science.gov (United States)

    Viertler, C; Zatloukal, K

    2008-11-01

    High quality human biological samples (e.g. blood, tissue or DNA) with associated, well documented clinical and research data are key resources for advancement of life sciences, biotechnology, clinical medicine, drug development and also molecular pathology. Millions of samples of diseased tissues have been collected in the context of routine histopathological diagnosis and are stored in the archives of hospitals and institutes of pathology. A concerted effort is necessary to overcome the current fragmentation of the European biobanking community in order to tap the full research potential of existing biobanks. A pan-European research infrastructure for biobanking and biomolecular resources (BBMRI) is currently in its planning phase. The mission is to link and provide access to local biobanks of different formats, including tissue collections, harmonize standards, establish operational procedures which properly consider ethical, legal, societal aspects, and to secure sustainable funding. Pathology plays a key role in development and administration of tissue banks and is, thus, a major partner for collaboration, expertise and construction of this pan-European research infrastructure.

  12. Biomolecular simulation on thousands of processors

    Science.gov (United States)

    Phillips, James Christopher

    Classical molecular dynamics simulation is a generally applicable method for the study of biomolecular aggregates of proteins, lipids, and nucleic acids. As experimental techniques have revealed the structures of larger and more complex biomolecular machines, the time required to complete even a single meaningful simulation of such systems has become prohibitive. We have developed the program NAMD to simulate systems of 50,000--500,000 atoms efficiently with full electrostatics on parallel computers with 1000 and more processors. NAMD's scalability is achieved through latency tolerant adaptive message-driven execution and measurement-based load balancing. NAMD is implemented in C++ and uses object-oriented design and threads to shield the basic algorithms from the necessary complexity of high-performance parallel execution. Apolipoprotein A-I is the primary protein constituent of high density lipoprotein particles, which transport cholesterol in the bloodstream. In collaboration with A. Jonas, we have constructed and simulated models of the nascent discoidal form of these particles, providing theoretical insight to the debate regarding the lipid-bound structure of the protein. Recently, S. Sligar and coworkers have created 10 nm phospholipid bilayer nanoparticles comprising a small lipid bilayer disk solubilized by synthetic membrane scaffold proteins derived from apolipoprotein A-I. Membrane proteins may be embedded in the water-soluble disks, with various medical and technological applications. We are working to develop variant scaffold proteins that produce disks of greater size, stability, and homogeneity. Our simulations have demonstrated a significant deviation from idealized cylindrical structure, and are being used in the interpretation of small angle x-ray scattering data.

  13. Solvent substitution

    Energy Technology Data Exchange (ETDEWEB)

    1990-01-01

    The DOE Environmental Restoration and Waste Management Office of Technology Development and the Air Force Engineering and Services Center convened the First Annual International Workshop on Solvent Substitution on December 4--7, 1990. The primary objectives of this joint effort were to share information and ideas among attendees in order to enhance the development and implementation of required new technologies for the elimination of pollutants associated with industrial use of hazardous and toxic solvents; and to aid in accelerating collaborative efforts and technology transfer between government and industry for solvent substitution. There were workshop sessions focusing on Alternative Technologies, Alternative Solvents, Recovery/Recycling, Low VOC Materials and Treatment for Environmentally Safe Disposal. The 35 invited papers presented covered a wide range of solvent substitution activities including: hardware and weapons production and maintenance, paint stripping, coating applications, printed circuit boards, metal cleaning, metal finishing, manufacturing, compliance monitoring and process control monitoring. This publication includes the majority of these presentations. In addition, in order to further facilitate information exchange and technology transfer, the US Air Force and DOE solicited additional papers under a general Call for Papers.'' These papers, which underwent review and final selection by a peer review committee, are also included in this combined Proceedings/Compendium. For those involved in handling, using or managing hazardous and toxic solvents, this document should prove to be a valuable resource, providing the most up-to-date information on current technologies and practices in solvent substitution. Individual papers are abstracted separated.

  14. Solvent substitution

    International Nuclear Information System (INIS)

    The DOE Environmental Restoration and Waste Management Office of Technology Development and the Air Force Engineering and Services Center convened the First Annual International Workshop on Solvent Substitution on December 4--7, 1990. The primary objectives of this joint effort were to share information and ideas among attendees in order to enhance the development and implementation of required new technologies for the elimination of pollutants associated with industrial use of hazardous and toxic solvents; and to aid in accelerating collaborative efforts and technology transfer between government and industry for solvent substitution. There were workshop sessions focusing on Alternative Technologies, Alternative Solvents, Recovery/Recycling, Low VOC Materials and Treatment for Environmentally Safe Disposal. The 35 invited papers presented covered a wide range of solvent substitution activities including: hardware and weapons production and maintenance, paint stripping, coating applications, printed circuit boards, metal cleaning, metal finishing, manufacturing, compliance monitoring and process control monitoring. This publication includes the majority of these presentations. In addition, in order to further facilitate information exchange and technology transfer, the US Air Force and DOE solicited additional papers under a general ''Call for Papers.'' These papers, which underwent review and final selection by a peer review committee, are also included in this combined Proceedings/Compendium. For those involved in handling, using or managing hazardous and toxic solvents, this document should prove to be a valuable resource, providing the most up-to-date information on current technologies and practices in solvent substitution. Individual papers are abstracted separated

  15. Biomolecular crystals for material applications and a mechanistic study of an iron oxide nanoparticle synthesis

    Science.gov (United States)

    Falkner, Joshua Charles

    The three projects within this work address the difficulties of controlling biomolecular crystal formats (i.e. size and shape), producing 3-D ordered composite materials from biomolecular crystal templates, and understanding the mechanism of a practical iron oxide synthesis. The unifying thread consistent throughout these three topics is the development of methods to manipulate nanomaterials using a bottom-up approach. Biomolecular crystals are nanometer to millimeter sized crystals that have well ordered mesoporous solvent channels. The overall physical dimensions of these crystals are highly dependent on crystallization conditions. The controlled growth of micro- and nanoprotein crystals was studied to provide new pathways for creating smaller crystalline protein materials. This method produced tetragonal hen egg-white lysozyme crystals (250--100,000 nm) with near monodisperse size distributions (membranes or templates. In this work, the porous structure of larger cowpea mosaic virus crystals was used to template metal nanoparticle growth within the body centered cubic crystalline network. The final composite material was found to have long range ordering of palladium and platinum nonocrystal aggregates (10nm) with symmetry consistent to the virus template. Nanoparticle synthesis itself is an immense field of study with an array of diverse applications. The final piece of this work investigates the mechanism behind a previously developed iron oxide synthesis to gain more understanding and direction to future synthesis strategies. The particle growth mechanism was found to proceed by the formation of a solvated iron(III)oleate complex followed by a reduction of iron (III) to iron (II). This unstable iron(II) nucleates to form a wustite (FeO) core which serves as an epitaxial surface for the magnetite (Fe3O4) shell growth. This method produces spherical particles (6-60nm) with relative size distributions of less than 15%.

  16. Microwave spectroscopy of biomolecular building blocks.

    Science.gov (United States)

    Alonso, José L; López, Juan C

    2015-01-01

    Microwave spectroscopy, considered as the most definitive gas phase structural probe, is able to distinguish between different conformational structures of a molecule, because they have unique spectroscopic constants and give rise to distinct individual rotational spectra.Previously, application of this technique was limited to molecular specimens possessing appreciable vapor pressures, thus discarding the possibility of studying many other molecules of biological importance, in particular those with high melting points, which had a tendency to undergo thermal reactions, and ultimately degradation, upon heating.Nowadays, the combination of laser ablation with Fourier transform microwave spectroscopy techniques, in supersonic jets, has enabled the gas-phase study of such systems. In this chapter, these techniques, including broadband spectroscopy, as well as results of their application into the study of the conformational panorama and structure of biomolecular building blocks, such as amino acids, nucleic bases, and monosaccharides, are briefly discussed, and with them, the tools for conformational assignation - rotational constants, nuclear quadrupole coupling interaction, and dipole moment. PMID:25721775

  17. 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.

  18. 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.

  19. Solvent substitutes

    International Nuclear Information System (INIS)

    The environmental and industrial hygiene regulations promulgated since 1980, most notably the Superfund Amendments and Reauthorization Act (SARA), the Hazardous and Solid Waste Amendments to the Resources Conservation and Recovery Act (RCRA), and the Clean Air Act Amendments of 1990, have brought about an increased emphasis on user exposure, hazardous waste generation, and air emissions. As a result, industry is performing a fundamental reassessment of cleaning solvents, processes, and procedures. The more progressive organizations have made their goal the elimination of solvents that may pose significant potential human health and environmental hazards. This chapter discusses solvent cleaning in metal-finishing, metal-manufacturing, and industrial maintenance applications; precision cleaning; and electronics manufacturing. Nonmetallic cleaning, adhesives, coatings, inks, and aerosols also will be addressed, but in a more cursory manner

  20. Biomolecular Modification of Inorganic Crystal Growth

    Energy Technology Data Exchange (ETDEWEB)

    De Yoreo, J J

    2007-04-27

    The fascinating shapes and hierarchical designs of biomineralized structures are an inspiration to materials scientists because of the potential they suggest for biomolecular control over materials synthesis. Conversely, the failure to prevent or limit tissue mineralization in the vascular, skeletal, and urinary systems is a common source of disease. Understanding the mechanisms by which organisms direct or limit crystallization has long been a central challenge to the biomineralization community. One prevailing view is that mineral-associated macromolecules are responsible for either inhibiting crystallization or initiating and stabilizing non-equilibrium crystal polymorphs and morphologies through interactions between anionic moieties and cations in solution or at mineralizing surfaces. In particular, biomolecules that present carboxyl groups to the growing crystal have been implicated as primary modulators of growth. Here we review the results from a combination of in situ atomic force microscopy (AFM) and molecular modeling (MM) studies to investigate the effect of specific interactions between carboxylate-rich biomolecules and atomic steps on crystal surfaces during the growth of carbonates, oxalates and phosphates of calcium. Specifically, we how the growth kinetics and morphology depend on the concentration of additives that include citrate, simple amino acids, synthetic Asp-rich polypeptides, and naturally occurring Asp-rich proteins found in both functional and pathological mineral tissues. The results reveal a consistent picture of shape modification in which stereochemical matching of modifiers to specific atomic steps drives shape modification. Inhibition and other changes in growth kinetics are shown to be due to a range of mechanisms that depend on chemistry and molecular size. Some effects are well described by classic crystal growth theories, but others, such as step acceleration due to peptide charge and hydrophylicity, were previously unrealized

  1. Nanoscale field effect transistor for biomolecular signal amplification

    CERN Document Server

    Chen, Yu; Hong, Mi K; Erramilli, Shyamsunder; Rosenberg, Carol; Mohanty, Pritiraj

    2008-01-01

    We report amplification of biomolecular recognition signal in lithographically defined silicon nanochannel devices. The devices are configured as field effect transistors (FET) in the reversed source-drain bias region. The measurement of the differential conductance of the nanowire channels in the FET allows sensitive detection of changes in the surface potential due to biomolecular binding. Narrower silicon channels demonstrate higher sensitivity to binding due to increased surface-to-volume ratio. The operation of the device in the negative source-drain region demonstrates signal amplification. The equivalence between protein binding and change in the surface potential is described.

  2. Solvent Immersion Imprint Lithography

    Energy Technology Data Exchange (ETDEWEB)

    Vasdekis, Andreas E.; Wilkins, Michael J.; Grate, Jay W.; Kelly, Ryan T.; Konopka, Allan; Xantheas, Sotiris S.; Chang, M. T.

    2014-06-21

    The mechanism of polymer disolution was explored for polymer microsystem prototyping, including microfluidics and optofluidics. Polymer films are immersed in a solvent, imprinted and finally brought into contact with a non-modified surface to permanently bond. The underlying polymer-solvent interactions were experimentally and theoretically investigated, and enabled rapid polymer microsystem prototyping. During imprinting, small molecule integration in the molded surfaces was feasible, a principle applied to oxygen sensing. Polystyrene (PS) was employed for microbiological studies at extreme environmental conditions. The thermophile anaerobe Clostridium Thermocellum was grown in PS pore-scale micromodels, revealing a double mean generation lifetime than under ideal culture conditions. Microsystem prototyping through directed polymer dissolution is simple and accessible, while simultaneous patterning, bonding, and surface/volume functionalization are possible in less than one minute.

  3. 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.

  4. Solvent cavitation under solvophobic confinement.

    Science.gov (United States)

    Ashbaugh, Henry S

    2013-08-14

    The stability of liquids under solvophobic confinement can tip in favor of the vapor phase, nucleating a liquid-to-vapor phase transition that induces attractive forces between confining surfaces. In the case of water adjacent to hydrophobic surfaces, experimental and theoretical evidence support confinement-mediated evaporation stabilization of biomolecular and colloidal assemblies. The macroscopic thermodynamic theory of cavitation under confinement establishes the connection between the size of the confining surfaces, interfacial free energies, and bulk solvent pressure with the critical evaporation separation and interfacial forces. While molecular simulations have confirmed the broad theoretical trends, a quantitative comparison based on independent measurements of the interfacial free energies and liquid-vapor coexistence properties has, to the best of our knowledge, not yet been performed. To overcome the challenges of simulating a large number of systems to validate scaling predictions for a three-dimensional fluid, we simulate both the forces and liquid-vapor coexistence properties of a two-dimensional Lennard-Jones fluid confined between solvophobic plates over a range of plate sizes and reservoir pressures. Our simulations quantitatively agree with theoretical predictions for solvent-mediated forces and critical evaporation separations once the length dependence of the solvation free energy of an individual confining plate is taken into account. The effective solid-liquid line tension length dependence results from molecular scale correlations for solvating microscopic plates and asymptotically decays to the macroscopic value for plates longer than 150 solvent diameters. The success of the macroscopic thermodynamic theory at describing two-dimensional liquids suggests application to surfactant monolayers to experimentally confirm confinement-mediated cavitation. PMID:23947875

  5. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy

    DEFF Research Database (Denmark)

    Ardenkjær-Larsen, Jan Henrik; Boebinger, Gregory S.; Comment, Arnaud;

    2015-01-01

    In the Spring of 2013, NMR spectroscopists convened at the Weizmann Institute in Israel to brainstorm on approaches to improve the sensitivity of NMR experiments, particularly when applied in biomolecular settings. This multi‐author interdisciplinary Review presents a state‐of‐the‐art description...

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

    NARCIS (Netherlands)

    de Vries, S.J.; van Dijk, M.; Bonvin, A.M.J.J.

    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

  7. 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 method

  8. Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Hummer, G.; Garcia, A.E. [Los Alamos National Lab., NM (United States). Theoretical Biology and Biophysics Group; Soumpasis, D.M. [Max-Planck-Inst for Biophysical Chemistry, Goettingen (Germany). Biocomputation Group

    1994-10-01

    To understand the functioning of living organisms on a molecular level, it is crucial to dissect the intricate interplay of the immense number of biological molecules. Most of the biochemical processes in cells occur in a liquid environment formed mainly by water and ions. This solvent environment plays an important role in biological systems. The potential-of-mean-force (PMF) formalism attempts to describe quantitatively the interactions of the solvent with biological macromolecules on the basis of an approximate statistical-mechanical representation. At its current status of development, it deals with ionic effects on the biomolecular structure and with the structural hydration of biomolecules. The underlying idea of the PMF formalism is to identify the dominant sources of interactions and incorporate these interactions into the theoretical formalism using PMF`s (or particle correlation functions) extracted from bulk-liquid systems. In the following, the authors shall briefly outline the statistical-mechanical foundation of the PMF formalism and introduce the PMF expansion formalism, which is intimately linked to superposition approximations for higher-order particle correlation functions. The authors shall then sketch applications, which describe the effects of the ionic environment on nucleic-acid structure. Finally, the authors shall present the more recent extension of the PMF idea to describe quantitatively the structural hydration of biomolecules. Results for the interface of ice and water and for the hydration of deoxyribonucleic acid (DNA) will be discussed.

  9. A self-regulating biomolecular comparator for processing oscillatory signals.

    Science.gov (United States)

    Agrawal, Deepak K; Franco, Elisa; Schulman, Rebecca

    2015-10-01

    While many cellular processes are driven by biomolecular oscillators, precise control of a downstream on/off process by a biochemical oscillator signal can be difficult: over an oscillator's period, its output signal varies continuously between its amplitude limits and spends a significant fraction of the time at intermediate values between these limits. Further, the oscillator's output is often noisy, with particularly large variations in the amplitude. In electronic systems, an oscillating signal is generally processed by a downstream device such as a comparator that converts a potentially noisy oscillatory input into a square wave output that is predominantly in one of two well-defined on and off states. The comparator's output then controls downstream processes. We describe a method for constructing a synthetic biochemical device that likewise produces a square-wave-type biomolecular output for a variety of oscillatory inputs. The method relies on a separation of time scales between the slow rate of production of an oscillatory signal molecule and the fast rates of intermolecular binding and conformational changes. We show how to control the characteristics of the output by varying the concentrations of the species and the reaction rates. We then use this control to show how our approach could be applied to process different in vitro and in vivo biomolecular oscillators, including the p53-Mdm2 transcriptional oscillator and two types of in vitro transcriptional oscillators. These results demonstrate how modular biomolecular circuits could, in principle, be combined to build complex dynamical systems. The simplicity of our approach also suggests that natural molecular circuits may process some biomolecular oscillator outputs before they are applied downstream. PMID:26378119

  10. Prediction of Water Binding to Protein Hydration Sites with a Discrete, Semiexplicit Solvent Model.

    Science.gov (United States)

    Setny, Piotr

    2015-12-01

    Buried water molecules are ubiquitous in protein structures and are found at the interface of most protein-ligand complexes. Determining their distribution and thermodynamic effect is a challenging yet important task, of great of practical value for the modeling of biomolecular structures and their interactions. In this study, we present a novel method aimed at the prediction of buried water molecules in protein structures and estimation of their binding free energies. It is based on a semiexplicit, discrete solvation model, which we previously introduced in the context of small molecule hydration. The method is applicable to all macromolecular structures described by a standard all-atom force field, and predicts complete solvent distribution within a single run with modest computational cost. We demonstrate that it indicates positions of buried hydration sites, including those filled by more than one water molecule, and accurately differentiates them from sterically accessible to water but void regions. The obtained estimates of water binding free energies are in fair agreement with reference results determined with the double decoupling method. PMID:26642995

  11. 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...

  12. Association of Biomolecular Resource Facilities Survey: Service Laboratory Funding

    OpenAIRE

    Ogorzalek Loo, Rachel; Nicolet, Charles M.; Niece, Ronald L.; Young, Mary; Simpson, John T.

    2009-01-01

    In 2007, The Association of Biomolecular Resource Facilities (ABRF) Survey Committee surveyed the ABRF membership and scientists at-large concerning the current state of funding in service-oriented laboratories. Questions pertained to services offered, cost recovery, capital equipment funding, and future outlook. The web-based survey, available for 3 weeks, achieved participation from 209 respondents in 13 countries, 77% of which represented academic laboratories. Most respondents (75%) direc...

  13. Biomolecular Detection employing the Interferometric Reflectance Imaging Sensor (IRIS)

    OpenAIRE

    Carlos A Lopez; George G Daaboul; Ahn, Sunmin; Reddington, Alexander P.; Monroe, Margo R.; Zhang, Xirui; Irani, Rostem J.; Yu, Chunxiao; Genco, Caroline A.; Cretich, Marina; Chiari, Marcella; Goldberg, Bennett B.; Connor, John H.; Ünlü, M. Selim

    2011-01-01

    The sensitive measurement of biomolecular interactions has use in many fields and industries such as basic biology and microbiology, environmental/agricultural/biodefense monitoring, nanobiotechnology, and more. For diagnostic applications, monitoring (detecting) the presence, absence, or abnormal expression of targeted proteomic or genomic biomarkers found in patient samples can be used to determine treatment approaches or therapy efficacy. In the research arena, information on molecular aff...

  14. Retroactivity in the Context of Modularly Structured Biomolecular Systems

    Science.gov (United States)

    Pantoja-Hernández, Libertad; Martínez-García, Juan Carlos

    2015-01-01

    Synthetic biology has intensively promoted the technical implementation of modular strategies in the fabrication of biological devices. Modules are considered as networks of reactions. The behavior displayed by biomolecular systems results from the information processes carried out by the interconnection of the involved modules. However, in natural systems, module wiring is not a free-of-charge process; as a consequence of interconnection, a reactive phenomenon called retroactivity emerges. This phenomenon is characterized by signals that propagate from downstream modules (the modules that receive the incoming signals upon interconnection) to upstream ones (the modules that send the signals upon interconnection). Such retroactivity signals, depending of their strength, may change and sometimes even disrupt the behavior of modular biomolecular systems. Thus, analysis of retroactivity effects in natural biological and biosynthetic systems is crucial to achieve a deeper understanding of how this interconnection between functionally characterized modules takes place and how it impacts the overall behavior of the involved cell. By discussing the modules interconnection in natural and synthetic biomolecular systems, we propose that such systems should be considered as quasi-modular. PMID:26137457

  15. Solvent wash solution

    Science.gov (United States)

    Neace, James C.

    1986-01-01

    Process for removing diluent degradation products from a solvent extraction solution, which has been used to recover uranium and plutonium from spent nuclear fuel. A wash solution and the solvent extraction solution are combined. The wash solution contains (a) water and (b) up to about, and including, 50 volume percent of at least one-polar water-miscible organic solvent based on the total volume of the water and the highly-polar organic solvent. The wash solution also preferably contains at least one inorganic salt. The diluent degradation products dissolve in the highly-polar organic solvent and the organic solvent extraction solvent do not dissolve in the highly-polar organic solvent. The highly-polar organic solvent and the extraction solvent are separated.

  16. Deep eutectic solvents: sustainable media for nanoscale and functional materials.

    Science.gov (United States)

    Wagle, Durgesh V; Zhao, Hua; Baker, Gary A

    2014-08-19

    Deep eutectic solvents (DESs) represent an alternative class of ionic fluids closely resembling room-temperature ionic liquids (RTILs), although, strictly speaking, they are distinguished by the fact that they also contain an organic molecular component (typically, a hydrogen bond donor like a urea, amide, acid, or polyol), frequently as the predominant constituent. Practically speaking, DESs are attractive alternatives to RTILs, sharing most of their remarkable qualities (e.g., tolerance to humidity, negligible vapor pressure, thermostability, wide electrochemical potential windows, tunability) while overcoming several limitations associated with their RTIL cousins. Particularly, DESs are typically, less expensive, more synthetically accessible (typically, from bulk commodity chemicals using solvent/waste-free processes), nontoxic, and biodegradable. In this Account, we provide an overview of DESs as designer solvents to create well-defined nanomaterials including shape-controlled nanoparticles, electrodeposited films, metal-organic frameworks, colloidal assemblies, hierarchically porous carbons, and DNA/RNA architectures. These breakthroughs illustrate how DESs can fulfill multiple roles in directing chemistry at the nanoscale: acting as supramolecular template, metal/carbon source, sacrificial agent (e.g., ammonia release from urea), and/or redox agent, all in the absence of formal stabilizing ligand (here, solvent and stabilizer are one and the same). The ability to tailor the physicochemical properties of DESs is central to controlling their interfacial behavior. The preorganized "supramolecular" nature of DESs provides a soft template to guide the formation of bimodal porous carbon networks or the evolution of electrodeposits. A number of essential parameters (viscosity, polarity, surface tension, hydrogen bonding), plus coordination with solutes/surfaces, all play significant roles in modulating species reactivity and mass transport properties governing the

  17. 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.

  18. Perspective: Coarse-grained models for biomolecular systems

    Science.gov (United States)

    Noid, W. G.

    2013-09-01

    By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.

  19. 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.

  20. Knowledge based cluster ensemble for cancer discovery from biomolecular data.

    Science.gov (United States)

    Yu, Zhiwen; Wongb, Hau-San; You, Jane; Yang, Qinmin; Liao, Hongying

    2011-06-01

    The adoption of microarray techniques in biological and medical research provides a new way for cancer diagnosis and treatment. In order to perform successful diagnosis and treatment of cancer, discovering and classifying cancer types correctly is essential. Class discovery is one of the most important tasks in cancer classification using biomolecular data. Most of the existing works adopt single clustering algorithms to perform class discovery from biomolecular data. However, single clustering algorithms have limitations, which include a lack of robustness, stability, and accuracy. In this paper, we propose a new cluster ensemble approach called knowledge based cluster ensemble (KCE) which incorporates the prior knowledge of the data sets into the cluster ensemble framework. Specifically, KCE represents the prior knowledge of a data set in the form of pairwise constraints. Then, the spectral clustering algorithm (SC) is adopted to generate a set of clustering solutions. Next, KCE transforms pairwise constraints into confidence factors for these clustering solutions. After that, a consensus matrix is constructed by considering all the clustering solutions and their corresponding confidence factors. The final clustering result is obtained by partitioning the consensus matrix. Comparison with single clustering algorithms and conventional cluster ensemble approaches, knowledge based cluster ensemble approaches are more robust, stable and accurate. The experiments on cancer data sets show that: 1) KCE works well on these data sets; 2) KCE not only outperforms most of the state-of-the-art single clustering algorithms, but also outperforms most of the state-of-the-art cluster ensemble approaches.

  1. 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.

  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. Programming in Biomolecular Computation: Programs, Self-Interpretation and Visualisation

    Directory of Open Access Journals (Sweden)

    J.G. Simonsen

    2011-01-01

    Full Text Available 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 and without arcane encodings of data and algorithm; it is also uniform: new ``hardware'' is not needed to solve new problems; and (last but not least it is Turing complete in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient.

  4. Solvent resistant nanofiltration membranes

    OpenAIRE

    Dutczak, Szymon Maria

    2011-01-01

    This thesis describes preparation and characterization of membranes for organic solvent filtration (OSF). The main aim was developing membranes for solvent resistant nanofiltration (SRNF) with molecular weight cut-off below 500 g mol-1.

  5. Organic Solvent Tropical Report

    International Nuclear Information System (INIS)

    This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an unmitigated organic solvent fire is within risk evaluation guidelines

  6. Predispersed solvent extraction

    OpenAIRE

    Rodarte, Alma Isabel Marín

    1988-01-01

    A new solvent extraction method has been developed for the extraction of metal and organic ions from very dilute aqueous solutions. The new method, which has been named Predispersed Solvent Extraction (POSE), is based on the principle that 1 there is no need to comminute both phases. All that is necessary is to comminute the solvent phase prior to contacting it with the feed. This is done by converting the solvent into aphrons, which are micron-sized globules encapsulated in a ...

  7. Solvent recycle/recovery

    Energy Technology Data Exchange (ETDEWEB)

    Paffhausen, M.W.; Smith, D.L.; Ugaki, S.N.

    1990-09-01

    This report describes Phase I of the Solvent Recycle/Recovery Task of the DOE Chlorinated Solvent Substitution Program for the US Air Force by the Idaho National Engineering Laboratory, EG G Idaho, Inc., through the US Department of Energy, Idaho Operations Office. The purpose of the task is to identify and test recovery and recycling technologies for proposed substitution solvents identified by the Biodegradable Solvent Substitution Program and the Alternative Solvents/Technologies for Paint Stripping Program with the overall objective of minimizing hazardous wastes. A literature search to identify recycle/recovery technologies and initial distillation studies has been conducted. 4 refs.

  8. Flavin mononucleotide biomolecular laser: longitudinal mode structure, polarization, and temporal characteristics as probes of local chemical environment.

    Science.gov (United States)

    Rivera, José A; Eden, J Gary

    2016-05-16

    A detailed characterization of the flavin mononucleotide (FMN) biomolecular laser, optically pumped in a stable resonator, is reported here. Photoexcitation of the molecule at 355 nm results in lasing over the ~566.5-573.5 nm spectral region, and the threshold pump energy density is measured to be 110 ± 10 µJ/mm2 for a 10 mM FMN/water solution. Over twenty longitudinal modes are observed when the cavity length L and the energy pump fluence Ep are 375 µm and 300 µJ/mm2, respectively. Partial substitution of glycerol for water as the solvent results in a factor of four reduction in the threshold pump energy fluence (to 2) and a quadrupling of the slope efficiency. This effect is attributed to the O2 - mediated photoconversion of FMN molecules in the triplet state to the singlet species. For pump intensities a factor of 2.5 above threshold, the laser pulse width is ~2 ns FWHM, and the output intensity decays exponentially with a photon lifetime of 1.7 ns. The addition of glycerol to a FMN/water solution also suppresses s-polarized emission (yielding P = 0.78 ± 0.08), presumably as a result of the inhibition of FMN rotational diffusion. The sensitivity of the spectral and optical properties of this and other biomolecular lasers to the chemical environment underscores the value of coherent emission as a biochemical or biomedical diagnostic tool, particularly insofar as molecule-molecule interactions are concerned. PMID:27409906

  9. The biomolecular corona of nanoparticles in circulating biological media

    Science.gov (United States)

    Pozzi, D.; Caracciolo, G.; Digiacomo, L.; Colapicchioni, V.; Palchetti, S.; Capriotti, A. L.; Cavaliere, C.; Zenezini Chiozzi, R.; Puglisi, A.; Laganà, A.

    2015-08-01

    When nanoparticles come into contact with biological media, they are covered by a biomolecular `corona', which confers a new identity to the particles. In all the studies reported so far nanoparticles are incubated with isolated plasma or serum that are used as a model for protein adsorption. Anyway, bodily fluids are dynamic in nature so the question arises on whether the incubation protocol, i.e. dynamic vs. static incubation, could affect the composition and structure of the biomolecular corona. Here we let multicomponent liposomes interact with fetal bovine serum (FBS) both statically and dynamically, i.e. in contact with circulating FBS (~40 cm s-1). The structure and composition of the liposome-protein corona, as determined by dynamic light scattering, electrophoretic light scattering and liquid chromatography tandem mass spectrometry, were found to be dependent on the incubation protocol. Specifically, following dynamic exposure to FBS, multicomponent liposomes were less enriched in complement proteins and appreciably more enriched in apolipoproteins and acute phase proteins (e.g. alpha-1-antitrypsin and inter-alpha-trypsin inhibitor heavy chain H3) that are involved in relevant interactions between nanoparticles and living systems. Supported by our results, we speculate that efficient predictive modeling of nanoparticle behavior in vivo will require accurate knowledge of nanoparticle-specific protein fingerprints in circulating biological media.When nanoparticles come into contact with biological media, they are covered by a biomolecular `corona', which confers a new identity to the particles. In all the studies reported so far nanoparticles are incubated with isolated plasma or serum that are used as a model for protein adsorption. Anyway, bodily fluids are dynamic in nature so the question arises on whether the incubation protocol, i.e. dynamic vs. static incubation, could affect the composition and structure of the biomolecular corona. Here we let

  10. Biomolecular Simulation of Base Excision Repair and Protein Signaling

    Energy Technology Data Exchange (ETDEWEB)

    Straatsma, TP; McCammon, J A; Miller, John H; Smith, Paul E; Vorpagel, Erich R; Wong, Chung F; Zacharias, Martin W

    2006-03-03

    The goal of the Biomolecular Simulation of Base Excision Repair and Protein Signaling project is to enhance our understanding of the mechanism of human polymerase-β, one of the key enzymes in base excision repair (BER) and the cell-signaling enzymes cyclic-AMP-dependent protein kinase. This work used molecular modeling and simulation studies to specifically focus on the • dynamics of DNA and damaged DNA • dynamics and energetics of base flipping in DNA • mechanism and fidelity of nucleotide insertion by BER enzyme human polymerase-β • mechanism and inhibitor design for cyclic-AMP-dependent protein kinase. Molecular dynamics simulations and electronic structure calculations have been performed using the computer resources at the Molecular Science Computing Facility at the Environmental Molecular Sciences Laboratory.

  11. Insights into cancer severity from biomolecular interaction mechanisms

    Science.gov (United States)

    Raimondi, Francesco; Singh, Gurdeep; Betts, Matthew J.; Apic, Gordana; Vukotic, Ranka; Andreone, Pietro; Stein, Lincoln; Russell, Robert B.

    2016-01-01

    To attain a deeper understanding of diseases like cancer, it is critical to couple genetics with biomolecular mechanisms. High-throughput sequencing has identified thousands of somatic mutations across dozens of cancers, and there is a pressing need to identify the few that are pathologically relevant. Here we use protein structure and interaction data to interrogate nonsynonymous somatic cancer mutations, identifying a set of 213 molecular interfaces (protein-protein, -small molecule or –nucleic acid) most often perturbed in cancer, highlighting several potentially novel cancer genes. Over half of these interfaces involve protein-small-molecule interactions highlighting their overall importance in cancer. We found distinct differences in the predominance of perturbed interfaces between cancers and histological subtypes and presence or absence of certain interfaces appears to correlate with cancer severity. PMID:27698488

  12. Simulation of Parallel Logical Operations with Biomolecular Computing

    Directory of Open Access Journals (Sweden)

    Mahnaz Kadkhoda

    2008-01-01

    Full Text Available Biomolecular computing is the computational method that uses the potential of DNA as a parallel computing device. DNA computing can be used to solve NP-complete problems. An appropriate application of DNA computation is large-scale evaluation of parallel computation models such as Boolean Circuits. In this study, we present a molecular-based algorithm for evaluation of Nand-based Boolean Circuits. The contribution of this paper is that the proposed algorithm has been implemented using only three molecular operations and the number of passes in each level is decreased to less than half of previously addressed in the literature. Thus, the proposed algorithm is much easier to implement in the laboratory.

  13. Structure and Interactions of Isolated Biomolecular Building Blocks.

    Science.gov (United States)

    de Vries, Mattanjah

    2006-03-01

    We investigate biomolecular building blocks and their clusters with each other and with water on a single molecular level. The motivation is the need to distinguish between intrinsic molecular properties and those that result from the biological environment. This is achieved by a combination of laser desorption and jet cooling, applied to aromatic amino acids, small peptides containing those, nucleobases and nucleosides. This approach is coupled with a number of laser spectroscopic techniques, including resonant multi-photon ionization, spectral hole burning and infra-red ion-dip spectroscopy. We will discuss examples illustrating how information can be obtained on spatial structure of individual biomolecules, including peptide conformations and details of DNA base-pairing.

  14. Perspective: Markov Models for Long-Timescale Biomolecular Dynamics

    CERN Document Server

    Schwantes, Christian R; Pande, Vijay 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.

  15. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

    Energy Technology Data Exchange (ETDEWEB)

    Fluitt, Aaron M. [Univ. of Chicago, IL (United States); de Pablo, Juan J. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-09-01

    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.

  16. A Nonlinear Boundary Condition for Continuum Models of Biomolecular Electrostatics

    OpenAIRE

    Bardhan, J. P.; Tejani, D. A.; Wieckowski, N. S.; Ramaswamy, A; Knepley, M. G.

    2015-01-01

    Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully atomistic simulations of biomolecules, surrounded by thousands of water molecules and ions are too computationally slow. Continuum solvent models based on macroscopic dielectric theory (e.g. the Poisson equation) are popular alternatives, but their simplicity ...

  17. Children's access to medicines

    OpenAIRE

    Alkahtani, Saad Ahmed

    2013-01-01

    Access to health care for children is important. It is dependent on access to health professionals and also parental attitudes towards illness. Children have the right to receive medicines that are scientifically evaluated for both efficacy and safety. Counterfeit and substandard medicines unfortunately result in the death of many children worldwide. There have been particular problems with diethylene glycol which has been used as a solvent in counterfeit medicines. It has also been foun...

  18. Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

    Institute of Scientific and Technical Information of China (English)

    ZHOU Shi-Qi

    2005-01-01

    A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.

  19. Biomolecular detection employing the Interferometric Reflectance Imaging Sensor (IRIS).

    Science.gov (United States)

    Lopez, Carlos A; Daaboul, George G; Ahn, Sunmin; Reddington, Alexander P; Monroe, Margo R; Zhang, Xirui; Irani, Rostem J; Yu, Chunxiao; Genco, Caroline A; Cretich, Marina; Chiari, Marcella; Goldberg, Bennett B; Connor, John H; Ünlü, M Selim

    2011-01-01

    The sensitive measurement of biomolecular interactions has use in many fields and industries such as basic biology and microbiology, environmental/agricultural/biodefense monitoring, nanobiotechnology, and more. For diagnostic applications, monitoring (detecting) the presence, absence, or abnormal expression of targeted proteomic or genomic biomarkers found in patient samples can be used to determine treatment approaches or therapy efficacy. In the research arena, information on molecular affinities and specificities are useful for fully characterizing the systems under investigation. Many of the current systems employed to determine molecular concentrations or affinities rely on the use of labels. Examples of these systems include immunoassays such as the enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR) techniques, gel electrophoresis assays, and mass spectrometry (MS). Generally, these labels are fluorescent, radiological, or colorimetric in nature and are directly or indirectly attached to the molecular target of interest. Though the use of labels is widely accepted and has some benefits, there are drawbacks which are stimulating the development of new label-free methods for measuring these interactions. These drawbacks include practical facets such as increased assay cost, reagent lifespan and usability, storage and safety concerns, wasted time and effort in labelling, and variability among the different reagents due to the labelling processes or labels themselves. On a scientific research basis, the use of these labels can also introduce difficulties such as concerns with effects on protein functionality/structure due to the presence of the attached labels and the inability to directly measure the interactions in real time. Presented here is the use of a new label-free optical biosensor that is amenable to microarray studies, termed the Interferometric Reflectance Imaging Sensor (IRIS), for detecting proteins, DNA, antigenic material

  20. Alternative Green Solvents Project

    Science.gov (United States)

    Maloney, Phillip R.

    2012-01-01

    Necessary for safe and proper functioning of equipment. Mainly halogenated solvents. Tetrachloride, Trichloroethylene (TCE), CFC-113. No longer used due to regulatory/safety concerns. Precision Cleaning at KSC: Small % of total parts. Used for liquid oxygen (LOX) systems. Dual solvent process. Vertrel MCA (decafluoropentane (DFP) and trons-dichloroethylene) HFE-7100. DFP has long term environmental concerns. Project Goals: a) Identify potential replacements. b) 22 wet chemical processes. c) 3 alternative processes. d) Develop test procedures. e) Contamination and cleaning. f) Analysis. g) Use results to recommend alternative processes. Conclusions: a) No alternative matched Vertrel in this study. b) No clear second place solvent. c) Hydrocarbons- easy; Fluorinated greases- difficult. d) Fluorinated component may be needed in replacement solvent. e) Process may need to make up for shortcoming of the solvent. f) Plasma and SCC02 warrant further testing.

  1. The fidelity of dynamic signaling by noisy biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Clive G Bowsher

    Full Text Available Cells live in changing, dynamic environments. To understand cellular decision-making, we must therefore understand how fluctuating inputs are processed by noisy biomolecular networks. Here we present a general methodology for analyzing the fidelity with which different statistics of a fluctuating input are represented, or encoded, in the output of a signaling system over time. We identify two orthogonal sources of error that corrupt perfect representation of the signal: dynamical error, which occurs when the network responds on average to other features of the input trajectory as well as to the signal of interest, and mechanistic error, which occurs because biochemical reactions comprising the signaling mechanism are stochastic. Trade-offs between these two errors can determine the system's fidelity. By developing mathematical approaches to derive dynamics conditional on input trajectories we can show, for example, that increased biochemical noise (mechanistic error can improve fidelity and that both negative and positive feedback degrade fidelity, for standard models of genetic autoregulation. For a group of cells, the fidelity of the collective output exceeds that of an individual cell and negative feedback then typically becomes beneficial. We can also predict the dynamic signal for which a given system has highest fidelity and, conversely, how to modify the network design to maximize fidelity for a given dynamic signal. Our approach is general, has applications to both systems and synthetic biology, and will help underpin studies of cellular behavior in natural, dynamic environments.

  2. A programmable biomolecular computing machine with bacterial phenotype output.

    Science.gov (United States)

    Kossoy, Elizaveta; Lavid, Noa; Soreni-Harari, Michal; Shoham, Yuval; Keinan, Ehud

    2007-07-23

    The main advantage of autonomous biomolecular computing devices over electronic computers is their ability to interact directly with biological systems. No interface is required since all components of molecular computers, including hardware, software, input, and output are molecules that interact in solution along a cascade of programmable chemical events. Here, we demonstrate for the first time that the output of a computation preduced by a molecular finite automaton can be a visible bacterial phenotype. Our 2-symbol-2-state finite automaton utilized linear double-stranded DNA inputs that were prepared by inserting a string of six base pair symbols into the lacZ gene on the pUC18 plasmid. The computation resulted in a circular plasmid that differed from the original pUC18 by either a 9 base pair (accepting state) or 11 base pair insert (unaccepting state) within the lacZ alpha region gene. Upon transformation and expression of the resultant plasmids in E. coli, the accepting state was represented by production of functional beta-galactosidase and formation of blue colonies on X-gal medium. In contrast, the unaccepting state was represented by white colonies due to a shift in the open reading frame of lacZ. PMID:17562552

  3. Stochastic Simulation of Biomolecular Networks in Dynamic Environments.

    Directory of Open Access Journals (Sweden)

    Margaritis Voliotis

    2016-06-01

    Full Text Available Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate-using decision-making by a large population of quorum sensing bacteria-that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits.

  4. Hazardous Solvent Substitution Data System reference manual

    International Nuclear Information System (INIS)

    Concern for the environment, in addition to Federal regulation, mandate the replacement of hazardous solvents with safer cleaning agents. Manufacturers are working to produce these replacement solvents. As these products are developed, potential users need to be informed of their availability. To promote the use of these new products instead of traditional solvents, the Idaho National Engineering Laboratory (INEL) has developed the Hazardous Solvent Substitution Data System (HSSDS). The HSSDS provides a comprehensive system of information on alternatives to hazardous solvents and related subjects, and it makes that information available to solvent users, industrial hygienists, and process engineers. The HSSDS uses TOPIC reg-sign, a text retrieval system produced by Verity, Inc., to allow a user to search for information on a particular subject. TOPIC reg-sign produces a listing of the retrieved documents and allows the use to examine the documents individually and to use the information contained in them. This reference manual does not replace the comprehensive TOPIC reg-sign user documentation (available from Verity, Inc.), or the HSSDS Tutorial (available from the INEL). The purpose of this reference manual is to provide enough instruction on TOPIC reg-sign so the user may begin accessing the data contained in the HSSDS

  5. Photoabsorption and resonance energy transfer phenomenon in CdTe-protein bioconjugates: an insight into QD-biomolecular interactions.

    Science.gov (United States)

    Vinayaka, Aaydha C; Thakur, Munna S

    2011-05-18

    Luminescent quantum dots (QDs) possess unique photophysical properties, which are advantageous in the development of new generation robust fluorescent probes based on Forster resonance energy transfer (FRET) phenomena. Bioconjugation of these QDs with biomolecules create hybrid materials having unique photophysical properties along with biological activity. The present study is aimed at characterizing QD bioconjugates in terms of optical behavior. Colloidal CdTe QDs capped with 3-mercaptopropionic acid (MPA) were conjugated to different proteins by the carbodiimide protocol using N-(3-dimethylaminopropyl)-N-ethylcarbodiimide hydrochloride (EDC) and a coupling reagent like N-hydroxysuccinimide (NHS). The photoabsorption of these QD-protein bioconjugates demonstrated an effective coupling of electronic orbitals of constituents. A linear variation in absorbance of bioconjugates at 330 nm proportionate to conjugation suggests a covalent attachment as confirmed by gel electrophoresis. A red shift in the fluorescence of bovine serum albumin (BSA) due to conjugation inferred a decrease in Stokes shift and solvent polarization effects on protein. A proportionate quenching in BSA fluorescence followed by an enhancement of QD fluorescence point toward nonradiative dipolar interactions. Further, reduction in photobleaching of BSA suggests QD-biomolecular interactions. Bioconjugation has significantly influenced the photoabsorption spectrum of QD bioconjugates suggesting the formation of a possible protein shell on the surface of QD. The experimental result suggests that these bioconjugates can be considered nanoparticle (NP) superstructures for the development of a new generation of robust nanoprobes. PMID:21452896

  6. Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.

    Science.gov (United States)

    Yu, Wenbo; He, Xibing; Vanommeslaeghe, Kenno; MacKerell, Alexander D

    2012-12-01

    Presented is an extension of the CHARMM General Force Field (CGenFF) to enable the modeling of sulfonyl-containing compounds. Model compounds containing chemical moieties such as sulfone, sulfonamide, sulfonate, and sulfamate were used as the basis for the parameter optimization. Targeting high-level quantum mechanical and experimental crystal data, the new parameters were optimized in a hierarchical fashion designed to maintain compatibility with the remainder of the CHARMM additive force field. The optimized parameters satisfactorily reproduced equilibrium geometries, vibrational frequencies, interactions with water, gas phase dipole moments, and dihedral potential energy scans. Validation involved both crystalline and liquid phase calculations showing the newly developed parameters to satisfactorily reproduce experimental unit cell geometries, crystal intramolecular geometries, and pure solvent densities. The force field was subsequently applied to study conformational preference of a sulfonamide based peptide system. Good agreement with experimental IR/NMR data further validated the newly developed CGenFF parameters as a tool to investigate the dynamic behavior of sulfonyl groups in a biological environment. CGenFF now covers sulfonyl group containing moieties allowing for modeling and simulation of sulfonyl-containing compounds in the context of biomolecular systems including compounds of medicinal interest. PMID:22821581

  7. 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 Iii, 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. PMID:26387907

  8. 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).

  9. Bridging Nano- and Microtribology in Mechanical and Biomolecular Layers

    Science.gov (United States)

    Tomala, Agnieszka; Göçerler, Hakan; Gebeshuber, Ille C.

    The physical and chemical composition of surfaces determine various important properties of solids such as corrosion rates, adhesive properties, frictional properties, catalytic activity, wettability, contact potential and - finally and most importantly - failure mechanisms. Very thin, weak layers (of man-made and biological origin) on much harder substrates that reduce friction are the focus of the micro- and nanotribological investigations presented in this chapter.Biomolecular layers fulfil various functions in organs of the human body. Examples comprise the skin that provides a protective physical barrier between the body and the environment, preventing unwanted inward and outward passage of water and electrolytes, reducing penetration by destructive chemicals, arresting the penetration of microorganisms and external antigens and absorbing radiation from the sun, or the epithelium of the cornea that blocks the passage of foreign material, such as dust, water and bacteria, into the eye and that contributes to the lubrication layer that ensures smooth movement of the eyelids over the eyeballs.Monomolecular thin films, additive-derived reaction layers and hard coatings are widely used to tailor tribological properties of surfaces. Nanotribological investigations on these substrates can reveal novel properties regarding the orientation of chemisorbed additive layers, development of rubbing films with time and the relation of frictional properties to surface characteristics in diamond coatings.Depending on the questions to be answered with the tribological research, various micro- and nanotribological measurement methods are applied, including scanning probe microscopy (AFM, FFM), scanning electron microscopy, microtribometer investigations, angle-resolved photoelectron spectroscopy and optical microscopy. Thoughts on the feasibility of a unified approach to energy-dissipating systems and how it might be reached (touching upon new ways of scientific publishing

  10. Supercritical solvent coal extraction

    Science.gov (United States)

    Compton, L. E. (Inventor)

    1984-01-01

    Yields of soluble organic extract are increased up to about 50% by the supercritical extraction of particulate coal at a temperature below the polymerization temperature for coal extract fragments (450 C.) and a pressure from 500 psig to 5,000 psig by the conjoint use of a solvent mixture containing a low volatility, high critical temperature coal dissolution catalyst such as phenanthrene and a high volatility, low critical temperature solvent such as toluene.

  11. SOLVENT EXTRACTION OF RUTHENIUM

    Science.gov (United States)

    Hyman, H.H.; Leader, G.R.

    1959-07-14

    The separation of rathenium from aqueous solutions by solvent extraction is described. According to the invention, a nitrite selected from the group consisting of alkali nitrite and alkaline earth nitrite in an equimolecular quantity with regard to the quantity of rathenium present is added to an aqueous solution containing ruthenium tetrantrate to form a ruthenium complex. Adding an organic solvent such as ethyl ether to the resulting mixture selectively extracts the rathenium complex.

  12. Recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices.

    Science.gov (United States)

    Sasaki, Naoki

    2012-01-01

    AC electrokinetics is a generic term that refers to an induced motion of particles and fluids under nonuniform AC electric fields. The AC electric fields are formed by application of AC voltages to microelectrodes, which can be easily integrated into microfluidic devices by standard microfabrication techniques. Moreover, the magnitude of the motion is large enough to control the mass transfer on the devices. These advantages are attractive for biomolecular analysis on the microfluidic devices, in which the characteristics of small space and microfluidics have been mainly employed. In this review, I describe recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices. The applications include fluid pumping and mixing by AC electrokinetic flow, and manipulation of biomolecules such as DNA and proteins by various AC electrokinetic techniques. Future prospects for highly functional biomolecular analysis on microfluidic devices with the aid of AC electrokinetics are also discussed.

  13. Multiple Features Based Approach to Extract Bio-molecular Event Triggers Using Conditional Random Field

    Directory of Open Access Journals (Sweden)

    Amit Majumder

    2012-11-01

    Full Text Available The purpose of Biomedical Natural Language Processing (BioNLP is to capture biomedical phenomena from textual data by extracting relevant entities, information and relations between biomedical entities (i.e. proteins and genes. In general, in most of the published papers, only binary relations were extracted. In a recent past, the focus is shifted towards extracting more complex relations in the form of bio-molecular events that may include several entities or other relations. In this paper we propose an approach that enables event trigger extraction of relatively complex bio-molecular events. We approach this problem as a detection of bio-molecular event trigger using the well-known algorithm, namely Conditional Random Field (CRF. We apply our experiments on development set. It shows the overall average recall, precision and F-measure values of 64.27504%, 69.97559% and 67.00429%, respectively for the event detection.

  14. Purex process solvent: literature review

    International Nuclear Information System (INIS)

    This document summarizes the data on Purex process solvent presently published in a variety of sources. Extracts from these various sources are presented herein and contain the work done, the salient results obtained, and the original, unaltered conclusions of the author of each paper. Three major areas are addressed: solvent stability, solvent quality testing, and solvent treatment processes. 34 references, 44 tables

  15. iBIOMES: managing and sharing biomolecular simulation data in a distributed environment.

    Science.gov (United States)

    Thibault, Julien C; Facelli, Julio C; Cheatham, Thomas E

    2013-03-25

    Biomolecular simulations, which were once batch queue or compute limited, have now become data analysis and management limited. In this paper we introduce a new management system for large biomolecular simulation and computational chemistry data sets. The system can be easily deployed on distributed servers to create a mini-grid at the researcher's site. The system not only offers a simple data deposition mechanism but also a way to register data into the system without moving the data from their original location. Any registered data set can be searched and downloaded using a set of defined metadata for molecular dynamics and quantum mechanics and visualized through a dynamic Web interface.

  16. 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

  17. Output-input ratio in thermally fluctuating biomolecular machines.

    Science.gov (United States)

    Kurzynski, Michal; Torchala, Mieczyslaw; Chelminiak, Przemyslaw

    2014-01-01

    Biological molecular machines are proteins that operate under isothermal conditions and hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free energy-donating (input) reaction and the free energy-accepting (output) one. Most if not all biologically active proteins display a slow stochastic dynamics of transitions between a variety of conformational substates composing their native state. This makes the description of the enzymatic reaction kinetics in terms of conventional rate constants insufficient. In the steady state, upon taking advantage of the assumption that each reaction proceeds through a single pair (the gate) of transition conformational substates of the enzyme-substrates complex, the degree of coupling between the output and the input reaction fluxes has been expressed in terms of the mean first-passage times on a conformational transition network between the distinguished substates. The theory is confronted with the results of random-walk simulations on the five-dimensional hypercube. The formal proof is given that, for single input and output gates, the output-input degree of coupling cannot exceed unity. As some experiments suggest such exceeding, looking for the conditions for increasing the degree of coupling value over unity challenges the theory. Performed simulations of random walks on several model networks involving more extended gates indicate that the case of the degree of coupling value higher than 1 is realized in a natural way on critical branching trees extended by long-range shortcuts. Such networks are scale-free and display the property of the small world. For short-range shortcuts, the networks are scale-free and fractal, representing a reasonable model for biomolecular machines displaying tight coupling, i.e., the degree of coupling equal exactly to unity. A hypothesis is stated that the protein conformational transition networks, as

  18. Safe battery solvents

    Science.gov (United States)

    Harrup, Mason K.; Delmastro, Joseph R.; Stewart, Frederick F.; Luther, Thomas A.

    2007-10-23

    An ion transporting solvent maintains very low vapor pressure, contains flame retarding elements, and is nontoxic. The solvent in combination with common battery electrolyte salts can be used to replace the current carbonate electrolyte solution, creating a safer battery. It can also be used in combination with polymer gels or solid polymer electrolytes to produce polymer batteries with enhanced conductivity characteristics. The solvents may comprise a class of cyclic and acyclic low molecular weight phosphazenes compounds, comprising repeating phosphorus and nitrogen units forming a core backbone and ion-carrying pendent groups bound to the phosphorus. In preferred embodiments, the cyclic phosphazene comprises at least 3 phosphorus and nitrogen units, and the pendent groups are polyethers, polythioethers, polyether/polythioethers or any combination thereof, and/or other groups preferably comprising other atoms from Group 6B of the periodic table of elements.

  19. Automated solvent concentrator

    Science.gov (United States)

    Griffith, J. S.; Stuart, J. L.

    1976-01-01

    Designed for automated drug identification system (AUDRI), device increases concentration by 100. Sample is first filtered, removing particulate contaminants and reducing water content of sample. Sample is extracted from filtered residue by specific solvent. Concentrator provides input material to analysis subsystem.

  20. Organic solvent topical report

    Energy Technology Data Exchange (ETDEWEB)

    Cowley, W.L.

    1998-04-30

    This report is the technical basis for the accident and consequence analyses used in the Hanford Tank Farms Basis for Interim Operation. The report also contains the scientific and engineering information and reference material needed to understand the organic solvent safety issue. This report includes comments received from the Chemical Reactions Subcommittee of the Tank Advisory Panel.

  1. Organic solvent topical report

    Energy Technology Data Exchange (ETDEWEB)

    COWLEY, W.L.

    1999-05-13

    This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an organic solvent fire is within risk evaluation guidelines. This report updates information contained in Analysis of Consequences of Postulated Solvent Fires in Hanford Site Waste Tanks. WHC-SD-WM-CN-032. Rev. 0A (Cowley et al. 1996). However, this document will not replace Cowley et al (1996) as the primary reference for the Basis for Interim Operation (BIO) until the recently submitted BIO amendment (Hanson 1999) is approved by the US Department of Energy. This conclusion depends on the use of controls for preventing vehicle fuel fires and for limiting the use of flame cutting in areas where hot metal can fall on the waste surface.The required controls are given in the Tank Waste Remediation System Technical Safety Requirements (Noorani 1997b). This is a significant change from the conclusions presented in Revision 0 of this report. Revision 0 of this calcnote concluded that some organic solvent fire scenarios exceeded risk evaluation guidelines, even with controls imposed.

  2. Organic solvent topical report

    International Nuclear Information System (INIS)

    This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an organic solvent fire is within risk evaluation guidelines. This report updates information contained in Analysis of Consequences of Postulated Solvent Fires in Hanford Site Waste Tanks. WHC-SD-WM-CN-032. Rev. 0A (Cowley et al. 1996). However, this document will not replace Cowley et al (1996) as the primary reference for the Basis for Interim Operation (BIO) until the recently submitted BIO amendment (Hanson 1999) is approved by the US Department of Energy. This conclusion depends on the use of controls for preventing vehicle fuel fires and for limiting the use of flame cutting in areas where hot metal can fall on the waste surface.The required controls are given in the Tank Waste Remediation System Technical Safety Requirements (Noorani 1997b). This is a significant change from the conclusions presented in Revision 0 of this report. Revision 0 of this calcnote concluded that some organic solvent fire scenarios exceeded risk evaluation guidelines, even with controls imposed

  3. Organic solvent topical report

    International Nuclear Information System (INIS)

    This report is the technical basis for the accident and consequence analyses used in the Hanford Tank Farms Basis for Interim Operation. The report also contains the scientific and engineering information and reference material needed to understand the organic solvent safety issue. This report includes comments received from the Chemical Reactions Subcommittee of the Tank Advisory Panel

  4. Transition metal bioconjugates with an organometallic link between the metal and the biomolecular scaffold

    OpenAIRE

    Monney, Angèle; Albrecht, Martin

    2013-01-01

    This overview compiles recent advances in the synthesis and application of organometallic bioconjugates that comprise a metal–carbon linkage between the metal and the biomolecular scaffold. This specific area of bioorganometallic chemistry has been spurred by the discovery of naturally occurring bioorganometallic compounds and afforded organometallic bioconjugates from transition metals binding to amino acids, nucleic acids and other biomolecules. These artificial bioorganometallic compounds ...

  5. 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 (BC...

  6. 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…

  7. Optical Coherence Tomography and Biomolecular Imaging with Coherent Raman Scattering Microscopy

    DEFF Research Database (Denmark)

    Andersson-Engels, Stefan; Andersen, Peter E.

    2014-01-01

    The Special Section on Selected Topics in Biophotonics: Optical Coherence Tomography and Biomolecular Imaging with Coherent Raman Scattering Microscopy comprises two invited review papers and several contributed papers from the summer school Biophotonics ’13, as well as contributed papers within...

  8. Global analysis of time-resolved fluorescence microspectroscopy and applications in biomolecular studies

    NARCIS (Netherlands)

    Laptenok, S.

    2009-01-01

    Understanding the properties of biomolecular networks is of central importance in life sciences. Optical microscopy has been very useful to determine the sub-cellular localisation of proteins but it cannot reveal whether proteins interact with one another. Micro-spectroscopic techniques (combining m

  9. Theoretical description of biomolecular hydration - Application to A-DNA

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, A.E.; Hummer, G. [Los Alamos National Laboratory, NM (United States); Soumpasis, D.M. [Max Planck Inst. for Biophysical Chemistry, Goettingen (Germany)

    1994-12-31

    The local density of water molecules around a biomolecule is constructed from calculated two- and three-points correlation functions of polar solvents in water using a Potential-of-Mean-Force (PMF) expansion. As a simple approximation, the hydration of all polar (including charged) groups in a biomolecule is represented by the hydration of water oxygen in bulk water, and the effect of non-polar groups on hydration are neglected, except for excluded volume effects. Pair and triplet correlation functions are calculated by molecular dynamics simulations. We present calculations of the structural hydration for ideal A-DNA molecules with sequences [d(CG){sub 5}]{sub 2} and [d(C{sub 5}G{sub 5})]{sub 2}. We find that this method can accurately reproduce the hydration patterns of A-DNA observed in neutron diffraction experiments on oriented DNA fibers.

  10. Poor-solvent polyelectrolytes

    International Nuclear Information System (INIS)

    Using extensive molecular dynamics simulations we study the behaviour of polyelectrolytes (PEs) in poor solvents, explicitly taking the counterions into account. The resulting pearl-necklace structures are subject to strong conformational fluctuations. These lead to small signatures in the form factor and the force-extension relation, which is a severe obstacle to experimental observations. In addition, we study how the necklace collapses as a function of the Bjerrum length. Finally, we demonstrate that the position of the first peak in the inter-chain structure factor varies with the monomer density as ∼ ρm0.35 for all densities, which shows a pertinent different behaviour as compared to that of PE solutions in good solvent

  11. Hazardous solvent substitution

    International Nuclear Information System (INIS)

    Eliminating hazardous solvents is good for the environment, worker safety, and the bottom line. However, even though we are motivated to find replacements, the big question is 'What can we use as replacements for hazardous solvents?'You, too, can find replacements for your hazardous solvents. All you have to do is search for them. Search through the vendor literature of hundreds of companies with thousands of products. Ponder the associated material safety data sheets, assuming of course that you can obtain them and, having obtained them, that you can read them. You will want to search the trade magazines and other sources for product reviews. You will want to talk to users about how well the product actually works. You may also want to check US Environmental Protection Agency (EPA) and other government reports for toxicity and other safety information. And, of course, you will want to compare the product's constituent chemicals with the many hazardous constituency lists to ensure the safe and legal use of the product in your workplace

  12. Diluent effects in solvent extraction. The Effects of Diluents in Solvent Extraction - a literature study

    International Nuclear Information System (INIS)

    The fact that the choice of organic diluent is important for a solvent extraction process goes without saying. Several factors, such as e.g. price, flash point, viscosity, polarity etc. each have their place in the planning of a solvent extraction system. This high number of variables makes the lack of compilations concerning diluent effects to an interesting topic. Often the interest for the research concerning a specific extraction system focuses on the extractant used and the complexes built up during an extraction. The diluents used are often classical ones, even if it has been shown that choice of diluent can affect extraction as well as separation in an extraction system. An attempt to point out important steps in the understanding of diluent effects in solvent extraction is here presented. This large field is, of course, not summarized in this article, but an attempt is made to present important steps in the understanding of diluents effects in solvent extraction. Trying to make the information concerning diluent effects and applications more easily accessible this review offers a selected summarizing of literature concerning diluents effects in solvent extraction. (authors)

  13. Occupational solvent exposure and cognition

    Science.gov (United States)

    Sabbath, E.L.; Glymour, M.M.; Berr, C.; Singh-Manoux, A.; Zins, M.; Goldberg, M.

    2012-01-01

    Objective: Chronic occupational solvent exposure is associated with long-term cognitive deficits. Cognitive reserve may protect solvent-exposed workers from cognitive impairment. We tested whether the association between chronic solvent exposure and cognition varied by educational attainment, a proxy for cognitive reserve. Methods: Data were drawn from a prospective cohort of French national gas and electricity (GAZEL) employees (n = 4,134). Lifetime exposure to 4 solvent types (chlorinated solvents, petroleum solvents, benzene, and nonbenzene aromatic solvents) was assessed using a validated job-exposure matrix. Education was dichotomized at less than secondary school or below. Cognitive impairment was defined as scoring below the 25th percentile on the Digit Symbol Substitution Test at mean age 59 (SD 2.8; 88% of participants were retired at testing). Log-binomial regression was used to model risk ratios (RRs) for poor cognition as predicted by solvent exposure, stratified by education and adjusted for sociodemographic and behavioral factors. Results: Solvent exposure rates were higher among less-educated patients. Within this group, there was a dose-response relationship between lifetime exposure to each solvent type and RR for poor cognition (e.g., for high exposure to benzene, RR = 1.24, 95% confidence interval 1.09–1.41), with significant linear trends (p < 0.05) in 3 out of 4 solvent types. Recency of solvent exposure also predicted worse cognition among less-educated patients. Among those with secondary education or higher, there was no significant or near-significant relationship between any quantification of solvent exposure and cognition. Conclusions: Solvent exposure is associated with poor cognition only among less-educated individuals. Higher cognitive reserve in the more-educated group may explain this finding. PMID:22641403

  14. Constructing Bio-molecular Databases on a DNA-based Computer

    CERN Document Server

    Chang, Weng-Long; Ho,; Guo, Minyi

    2007-01-01

    Codd [Codd 1970] wrote the first paper in which the model of a relational database was proposed. Adleman [Adleman 1994] wrote the first paper in which DNA strands in a test tube were used to solve an instance of the Hamiltonian path problem. From [Adleman 1994], it is obviously indicated that for storing information in molecules of DNA allows for an information density of approximately 1 bit per cubic nm (nanometer) and a dramatic improvement over existing storage media such as video tape which store information at a density of approximately 1 bit per 1012 cubic nanometers. This paper demonstrates that biological operations can be applied to construct bio-molecular databases where data records in relational tables are encoded as DNA strands. In order to achieve the goal, DNA algorithms are proposed to perform eight operations of relational algebra (calculus) on bio-molecular relational databases, which include Cartesian product, union, set difference, selection, projection, intersection, join and division. Fu...

  15. PREFACE: India-Japan Workshop on Biomolecular Electronics & Organic Nanotechnology for Environment Preservation

    Science.gov (United States)

    Onoda, Mitsuyoshi; Malhotra, Bansi D.

    2012-04-01

    The 'India-Japan Workshop on Biomolecular Electronics & Organic Nanotechnology for Environment Preservation' (IJWBME 2011) will be held on 7-10 December 2011 at EGRET Himeji, Himeji, Hyogo, Japan. This workshop was held for the first time on 17-19 December 2009 at NPL, New Delhi. Keeping in mind the importance of organic nanotechnology and biomolecular electronics for environmental preservation and their anticipated impact on the economics of both the developing and the developed world, IJWBME 2009 was jointly organized by the Department of Biological Functions, Graduate School of Life Sciences and Systems Engineering, the Kyushu Institute of Technology (KIT), Kitakyushu, Japan, and the Department of Science & Technology Centre on Biomolecular Electronics (DSTCBE), National Physical Laboratory (NPL). Much progress in the field of biomolecular electronics and organic nanotechnology for environmental preservation is expected for the 21st Century. Organic optoelectronic devices, such as organic electroluminescent devices, organic thin-film transistors, organic sensors, biological systems and so on have especially attracted much attention. The main purpose of this workshop is to provide an opportunity for researchers interested in biomolecular electronics and organic nanotechnology for environmental preservation, to come together in an informal and friendly atmosphere and exchange technical knowledge and experience. We are sure that this workshop will be very useful and fruitful for all participants in summarizing the recent progress in biomolecular electronics and organic nanotechnology for environmental preservation and preparing new ground for the next generation. Many papers have been submitted from India and Japan and more than 30 papers have been accepted for presentation. The main topics of interest are as follows: Bioelectronics Biomolecular Electronics Fabrication Techniques Self-assembled Monolayers Nano-sensors Environmental Monitoring Organic Devices

  16. Biochemical filter with sigmoidal response: increasing the complexity of biomolecular logic.

    Science.gov (United States)

    Privman, Vladimir; Halámek, Jan; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny

    2010-11-11

    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by H(2)O(2) was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved capabilities for design of scalable biomolecular information processing systems.

  17. Effect of antibody modifications on its biomolecular binding as determined by surface plasmon resonance.

    Science.gov (United States)

    Vashist, Sandeep Kumar

    2012-02-01

    A surface plasmon resonance (SPR)-based procedure was developed to determine the effect of antibody modifications on its biomolecular binding behavior. Mouse immunoglobulin G (IgG) was immobilized on a protein A-functionalized gold-coated SPR chip. Goat anti-mouse IgG and its various commercially available modifications (i.e., conjugated with atto 550, atto 647, tetramethylrhodamine isothiocyanate [TRITC], horseradish peroxidase [HRP], or biotin) were employed in exactly the same concentration for the detection of mouse IgG. The various modifications of goat anti-mouse IgG decreased its biomolecular binding to mouse IgG in the order of unmodified>HRP-labeled>atto 550-labeled>biotinylated>TRITC-labeled>atto 647-labeled. PMID:22093612

  18. Solvent effects in chemistry

    CERN Document Server

    Buncel, Erwin

    2015-01-01

    This book introduces the concepts, theory and experimental knowledge concerning solvent effects on the rate and equilibrium of chemical reactions of all kinds.  It begins with basic thermodynamics and kinetics, building on this foundation to demonstrate how a more detailed understanding of these effects may be used to aid in determination of reaction mechanisms, and to aid in planning syntheses. Consideration is given to theoretical calculations (quantum chemistry, molecular dynamics, etc.), to statistical methods (chemometrics), and to modern day concerns such as ""green"" chemistry, where ut

  19. Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids

    OpenAIRE

    Tessier, Matthew B; DeMarco, Mari L.; Yongye, Austin B.; Woods, Robert J.

    2008-01-01

    GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a c...

  20. Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES

    OpenAIRE

    Chennubhotla, Chakra; Bahar, Ivet

    2006-01-01

    We introduce a novel approach for elucidating the potential pathways of allosteric communication in biomolecular systems. The methodology, based on Markov propagation of ‘information' across the structure, permits us to partition the network of interactions into soft clusters distinguished by their coherent stochastics. Probabilistic participation of residues in these clusters defines the communication patterns inherent to the network architecture. Application to bacterial chaperonin complex ...

  1. Atomic force microscopy of self-assembled biomolecular structures and their interaction with metallic nanoparticles.

    OpenAIRE

    Gysemans, Maarten

    2009-01-01

    We applied AFM to study biomolecular wires, both out of interest in thei r biological functions and in the framework of nanotechnology based fabr ication. We have focused on two different kinds of protein wires: Insuli n fibrils and microtubules. Microtubules are an important constituent of the cytoskeleton and fulfill multiple vital functions in the cell. Insu lin fibrils on the other hand are amyloid fibrils without a clear biolog ical role, but with intriguing polymerization properties tha...

  2. Assembly of single wall carbon nanotube-metal nanohybrids using biomolecular components

    Science.gov (United States)

    Kim, Sang Nyon; Slocik, Joseph M.; Naik, Rajesh R.

    2010-08-01

    Biomaterials such as nucleic acids and proteins can be exploited to create higher order structures. The biomolecular components such as DNA and peptides have been used to assemble nanoparticles with high fidelity. Here, we use DNA and peptides, and their preferential interaction with inorganic and carbon nanomaterials to form homogeneous hybrids. The enhanced binding of Pt ions to both DNA and peptide functionalized nanoparticles mediates the assembly of carbon nanotubes functionalized with DNA with peptide coated gold nanoparticles.

  3. ssDNA-Functionalized Nanoceria: A Redox-Active Aptaswitch for Biomolecular Recognition.

    Science.gov (United States)

    Bülbül, Gonca; Hayat, Akhtar; Andreescu, Silvana

    2016-04-01

    Quantification of biomolecular binding events is a critical step for the development of biorecognition assays for diagnostics and therapeutic applications. This paper reports the design of redox-active switches based on aptamer conjugated nanoceria for detection and quantification of biomolecular recognition. It is shown that the conformational transition state of the aptamer on nanoceria, combined with the redox properties of these particles can be used to create surface based structure switchable aptasensing platforms. Changes in the redox properties at the nanoceria surface upon binding of the ssDNA and its target analyte enables rapid and highly sensitive measurement of biomolecular interactions. This concept is demonstrated as a general applicable method to the colorimetric detection of DNA binding events. An example of a nanoceria aptaswitch for the colorimetric sensing of Ochratoxin A (OTA) and applicability to other targets is provided. The system can sensitively and selectivity detect as low as 0.15 × 10(-9) m OTA. This novel assay is simple in design and does not involve oligonucleotide labeling or elaborate nanoparticle modification steps. The proposed mechanism discovered here opens up a new way of designing optical sensing methods based on aptamer recognition. This approach can be broadly applicable to many bimolecular recognition processes and related applications. PMID:26844813

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

    Science.gov (United States)

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

    2014-11-01

    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.

  5. Rational Design of Biomolecular Templates for Synthesizing Multifunctional Noble Metal Nanoclusters toward Personalized Theranostic Applications.

    Science.gov (United States)

    Yu, Yong; Mok, Beverly Y L; Loh, Xian Jun; Tan, Yen Nee

    2016-08-01

    Biomolecule-templated or biotemplated metal nanoclusters (NCs) are ultrasmall (<2 nm) metal (Au, Ag) particles stabilized by a certain type of biomolecular template (e.g., peptides, proteins, and DNA). Due to their unique physiochemical properties, biotemplated metal NCs have been widely used in sensing, imaging, delivery and therapy. The overwhelming applications in these individual areas imply the great promise of harnessing biotemplated metal NCs in more advanced biomedical aspects such as theranostics. Although applications of biotemplated metal NCs as theranostic agents are trending, the rational design of biomolecular templates suitable for the synthesis of multifunctional metal NCs for theranostics is comparatively underexplored. This progress report first identifies the essential attributes of biotemplated metal NCs for theranostics by reviewing the state-of-art applications in each of the four modalities of theranostics, namely sensing, imaging, delivery and therapy. To achieve high efficacy in these modalities, we elucidate the design principles underlying the use of biomolecules (proteins, peptides and nucleic acids) to control the NC size, emission color and surface chemistries for post-functionalization of therapeutic moieties. We then propose a unified strategy to engineer biomolecular templates that combine all these modalities to produce multifunctional biotemplated metal NCs that can serve as the next-generation personalized theranostic agents.

  6. Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

    Science.gov (United States)

    Cole, Daniel J; Vilseck, Jonah Z; Tirado-Rives, Julian; Payne, Mike C; Jorgensen, William L

    2016-05-10

    Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme. PMID:27057643

  7. An improved simple polarisable water model for use in biomolecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Bachmann, Stephan J.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich (Switzerland)

    2014-12-14

    The accuracy of biomolecular simulations depends to some degree on the accuracy of the water model used to solvate the biomolecules. Because many biomolecules such as proteins are electrostatically rather inhomogeneous, containing apolar, polar, and charged moieties or side chains, a water model should be able to represent the polarisation response to a local electrostatic field, while being compatible with the force field used to model the biomolecules or protein. The two polarisable water models, COS/G2 and COS/D, that are compatible with the GROMOS biomolecular force fields leave room for improvement. The COS/G2 model has a slightly too large dielectric permittivity and the COS/D model displays a much too slow dynamics. The proposed COS/D2 model has four interaction sites: only one Lennard-Jones interaction site, the oxygen atom, and three permanent charge sites, the two hydrogens, and one massless off-atom site that also serves as charge-on-spring (COS) polarisable site with a damped or sub-linear dependence of the induced dipole on the electric field strength for large values of the latter. These properties make it a cheap and yet realistic water model for biomolecular solvation.

  8. Perspectives for quantum interference with biomolecules and biomolecular clusters

    Science.gov (United States)

    Geyer, P.; Sezer, U.; Rodewald, J.; Mairhofer, L.; Dörre, N.; Haslinger, P.; Eibenberger, S.; Brand, C.; Arndt, M.

    2016-06-01

    Modern quantum optics encompasses a wide field of phenomena that are either related to the discrete quantum nature of light, the quantum wave nature of matter or light–matter interactions. We here discuss new perspectives for quantum optics with biological nanoparticles. We focus in particular on the prospects of matter-wave interferometry with amino acids, nucleotides, polypeptides or DNA strands. We motivate the challenge of preparing these objects in a ‘biomimetic’ environment and argue that hydrated molecular beam sources are promising tools for quantum-assisted metrology. The method exploits the high sensitivity of matter-wave interference fringes to dephasing and shifts in the presence of external perturbations to access and determine molecular properties.

  9. Solvent Blending Strategy to Upgrade MCU CSSX Solvent to Equivalent Next-Generation CSSX Solvent

    Energy Technology Data Exchange (ETDEWEB)

    Delmau, Laetitia Helene [ORNL; Moyer, Bruce A [ORNL

    2012-12-01

    The results of the present study have validated an equal-volume blending strategy for upgrading freshly prepared CSSX solvent to a blended solvent functionally equivalent to NG-CSSX solvent. It is shown that blending fresh CSSX solvent as currently used in MCU with an equal volume of an NG-CSSX solvent concentrate of appropriate composition yields a blended solvent composition (46.5 mM of MaxCalix, 3.5 mM of BOBCalixC6, 0.5 M of Cs-7SB, 3 mM of guanidine suppressor, and 1.5 mM of TOA in Isopar L) that exhibits equivalent batch ESS performance to that of the NG-CSSX solvent containing 50 mM of MaxCalix, 0.5 M of Cs-7SB, and 3 mM of guanidine suppressor in Isopar L. The solvent blend composition is robust to third-phase formation. Results also show that a blend containing up to 60% v/v of CSSX solvent could be accommodated with minimal risk. Extraction and density data for the effect of solvent concentration mimicking diluent evaporation or over-dilution of the equal-volume blended solvent are also given, providing input for setting operational limits. Given that the experiments employed all pristine chemicals, the results do not qualify a blended solvent starting with actual used MCU solvent, which can be expected to have undergone some degree of degradation. Consequently, further work should be considered to evaluate this risk and implement appropriate remediation if needed.

  10. Biomolecular Deuteration for Neutron Structural Biology and Dynamics.

    Science.gov (United States)

    Haertlein, Michael; Moulin, Martine; Devos, Juliette M; Laux, Valerie; Dunne, Orla; Forsyth, V Trevor

    2016-01-01

    Neutron scattering studies provide important information in structural biology that is not accessible using other approaches. The uniqueness of the technique, and its complementarity with X-ray scattering, is greatest when full use is made of deuterium labeling. The ability to produce tailor-made deuterium-labeled biological macromolecules allows neutron studies involving solution scattering, crystallography, reflection, and dynamics to be optimized in a manner that has major impact on the scope, quality, and throughput of work in these areas. Deuteration facilities have now been developed at many neutron centres throughout the world; these are having a crucial effect on neutron studies in the life sciences and on biologically related studies in soft matter. This chapter describes methods that have been developed for the efficient production of deuterium-labeled samples for a wide range of neutron scattering applications. Examples are given that illustrate the use of these samples for each of the main techniques. Perspectives for biological deuterium labeling are discussed in relation to developments at current facilities and those that are planned in the future.

  11. Multiresolution persistent homology for excessively large biomolecular datasets

    Science.gov (United States)

    Xia, Kelin; Zhao, Zhixiong; Wei, Guo-Wei

    2015-10-01

    Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

  12. Multiresolution persistent homology for excessively large biomolecular datasets

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Kelin; Zhao, Zhixiong [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (United States)

    2015-10-07

    Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

  13. Supercritical multicomponent solvent coal extraction

    Science.gov (United States)

    Corcoran, W. H.; Fong, W. S.; Pichaichanarong, P.; Chan, P. C. F.; Lawson, D. D. (Inventor)

    1983-01-01

    The yield of organic extract from the supercritical extraction of coal with larger diameter organic solvents such as toluene is increased by use of a minor amount of from 0.1 to 10% by weight of a second solvent such as methanol having a molecular diameter significantly smaller than the average pore diameter of the coal.

  14. Laboratory solvent reuse -- Liquid chromatography

    Energy Technology Data Exchange (ETDEWEB)

    Quinlin, W.T.; Schaffer, C.L.

    1992-11-01

    The objective of this work was to develop a method for reduction of waste solvent in the Process Engineering Chemistry Laboratory. The liquid chromatographs are the largest generators of explosive-contaminated waste in the laboratory. We developed a successful process for the reuse of solvents from the liquid chromatographs and demonstrated the utility of the process in the assay of hexanitrostilbene.

  15. SOLVENT EXTRACTION OF URANIUM VALUES

    Science.gov (United States)

    Feder, H.M.; Ader, M.; Ross, L.E.

    1959-02-01

    A process is presented for extracting uranium salt from aqueous acidic solutions by organic solvent extraction. It consists in contacting the uranium bearing solution with a water immiscible dialkylacetamide having at least 8 carbon atoms in the molecule. Mentioned as a preferred extractant is dibutylacetamide. The organic solvent is usually used with a diluent such as kerosene or CCl/sub 4/.

  16. Solvent degradation products in nuclear fuel processing solvents

    Energy Technology Data Exchange (ETDEWEB)

    Shook, H.E. Jr.

    1988-06-01

    The Savannah River Plant uses a modified Purex process to recover enriched uranium and separate fission products. This process uses 7.5% tri-n-butyl phosphate (TBP) dissolved in normal paraffin hydrocarbons for the solvent extraction of a nitric acid solution containing the materials to be separated. Periodic problems in product decontamination result from solvent degradation. A study to improve process efficiency has identified certain solvent degradation products and suggested mitigation measures. Undecanoic acid, lauric acid, and tridecanoic acid were tentatively identified as diluent degradation products in recycle solvent. These long-chain organic acids affect phase separation and lead to low decontamination factors. Solid phase extraction (SPE) was used to concentrate the organic acids in solvent prior to analysis by high performance liquid chromatography (HPLC). SPE and HPLC methods were optimized in this work for analysis of decanoic acid, undecanoic acid, and lauric acid in solvent. Accelerated solvent degradation studies with 7.5% TBP in normal paraffin hydrocarbons showed that long-chain organic acids and long-chain alkyl butyl phosphoric acids are formed by reactions with nitric acid. Degradation of both tributyl phosphate and hydrocarbon can be minimized with purified normal paraffin replacing the standard grade presently used. 12 refs., 1 fig., 3 tabs.

  17. COMPUTER AIDED SOLVENT DESIGN FOR THE ENVIRONMENT

    Science.gov (United States)

    Solvent substitution is an effective and useful means of eliminating the use of harmful solvents, but finding substitute solvents which are less harmful and as effective as currently used solvents presents significant difficulties. Solvent substitution is a form of reverse engin...

  18. Hazardous Solvent Substitution Data System reference manual. Revision 1

    Energy Technology Data Exchange (ETDEWEB)

    Branham-Haar, K.A.; Twitchell, K.E.

    1993-07-01

    Concern for the environment, in addition to Federal regulation, mandate the replacement of hazardous solvents with safer cleaning agents. Manufacturers are working to produce these replacement solvents. As these products are developed, potential users need to be informed of their availability. To promote the use of these new products instead of traditional solvents, the Idaho National Engineering Laboratory (INEL) has developed the Hazardous Solvent Substitution Data System (HSSDS). The HSSDS provides a comprehensive system of information on alternatives to hazardous solvents and related subjects, and it makes that information available to solvent users, industrial hygienists, and process engineers. The HSSDS uses TOPIC{reg_sign}, a text retrieval system produced by Verity, Inc., to allow a user to search for information on a particular subject. TOPIC{reg_sign} produces a listing of the retrieved documents and allows the use to examine the documents individually and to use the information contained in them. This reference manual does not replace the comprehensive TOPIC{reg_sign} user documentation (available from Verity, Inc.), or the HSSDS Tutorial (available from the INEL). The purpose of this reference manual is to provide enough instruction on TOPIC{reg_sign} so the user may begin accessing the data contained in the HSSDS.

  19. Structural Transitions of Solvent-Free Oligomer-Grafted Nanoparticles

    KAUST Repository

    Chremos, Alexandros

    2011-09-01

    Novel structural transitions of solvent-free oligomer-grafted nanoparticles are investigated by using molecular dynamics simulations of a coarse-grained bead-spring model. Variations in core size and grafting density lead to self-assembly of the nanoparticles into a variety of distinct structures. At the boundaries between different structures, the nanoparticle systems undergo thermoreversible transitions. This structural behavior, which has not been previously reported, deviates significantly from that of simple liquids. The reversible nature of these transitions in solvent-free conditions offers new ways to control self-assembly of nanoparticles at experimentally accessible conditions. © 2011 American Physical Society.

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

    Science.gov (United States)

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

    2016-03-01

    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

  1. 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

    Factors, Reporter Proteins and Reporter Complexes, and use this to decipher the logic of regulatory circuits playing a key role in yeast glucose repression and human diabetes. Conclusion: Reporter Features offer the opportunity to identify regulatory hot-spots in bio-molecular interaction networks...... that are significantly affected between or across conditions. Results of the Reporter Feature analysis not only provide a snapshot of the transcriptional regulatory program but also are biologically easy to interpret and provide a powerful way to generate new hypotheses. Our Reporter Features analyses of yeast glucose...

  2. In situ monitoring of biomolecular processes in living systems using surface-enhanced Raman scattering

    Science.gov (United States)

    Altunbek, Mine; Kelestemur, Seda; Culha, Mustafa

    2015-12-01

    Surface-enhanced Raman scattering (SERS) continues to strive to gather molecular level information from dynamic biological systems. It is our ongoing effort to utilize the technique for understanding of the biomolecular processes in living systems such as eukaryotic and prokaryotic cells. In this study, the technique is investigated to identify cell death mechanisms in 2D and 3D in vitro cell culture models, which is a very important process in tissue engineering and pharmaceutical applications. Second, in situ biofilm formation monitoring is investigated to understand how microorganisms respond to the environmental stimuli, which inferred information can be used to interfere with biofilm formation and fight against their pathogenic activity.

  3. Surface-plasmon-enhanced fluorescence from periodic quantum dot arrays through distance control using biomolecular linkers

    International Nuclear Information System (INIS)

    We have developed a protein-enabled strategy to fabricate quantum dot (QD) nanoarrays where up to a 15-fold increase in surface-plasmon-enhanced fluorescence has been achieved. This approach permits a comprehensive control both laterally (via lithographically defined gold nanoarrays) and vertically (via the QD-metal distance) of the collectively behaving assemblies of QDs and gold nanoarrays by way of biomolecular recognition. Specifically, we demonstrated the spectral tuning of plasmon resonant metal nanoarrays and self-assembly of protein-functionalized QDs in a stepwise fashion with a concomitant incremental increase in separation from the metal surface through biotin-streptavidin spacer units.

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

    Energy Technology Data Exchange (ETDEWEB)

    Lee, In-Hee; Yang, Kyung-Ae; Zhang, Byoung-Tak [School of Computer Science and Engineering, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Lee, Ji-Hoon [Center for Bioinformation Technology, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Park, Ji-Yoon; Chai, Young Gyu [Division of Molecular and Life Sciences, Hanyang University, 1271 Sa-dong, Sangnok-gu, Ansan, Gyeonggi-do 426-791 (Korea, Republic of); Lee, Jae-Hoon [Fachgebiet Mikrobiologie und Genetik, Institut fuer Biotechnologie, Technische Universitaet Berlin, Gustav-Meyer Allee 25, D-13355 Berlin (Germany)], E-mail: btzhang@bi.snu.ac.kr

    2008-10-01

    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.

  5. 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.

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

    Science.gov (United States)

    Fei, Yiyan; Landry, James P; Li, Yanhong; Yu, Hai; Lau, Kam; Huang, Shengshu; Chokhawala, Harshal A; Chen, Xi; Zhu, X D

    2013-11-01

    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.

  7. Selection and design of solvents

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    and design of solvents will be presented together with application examples. The selection problem is defined as finding known chemicals that match the desired functions of a solvent for a specified set of applications. The design problem is defined as finding the molecular structure (or mixture of molecules....... With increasing interest on issues such as waste, sustainability, environmental impact and green chemistry, the selection and design of solvents have become important problems that need to be addressed during chemical product-process design and development. Systematic methods and tools suitable for selection...

  8. Handbook of organic solvent properties

    CERN Document Server

    Smallwood, Ian

    2012-01-01

    The properties of 72 of the most commonly used solvents are given, tabulated in the most convenient way, making this book a joy for industrial chemists to use as a desk reference. The properties covered are those which answer the basic questions of: Will it do the job? Will it harm the user? Will it pollute the air? Is it easy to handle? Will it pollute the water? Can it be recovered or incinerated? These are all factors that need to be considered at the early stages of choosing a solvent for a new product or process.A collection of the physical properties of most commonly used solvents, their

  9. The Solvent Selection framework: solvents for organic synthesis, separation processes and ionic-organic synthesis

    DEFF Research Database (Denmark)

    Mitrofanov, Igor; Sansonetti, Sascha; Abildskov, Jens;

    2012-01-01

    problems are presented: 1) solvent selection and design for organic synthesis, 2) solvent screening and design of solvent mixtures for pharmaceutical applications and 3) ionic liquids selection and design as solvents. The application of the framework is highlighted successfully through case studies...... focusing on solvent replacement problem in organic synthesis and solvent mixture design for ibuprofen respectively....

  10. Hansen Cleaning Solvent Research Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Environmental regulation will force current baseline  precision cleaning solvent (AK-225) to be phased out starting 2015. We plan to develop  a new...

  11. 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.

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

    Science.gov (United States)

    Thurber, Kent R.; Tycko, Robert

    2009-01-01

    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 25 K using roughly 3 liters/hour 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 13C NMR data for two biomolecular samples, namely the peptide Aβ14–23 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 13C MAS NMR linewidths are discussed. PMID:18922715

  13. Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics.

    Science.gov (United States)

    Kubelka, Jan

    2009-04-01

    Many important biochemical processes occur on the time-scales of nanoseconds and microseconds. The introduction of the laser temperature-jump (T-jump) to biophysics more than a decade ago opened these previously inaccessible time regimes up to direct experimental observation. Since then, laser T-jump methodology has evolved into one of the most versatile and generally applicable methods for studying fast biomolecular kinetics. This perspective is a review of the principles and applications of the laser T-jump technique in biophysics. A brief overview of the T-jump relaxation kinetics and the historical development of laser T-jump methodology is presented. The physical principles and practical experimental considerations that are important for the design of the laser T-jump experiments are summarized. These include the Raman conversion for generating heating pulses, considerations of size, duration and uniformity of the temperature jump, as well as potential adverse effects due to photo-acoustic waves, cavitation and thermal lensing, and their elimination. The laser T-jump apparatus developed at the NIH Laboratory of Chemical Physics is described in detail along with a brief survey of other laser T-jump designs in use today. Finally, applications of the laser T-jump in biophysics are reviewed, with an emphasis on the broad range of problems where the laser T-jump methodology has provided important new results and insights into the dynamics of the biomolecular processes.

  14. DockScreen: A Database of In Silico Biomolecular Interactions to Support Computational Toxicology

    Directory of Open Access Journals (Sweden)

    Michael-Rock Goldsmith

    2014-01-01

    Full Text Available We have developed DockScreen, a database of in silico biomolecular interactions designed to enable rational molecular toxicological insight within a computational toxicology framework. This database is composed of chemical/target (receptor and enzyme binding scores calculated by molecular docking of more than 1000 chemicals into 150 protein targets and contains nearly 135 thousand unique ligand/target binding scores. Obtaining this dataset was achieved using eHiTS (Simbiosys Inc., a fragment-based molecular docking approach with an exhaustive search algorithm, on a heterogeneous distributed high-performance computing framework. The chemical landscape covered in DockScreen comprises selected environmental and therapeutic chemicals. The target landscape covered in DockScreen was selected based on the availability of high-quality crystal structures that covered the assay space of phase I ToxCast in vitro assays. This in silico data provides continuous information that establishes a means for quantitatively comparing, on a structural biophysical basis, a chemical’s profile of biomolecular interactions. The combined minimum-score chemical/target matrix is provided.

  15. Neutral-particle emission in collisions of electrons with biomolecular ions in an electrostatic storage ring

    International Nuclear Information System (INIS)

    Electron-biomolecular ion collisions were studied using an electrostatic storage ring with a merging electron beam device. Biomolecular ions produced by an electrospray ion source and accelerated to 20 keV/charge were injected into the ring after being mass-analyzed. The circulating ion beam was then merged with an electron beam. Neutral reaction products in collisions of electrons with ions were detected by a micro-channel plate outside of the ring. Electron-ion collisions were studied for multiply-deprotonated oligonucleotide and peptide anions as well as singly protonated oligonucleotide and peptide cations. For peptide cations, neutrals were resonantly emitted at an electron energy of around 6.5 eV, which was almost independent of the ion masses. This is deduced to come from electron-ion recombination, resulting in the cleavage of a peptide bond. For DNA oligonucleotide cations, resonant neutral particle emission was also observed. In electron and DNA anion collisions, neutrals started to increase from definite threshold energies, where the threshold energies increased in proportion to the ion charge. The same was found for peptide anions. The origin of this phenomenon is discussed

  16. Submicrometer Hall sensors for detection of magnetic nanoparticles in biomolecular sensing

    Science.gov (United States)

    Mihajlovic, Goran; Xiong, P.; von Molnar, S.; Ohtani, K.; Ohno, H.; Field, M.; Sullivan, G. J.

    2006-03-01

    Significant progress has been made in the recent years in synthesis and biomolecular functionalization of magnetic nanoparticles. These magnetic bio-nanolabels can be utilized as protein or gene markers in biomolecular sensing assays, in contrast to the much larger micron sized magnetic beads that are usually limited to cell labeling. However, the low magnetic moments of individual nanoparticles (10^4-10^5 μB) render their sensitive detection still a challenging task. In order to address this issue we are developing miniaturized Hall sensors from InAs/AlSb quantum well semiconductor heterostructures with active Hall cross areas down to 300 nm x 300 nm. Our preliminary characterization measurements performed at room temperature show functional devices with magnetic field resolution < 100 μT/√Hz at frequencies above 100 Hz, yielding a moment sensitivity ˜ 10^5 μB. In addition to the progress in improving the moment sensitivity of the submicrometer Hall detectors, we will also present efforts in device integration with on-chip microcoils for the generation of local magnetic excitation fields. Results on nanoparticle detection will also be presented.

  17. The detection of specific biomolecular interactions with micro-Hall magnetic sensors

    Science.gov (United States)

    Manandhar, Pradeep; Chen, Kan-Sheng; Aledealat, Khaled; Mihajlović, Goran; Yun, C. Steven; Field, Mark; Sullivan, Gerard J.; Strouse, Geoffrey F.; Bryant Chase, P.; von Molnár, Stephan; Xiong, Peng

    2009-09-01

    The detection of reagent-free specific biomolecular interactions through sensing of nanoscopic magnetic labels provides one of the most promising routes to biosensing with solid-state devices. In particular, Hall sensors based on semiconductor heterostructures have shown exceptional magnetic moment sensitivity over a large dynamic field range suitable for magnetic biosensing using superparamagnetic labels. Here we demonstrate the capability of such micro-Hall sensors to detect specific molecular binding using biotin-streptavidin as a model system. We apply dip-pen nanolithography to selectively biotinylate the active areas of InAs micro-Hall devices with nanoscale precision. Specific binding of complementarily functionalized streptavidin-coated superparamagnetic beads to the Hall crosses occurs via molecular recognition, and magnetic detection of the assembled beads is achieved at room temperature using phase sensitive micro-Hall magnetometry. The experiment constitutes the first unambiguous demonstration of magnetic detection of specific biomolecular interactions with semiconductor micro-Hall sensors, and the selective molecular functionalization and resulting localized bead assembly demonstrate the possibility of multiplexed sensing of multiple target molecules using a single device with an array of micro-Hall sensors.

  18. Access Denied

    Science.gov (United States)

    Villano, Matt

    2008-01-01

    Building access control (BAC)--a catchall phrase to describe the systems that control access to facilities across campus--has traditionally been handled with remarkably low-tech solutions: (1) manual locks; (2) electronic locks; and (3) ID cards with magnetic strips. Recent improvements have included smart cards and keyless solutions that make use…

  19. Solvent/Non-Solvent Sintering To Make Microsphere Scaffolds

    Science.gov (United States)

    Laurencin, Cato T.; Brown, Justin L.; Nair, Lakshmi

    2011-01-01

    A solvent/non-solvent sintering technique has been devised for joining polymeric microspheres to make porous matrices for use as drug-delivery devices or scaffolds that could be seeded with cells for growing tissues. Unlike traditional sintering at elevated temperature and pressure, this technique is practiced at room temperature and pressure and, therefore, does not cause thermal degradation of any drug, protein, or other biochemical with which the microspheres might be loaded to impart properties desired in a specific application. Also, properties of scaffolds made by this technique are more reproducible than are properties of comparable scaffolds made by traditional sintering. The technique involves the use of two miscible organic liquids: one that is and one that is not a solvent for the affected polymer. The polymeric microspheres are placed in a mold having the size and shape of the desired scaffold, then the solvent/non-solvent mixture is poured into the mold to fill the void volume between the microspheres, then the liquid mixture is allowed to evaporate. Some of the properties of the resulting scaffold can be tailored through choice of the proportions of the liquids and the diameter of the microspheres.

  20. Protease activation in glycerol-based deep eutectic solvents

    OpenAIRE

    Zhao, Hua; Baker, Gary A.; Holmes, Shaletha

    2011-01-01

    Deep eutectic solvents (DESs) consisting of mixtures of a choline salt (chloride or acetate form) and glycerol are prepared as easily accessible, biodegradable, and inexpensive alternatives to conventional aprotic cation-anion paired ionic liquids. These DES systems display excellent fluidity coupled with thermal stability to nearly 200 °C. In this work, the transesterification activities of cross-linked proteases (subtilisin and α-chymotrypsin), immobilized on chitosan, were individually exa...

  1. 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.

  2. Handbook of green chemistry, green solvents, supercritical solvents

    CERN Document Server

    Anastas, Paul T; Jessop, Philip G

    2014-01-01

    Green Chemistry is a vitally important subject area in a world where being as green and environmentally sound as possible is no longer a luxury but a necessity. Its applications include the design of chemical products and processes that help to reduce or eliminate the use and generation of hazardous substances. The Handbook of Green Chemistry comprises 12 volumes, split into subject-specific sets as follows: Set I: Green Catalysis Set II: Green Solvents Volume 4: Supercritical Solvents Volume 5: Reactions in Water Volume 6: Ionic Liquids

  3. Using Nature's "Tricks" To Rationally Tune the Binding Properties of Biomolecular Receptors.

    Science.gov (United States)

    Ricci, Francesco; Vallée-Bélisle, Alexis; Simon, Anna J; Porchetta, Alessandro; Plaxco, Kevin W

    2016-09-20

    The biosensor community has long focused on achieving the lowest possible detection limits, with specificity (the ability to differentiate between closely similar target molecules) and sensitivity (the ability to differentiate between closely similar target concentrations) largely being relegated to secondary considerations and solved by the inclusion of cumbersome washing and dilution steps or via careful control experimental conditions. Nature, in contrast, cannot afford the luxury of washing and dilution steps, nor can she arbitrarily change the conditions (temperature, pH, ionic strength) under which binding occurs in the homeostatically maintained environment within the cell. This forces evolution to focus at least as much effort on achieving optimal sensitivity and specificity as on achieving low detection limits, leading to the "invention" of a number of mechanisms, such as allostery and cooperativity, by which the useful dynamic range of receptors can be tuned, extended, narrowed, or otherwise optimized by design, rather than by sample manipulation. As the use of biomolecular receptors in artificial technologies matures (i.e., moves away from multistep, laboratory-bound processes and toward, for example, systems supporting continuous in vivo measurement) and these technologies begin to mimic the reagentless single-step convenience of naturally occurring chemoperception systems, the ability to artificially design receptors of enhanced sensitivity and specificity will likely also grow in importance. Thus motivated, we have begun to explore the adaptation of nature's solutions to these problems to the biomolecular receptors often employed in artificial biotechnologies. Using the population-shift mechanism, for example, we have generated nested sets of receptors and allosteric inhibitors that greatly expanded the normally limited (less than 100-fold) useful dynamic range of unmodified molecular and aptamer beacons, enabling the single-step (e.g., dilution

  4. Multiple sclerosis and organic solvents

    DEFF Research Database (Denmark)

    Mortensen, J T; Brønnum-Hansen, Henrik; Rasmussen, K

    1998-01-01

    We investigated a possible causal relation between exposure to organic solvents in Danish workers (housepainters, typographers/printers, carpenters/cabinetmakers) and onset of multiple sclerosis. Data on men included in the Danish Multiple Sclerosis Register (3,241 men) were linked with data from......, and butchers. Over a follow-up period of 20 years, we observed no increase in the incidence of multiple sclerosis among men presumed to be exposed to organic solvents. It was not possible to obtain data on potential confounders, and the study design has some potential for selection bias. Nevertheless......, the study does not support existing hypotheses regarding an association between occupational exposure to organic solvents and multiple sclerosis....

  5. Effect of temperature and magnetic field on the photocurrent response of biomolecular bulk-hetero junction

    Science.gov (United States)

    Tajima, Hiroyuki; Sekiguchi, Yusuke; Matsuda, Masaki

    2012-02-01

    The photocurrent responses were investigated for the biomolecular bulk-hetero junction of chlorophyll α (Chl-α) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-1-phenyl-(6,6)C61 (PCBM) in the temperature range between 300 K and 1.5 K under the magnetic field up to 8 T. The chopped-light photocurrent decreases on lowering the temperature. Below 10 K, photocurrent decrease was observed under the applied magnetic field. Decay of the photocurrent observed at 10 K was ascribed to the formation of the charged trap under light irradiation. The magnetic field effect (MFE) observed in this device was found to be very similar to that observed in P3HT:PCBM bulk-hetero junction at low temperatures.

  6. Biomolecular papain thin films grown by matrix assisted and conventional pulsed laser deposition: A comparative study

    Science.gov (United States)

    György, E.; Pérez del Pino, A.; Sauthier, G.; Figueras, A.

    2009-12-01

    Biomolecular papain thin films were grown both by matrix assisted pulsed laser evaporation (MAPLE) and conventional pulsed laser deposition (PLD) techniques with the aid of an UV KrF∗ (λ =248 nm, τFWHM≅20 ns) excimer laser source. For the MAPLE experiments the targets submitted to laser radiation consisted on frozen composites obtained by dissolving the biomaterial powder in distilled water at 10 wt % concentration. Conventional pressed biomaterial powder targets were used in the PLD experiments. The surface morphology of the obtained thin films was studied by atomic force microscopy and their structure and composition were investigated by Fourier transform infrared spectroscopy. The possible physical mechanisms implied in the ablation processes of the two techniques, under comparable experimental conditions were identified. The results showed that the growth mode, surface morphology as well as structure of the deposited biomaterial thin films are determined both by the incident laser fluence value as well as target preparation procedure.

  7. A Review of Salam Phase Transition in Protein Amino Acids Implication for Biomolecular Homochirality

    CERN Document Server

    Bai, F; Bai, Fan; Wang, Wenqing

    2002-01-01

    The origin of chirality, closely related to the evolution of life on the earth, has long been debated. In 1991, Abdus Salam suggested a novel approach to achieve biomolecular homochirality by a phase transition. In his subsequent publication, he predicted that this phase transition could eventually change D-amino acids to L-amino acids as C -H bond would break and H atom became a superconductive atom. Since many experiments denied the configuration change in amino acids, Salam hypothesis aroused suspicion. This paper is aimed to provide direct experimental evidence of a phase transition in alanine, valine single crystals but deny the configuration change of D- to L- enantiomers. New views on Salam phase transition are presented to revalidate its great importance in the origin of homochirality.

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

    International Nuclear Information System (INIS)

    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.

  9. Settlement specifics: Effective induction of abalone settlement and metamorphosis corresponds to biomolecular composition of natural cues.

    Science.gov (United States)

    Williams, Elizabeth A; Cummins, Scott; Degnan, Sandie M

    2009-07-01

    Chemical signaling plays a major role in shaping life history processes that drive ecology and evolution in marine systems, notably including habitat selection by marine invertebrate larvae that must settle out of the plankton onto the benthos.1 For larvae, the identification of appropriate habitats in which to settle and undergo metamorphosis to the adult form relies heavily on the recognition of cues indicative of a favorable environment. By documenting settlement responses of larvae of the tropical abalone, Haliotis asinina, to a range of coralline algae species, we recently highlighted the species-specific nature of this interaction.2 Here, we demonstrate that this specificity is likely driven by chemical, rather than physical, properties of the algae. Our initial characterization of the surface cell biomarkers from three different algal species shows that inductive cue biomolecular composition correlates with variations in larval settlement response.

  10. Biomolecular ion detection using high-temperature superconducting MgB2 strips

    Science.gov (United States)

    Zen, N.; Shibata, H.; Mawatari, Y.; Koike, M.; Ohkubo, M.

    2015-06-01

    Superconducting strip ion detectors (SSIDs) are promising for realization of ideal ion detection with 100% efficiency and nanosecond-scale time response in time-of-flight mass spectrometry. We have detected single biomolecular ions in the keV range using a 10-nm-thick and 250-nm-wide strip of a high temperature superconductor, magnesium diboride (MgB2), at temperatures of up to 13 K. The output pulse shape is explained remarkably well using circuit simulations and time-dependent Ginzburg-Landau simulations coupled with a heat diffusion equation. The simulations show that the hot spot model is applicable to the proposed MgB2-SSIDs and the normal region expansion is completed within 16 ps, which corresponds to a maximum length of 1010 nm.

  11. Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic

    CERN Document Server

    Privman, Vladimir; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny

    2010-01-01

    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by hydrogen peroxide, was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved...

  12. A program to calculate non-bonded interaction energy in biomolecular aggregates.

    Science.gov (United States)

    Sundaram, K; Prasad, C V

    1982-02-01

    This paper describes a program to calculate intermolecular as well as intramolecular electronic potential energy resulting from non-bonded interactions. The underlying theory is obtained by the application of Rayleigh-Schroedinger perturbation theory to non-overlap regions of a molecular system. The rigorous theoretical expressions for the energy terms are simplified by approximations consistent with those commonly employed in semi-empirical molecular orbital theories. The program is particularly suited for the study of biomolecular assemblies, and in situations where insight into contributions to total energy from various component interaction types is desired. The inclusion of the non-additive dispersion effects in this approach makes it especially interesting for the study of cooperative phenomena in the light of a recent finding [1]. PMID:7067416

  13. Accessible Knowledge - Knowledge on Accessibility

    DEFF Research Database (Denmark)

    Kirkeby, Inge Mette

    2015-01-01

    Although serious efforts are made internationally and nationally, it is a slow process to make our physical environment accessible. In the actual design process, architects play a major role. But what kinds of knowledge, including research-based knowledge, do practicing architects make use of when...... designing accessible environments? The answer to the question is crucially important since it affects how knowledge is distributed and how accessibility can be ensured. In order to get first-hand knowledge about the design process and the sources from which they gain knowledge, 11 qualitative interviews...... were conducted with architects with experience of designing for accessibility. The analysis draws on two theoretical distinctions. The first is research-based knowledge versus knowledge used by architects. The second is context-independent knowledge versus context-dependent knowledge. The practitioners...

  14. Biomolecular Characterization of Diazotrophs Isolated from the Tropical Soil in Malaysia

    Directory of Open Access Journals (Sweden)

    Zulkifli H Shamsuddin

    2013-08-01

    Full Text Available This study was conducted to evaluate selected biomolecular characteristics of rice root-associated diazotrophs isolated from the Tanjong Karang rice irrigation project area of Malaysia. Soil and rice plant samples were collected from seven soil series belonging to order Inceptisol (USDA soil taxonomy. A total of 38 diazotrophs were isolated using a nitrogen-free medium. The biochemical properties of the isolated bacteria, such as nitrogenase activity, indoleacetic acid (IAA production and sugar utilization, were measured. According to a cluster analysis of Jaccard’s similarity coefficients, the genetic similarities among the isolated diazotrophs ranged from 10% to 100%. A dendogram constructed using the unweighted pair-group method with arithmetic mean (UPGMA showed that the isolated diazotrophs clustered into 12 groups. The genomic DNA rep-PCR data were subjected to a principal component analysis, and the first four principal components (PC accounted for 52.46% of the total variation among the 38 diazotrophs. The 10 diazotrophs that tested highly positive in the acetylene reduction assay (ARA were identified as Bacillus spp. (9 diazotrophs and Burkholderia sp. (Sb16 using the partial 16S rRNA gene sequence analysis. In the analysis of the biochemical characteristics, three principal components were accounted for approximately 85% of the total variation among the identified diazotrophs. The examination of root colonization using scanning electron microscopy (SEM and transmission electron microscopy (TEM proved that two of the isolated diazotrophs (Sb16 and Sb26 were able to colonize the surface and interior of rice roots and fixed 22%–24% of the total tissue nitrogen from the atmosphere. In general, the tropical soils (Inceptisols of the Tanjong Karang rice irrigation project area in Malaysia harbor a diverse group of diazotrophs that exhibit a large variation of biomolecular characteristics.

  15. 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

  16. Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction.

    Science.gov (United States)

    Wang, Ling; Stumm, Boris; Helms, Volkhard

    2010-03-01

    Biomolecular association and dissociation reactions take place on complicated interaction free energy landscapes that are still very hard to characterize computationally. For large enough distances, though, it often suffices to consider the six relative translational and rotational degrees of freedom of the two particles treated as rigid bodies. Here, we computed the six-dimensional free energy surface of a dimer of water-soluble alpha-helices by scanning these six degrees of freedom in about one million grid points. In each point, the relative free energy difference was computed as the sum of the polar and nonpolar solvation free energies of the helix dimer and of the intermolecular coulombic interaction energy. The Dijkstra graph algorithm was then applied to search for the lowest cost dissociation pathways based on a weighted, directed graph, where the vertices represent the grid points, the edges connect the grid points and their neighbors, and the weights are the reaction costs between adjacent pairs of grid points. As an example, the configuration of the bound state was chosen as the source node, and the eight corners of the translational cube were chosen as the destination nodes. With the strong electrostatic interaction of the two helices giving rise to a clearly funnel-shaped energy landscape, the eight lowest-energy cost pathways coming from different orientations converge into a well-defined pathway for association. We believe that the methodology presented here will prove useful for identifying low-energy association and dissociation pathways in future studies of complicated free energy landscapes for biomolecular interaction. PMID:19603501

  17. Understanding the Results of Electrostatics Calculations: Visualizing Molecular 'Isopotential' Surfaces

    OpenAIRE

    Mura, Cameron

    2016-01-01

    This document attempts to clarify potential confusion regarding electrostatics calculations, specifically in the context of biomolecular structure and specifically as regards the units typically used to contour/visualize isopotential surfaces, potentials mapped onto molecular solvent-accessible surfaces, etc.

  18. Open access

    CERN Document Server

    Suber, Peter

    2012-01-01

    The Internet lets us share perfect copies of our work with a worldwide audience at virtually no cost. We take advantage of this revolutionary opportunity when we make our work "open access": digital, online, free of charge, and free of most copyright and licensing restrictions. Open access is made possible by the Internet and copyright-holder consent, and many authors, musicians, filmmakers, and other creators who depend on royalties are understandably unwilling to give their consent. But for 350 years, scholars have written peer-reviewed journal articles for impact, not for money, and are free to consent to open access without losing revenue. In this concise introduction, Peter Suber tells us what open access is and isn't, how it benefits authors and readers of research, how we pay for it, how it avoids copyright problems, how it has moved from the periphery to the mainstream, and what its future may hold. Distilling a decade of Suber's influential writing and thinking about open access, this is the indispe...

  19. Hemodialysis access - self care

    Science.gov (United States)

    Kidney failure - chronic-hemodialysis access; Renal failure - chronic-hemodialysis access; Chronic renal insufficiency - hemodialysis access; Chronic kidney failure - hemodialysis access; Chronic renal failure - hemodialysis access; dialysis - hemodialysis access

  20. Improved Purex solvent scrubbing methods

    Energy Technology Data Exchange (ETDEWEB)

    Mailen, J.C.; Tallent, O.K.

    1984-01-01

    Studies of hydrazine and hydroxylamine salts as solvent scrubbing agents that can be decomposed into gases are summarized. Results from testing of countercurrent scrubbers and solid sorber columns that produce lesser amounts of permanent salts are reported. The status of studies of the acid-degradation of paraffin diluent and the options for removal of long-chain organic acids is given.

  1. Which solvent for olfactory testing?

    Science.gov (United States)

    Philpott, C M; Goodenough, P C; Wolstenholme, C R; Murty, G E

    2004-12-01

    The physical properties of any carrier can deteriorate over time and thus alter the results in any olfactory test. The aim of this study was to evaluate clinically potential solvents as a clean odourless carrier for olfactory testing. Sweet almond oil, pure coconut oil, pure peach kernel oil, dipropylene glycol, monopropylene glycol, mineral oil and silicone oil were studied. The experimentation was conducted in two parts. First, an olfactory device was used to conduct air through the solvents on a weekly basis using a cohort of six volunteers to assess the perceived odour of each solvent at weekly intervals. Secondly a cross-reference test was performed using small bottled solutions of phenylethyl-alcohol and 1-butanol in 10-fold dilutions to compare any perceived difference in concentrations over a period of 8 weeks. We concluded that mineral oil is the most suitable carrier for the purpose of olfactory testing, possessing many desirable characteristics of an olfactory solvent, and that silicone oil may provide a suitable alternative for odorants with which it is miscible.

  2. Nanopapers for organic solvent nanofiltration.

    OpenAIRE

    Mautner, A.; Lee, K Y; P. Lahtinen; Hakalahti, M.; Tammelin, T. (Tuija); Li, K.; Bismarck, A.

    2014-01-01

    Would it not be nice to have an organic solvent nanofiltration membrane made from renewable resources that can be manufactured as simply as producing paper? Here the production of nanofiltration membranes made from nanocellulose by applying a papermaking process is demonstrated. Manufacture of the nanopapers was enabled by inducing flocculation of nanofibrils upon addition of trivalent ions.

  3. Access French

    CERN Document Server

    Grosz, Bernard

    2014-01-01

    Access is the major new language series designed with the needs of today's generation of students firmly in mind. Whether learning for leisure or business purposes or working towards a curriculum qualification, Access French is specially designed for adults of all ages and gives students a thorough grounding in all the skills required to understand, speak, read and write contemporary French from scratch. The coursebook consists of 10 units covering different topic areas, each of which includes Language Focus panels explaining the structures covered and a comprehensive glossary. Learning tips

  4. Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes.

    Science.gov (United States)

    Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C

    2014-07-24

    Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagates into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor-Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Therefore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface. PMID:24999844

  5. Dipolar correlations in structured solvents under nanoconfinement.

    Science.gov (United States)

    Buyukdagli, Sahin; Blossey, Ralf

    2014-06-21

    We study electrostatic correlations in structured solvents confined to nanoscale systems. We derive variational equations of Netz-Orland type for a model liquid composed of finite size dipoles. These equations are solved for both dilute solvents and solvents at physiological concentrations in a slit nanopore geometry. Correlation effects are of major importance for the dielectric reduction and anisotropy of the solvent resulting from dipole image interactions and also lead to a reduction of van der Waals attractions between low dielectric bodies. Finally, by comparison with other recently developed self-consistent theories and experiments, we scrutinize the effect of solvent-membrane interactions on the differential capacitance of the charged liquid in contact with low dielectric substrates. The interfacial solvent depletion driven by solvent-image interactions plays the major role in the observed low values of the experimental capacitance data, while non-locality associated with the extended charge structure of solvent molecules only brings a minor contribution. PMID:24952564

  6. Dipolar correlations in structured solvents under nanoconfinement

    OpenAIRE

    Buyukdagli, Sahin; Blossey, Ralf

    2014-01-01

    We study electrostatic correlations in structured solvents confined to nanoscale systems. We derive variational equations of Netz-Orland type for a model liquid composed of finite size dipoles. These equations are solved for both dilute solvents and solvents at physiological concentrations in a slit nanopore geometry. Correlation effects are of major importance for the dielectric reduction and anisotropy of the solvent resulting from dipole image interactions and also lead to a reduction of v...

  7. Detection and kinetic studies of triplex formation by oligodeoxynucleotides using real-time biomolecular interaction analysis (BIA).

    OpenAIRE

    Bates, P. J.; Dosanjh, H. S.; S. Kumar; Jenkins, T. C.; Laughton, C A; Neidle, S

    1995-01-01

    Real-time biomolecular interaction analysis (BIA) has been applied to triplex formation between oligodeoxynucleotides. 5'-Biotinylated oligonucleotides were immobilised on the streptavidin-coated surface of a biosensor chip and subsequently hybridised to their complementary strand. Sequence-specific triplex formation was observed when a suitable third-strand oligopyrimidine was injected over the surface-bound duplex. In addition, a single-stranded oligonucleotide immobilised on the chip surfa...

  8. Solvent Extraction of Furfural From Biomass

    Science.gov (United States)

    Humphrey, M. F.

    1984-01-01

    Solvent-extraction method reduces energy required to remove furfural produced during acid hydrolysis of biomass. Acid hydrolysis performed in vessel containing both solvents and reacting ingredients. With intimate contact between solvents and aqueous hydrolyis liqour, furfural removed form liquor almost as fast as it forms.

  9. The hype with ionic liquids as solvents

    Science.gov (United States)

    Kunz, Werner; Häckl, Katharina

    2016-09-01

    In this mini review, we give our personal opinion about the present state of the art concerning Ionic Liquids, proposed as alternative solvents. In particular, we consider their different drawbacks and disadvantages and discuss the critical aspects of the research of Ionic Liquids as solvents. Finally, we point out some aspects on potentially promising Ionic Liquid solvents.

  10. Reactions and Separations in Green Solvents

    NARCIS (Netherlands)

    Van Spronsen, J.

    2010-01-01

    Most chemical processes involve solvents in the reaction and the separation step. These solvents give rise to a heavy environmental and economical burden. Moreover, these solvents are based on non-sustainable resources like petroleum. The aim of this thesis has been to develop a number of alternativ

  11. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.

    Science.gov (United States)

    Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo

    2015-12-15

    Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to

  12. Single-Molecule Pull-down FRET (SiMPull-FRET) to dissect the mechanisms of biomolecular machines

    Science.gov (United States)

    Kahlscheuer, Matthew L.; Widom, Julia; Walter, Nils G.

    2016-01-01

    Spliceosomes are multi-megadalton RNA-protein complexes responsible for the faithful removal of non-coding segments (introns) from pre-messenger RNAs (pre-mRNAs), a process critical for the maturation of eukaryotic mRNAs for subsequent translation by the ribosome. Both the spliceosome and ribosome, as well as many other RNA and DNA processing machineries, contain central RNA components that endow biomolecular complexes with precise, sequence-specific nucleic acid recognition and versatile structural dynamics. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) microscopy is a powerful tool for the study of local and global conformational changes of both simple and complex biomolecular systems involving RNA. The integration of biochemical tools such as immunoprecipitation with advanced methods in smFRET microscopy and data analysis has opened up entirely new avenues towards studying the mechanisms of biomolecular machines isolated directly from complex biological specimens such as cell extracts. Here we detail the general steps for using prism-based total internal reflection fluorescence (TIRF) microscopy in exemplary single molecule pull-down FRET (SiMPull-FRET) studies of the yeast spliceosome and discuss the broad application potential of this technique. PMID:26068753

  13. Solvent cleaning system and method for removing contaminants from solvent used in resin recycling

    Science.gov (United States)

    Bohnert, George W.; Hand, Thomas E.; DeLaurentiis, Gary M.

    2009-01-06

    A two step solvent and carbon dioxide based system that produces essentially contaminant-free synthetic resin material and which further includes a solvent cleaning system for periodically removing the contaminants from the solvent so that the solvent can be reused and the contaminants can be collected and safely discarded in an environmentally safe manner.

  14. Hemodialysis access procedures

    Science.gov (United States)

    Kidney failure - chronic-dialysis access; Renal failure - chronic-dialysis access; Chronic renal insufficiency-dialysis access; Chronic kidney failure-dialysis access; Chronic renal failure-dialysis access

  15. Insecticide solvents: interference with insecticidal action.

    Science.gov (United States)

    Brattsten, L B; Wilkinson, C F

    1977-06-10

    Several commercial solvent mixtures commonly used as insecticide carriers in spray formulations increase by more than threefold the microsomal N-demethylation of p-chloro N-methylaniline in midgut preparations of southern army-worm (Spodoptera eridania) larvae exposed orally to the test solvents. Under laboratory conditions, the same solvent mixtures exhibit a protective action against the in vivo toxicity of the insecticide carbaryl to the larvae. The data are discussed with respect to possible solvent-insecticide interactions occurring under field conditions and, more broadly, to potential toxicological hazards of these solvents to humans. PMID:860135

  16. 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

    2016-01-01

    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. PMID:27506964

  17. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components.

    Science.gov (United States)

    Pardee, Keith; Green, Alexander A; Takahashi, Melissa K; Braff, Dana; Lambert, Guillaume; Lee, Jeong Wook; Ferrante, Tom; Ma, Duo; Donghia, Nina; Fan, Melina; Daringer, Nichole M; Bosch, Irene; Dudley, Dawn M; O'Connor, David H; Gehrke, Lee; Collins, James J

    2016-05-19

    The recent Zika virus outbreak highlights the need for low-cost diagnostics that can be rapidly developed for distribution and use in pandemic regions. Here, we report a pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome. By linking isothermal RNA amplification to toehold switch RNA sensors, we detect clinically relevant concentrations of Zika virus sequences and demonstrate specificity against closely related Dengue virus sequences. When coupled with a novel CRISPR/Cas9-based module, our sensors can discriminate between viral strains with single-base resolution. We successfully demonstrate a simple, field-ready sample-processing workflow and detect Zika virus from the plasma of a viremic macaque. Our freeze-dried biomolecular platform resolves important practical limitations to the deployment of molecular diagnostics in the field and demonstrates how synthetic biology can be used to develop diagnostic tools for confronting global health crises. PAPERCLIP. PMID:27160350

  18. A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis.

    Science.gov (United States)

    Larimer, Curtis; Winder, Eric; Jeters, Robert; Prowant, Matthew; Nettleship, Ian; Addleman, Raymond Shane; Bonheyo, George T

    2016-01-01

    The accumulation of bacteria in surface-attached biofilms can be detrimental to human health, dental hygiene, and many industrial processes. Natural biofilms are soft and often transparent, and they have heterogeneous biological composition and structure over micro- and macroscales. As a result, it is challenging to quantify the spatial distribution and overall intensity of biofilms. In this work, a new method was developed to enhance the visibility and quantification of bacterial biofilms. First, broad-spectrum biomolecular staining was used to enhance the visibility of the cells, nucleic acids, and proteins that make up biofilms. Then, an image analysis algorithm was developed to objectively and quantitatively measure biofilm accumulation from digital photographs and results were compared to independent measurements of cell density. This new method was used to quantify the growth intensity of Pseudomonas putida biofilms as they grew over time. This method is simple and fast, and can quantify biofilm growth over a large area with approximately the same precision as the more laborious cell counting method. Stained and processed images facilitate assessment of spatial heterogeneity of a biofilm across a surface. This new approach to biofilm analysis could be applied in studies of natural, industrial, and environmental biofilms.

  19. Toxicity evaluation of PEDOT/biomolecular composites intended for neural communication electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Asplund, M; Thaning, E; Von Holst, H [Division of Neuronic Engineering, School of Technology and Health, Royal Institute of Technology, SE-14152 Huddinge (Sweden); Lundberg, J [Section for Neuroradiology, R2:02 NKK-lab, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, Solna, SE-171 76, Stockholm (Sweden); Sandberg-Nordqvist, A C [Section of Clinical CNS Research, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, Solna, SE-171 76, Stockholm (Sweden); Kostyszyn, B [Center for Hearing and Communication Research, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, M1:01, SE-171 76 Stockholm (Sweden); Inganaes, O, E-mail: maria.asplund@sth.kth.s [Biomolecular and Organic Electronics, IFM, Linkoeping University, SE-581 83 Linkoeping (Sweden)

    2009-08-15

    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.

  20. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components.

    Science.gov (United States)

    Pardee, Keith; Green, Alexander A; Takahashi, Melissa K; Braff, Dana; Lambert, Guillaume; Lee, Jeong Wook; Ferrante, Tom; Ma, Duo; Donghia, Nina; Fan, Melina; Daringer, Nichole M; Bosch, Irene; Dudley, Dawn M; O'Connor, David H; Gehrke, Lee; Collins, James J

    2016-05-19

    The recent Zika virus outbreak highlights the need for low-cost diagnostics that can be rapidly developed for distribution and use in pandemic regions. Here, we report a pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome. By linking isothermal RNA amplification to toehold switch RNA sensors, we detect clinically relevant concentrations of Zika virus sequences and demonstrate specificity against closely related Dengue virus sequences. When coupled with a novel CRISPR/Cas9-based module, our sensors can discriminate between viral strains with single-base resolution. We successfully demonstrate a simple, field-ready sample-processing workflow and detect Zika virus from the plasma of a viremic macaque. Our freeze-dried biomolecular platform resolves important practical limitations to the deployment of molecular diagnostics in the field and demonstrates how synthetic biology can be used to develop diagnostic tools for confronting global health crises. PAPERCLIP.

  1. A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis.

    Science.gov (United States)

    Larimer, Curtis; Winder, Eric; Jeters, Robert; Prowant, Matthew; Nettleship, Ian; Addleman, Raymond Shane; Bonheyo, George T

    2016-01-01

    The accumulation of bacteria in surface-attached biofilms can be detrimental to human health, dental hygiene, and many industrial processes. Natural biofilms are soft and often transparent, and they have heterogeneous biological composition and structure over micro- and macroscales. As a result, it is challenging to quantify the spatial distribution and overall intensity of biofilms. In this work, a new method was developed to enhance the visibility and quantification of bacterial biofilms. First, broad-spectrum biomolecular staining was used to enhance the visibility of the cells, nucleic acids, and proteins that make up biofilms. Then, an image analysis algorithm was developed to objectively and quantitatively measure biofilm accumulation from digital photographs and results were compared to independent measurements of cell density. This new method was used to quantify the growth intensity of Pseudomonas putida biofilms as they grew over time. This method is simple and fast, and can quantify biofilm growth over a large area with approximately the same precision as the more laborious cell counting method. Stained and processed images facilitate assessment of spatial heterogeneity of a biofilm across a surface. This new approach to biofilm analysis could be applied in studies of natural, industrial, and environmental biofilms. PMID:26643074

  2. AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems

    Science.gov (United States)

    Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew

    2013-11-01

    A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of the fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/~lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage. Restrictions: Only three or six significant digits options are provided in this version. Unusual features: Most of the codes are in Fortran77 style. Memory allocation functions from Fortran90 and above are used in a few subroutines. Additional comments: The current version of the codes is designed and written for single core/processor desktop machines. Check http://lsec.cc.ac.cn/lubz/afmpb.html for updates and changes. Running time: The running time varies with the number of discretized elements (N) in the system and their distributions. In most cases, it scales linearly as a function of N.

  3. Amplified Immunoassay of Human IgG Using Real-time Biomolecular Interaction Analysis (BIA) Technology

    Institute of Scientific and Technical Information of China (English)

    PEI,Ren-Jun(裴仁军); CUI,Xiao-Qiang(崔小强); YANG,Xiu-Rong(杨秀荣); WANG,Er-Kang(汪尔康)

    2002-01-01

    An automated biomolecular interaction analysis instrument (BIAcore) based on surface plasmon resonance (SPR) has been used to determine human immunoglobulin G (IgG) in real time. Polyclonal anti-human IgG antibody was covalently immobilized to a carboxymethyldextran-modified gold film surface. The samples of human IgG prepared in HBS buffer were poured over the immobilized surface. The signal amplification antibody was applied to amplify the response signal. After each measurement, the surface was regenerated with 0.1 mol/L H3PO4. The assay was rapid, requiring only 30 min for antibody immobilization and 20 min for each subsequent process of immune binding, antibody amplification and regeneration. The antibody immobilized surface had good response to human IgG in the range of 0.12-60 nmol/L with a detection limit of 60 pmoL/L. The same antibody immobilized surface could be used for more than 110 cycles of binding, amplificafion and regeneration. The results demonstrate that the sensitivity, specificity and reproducibility of amplified immunoassay using real-time BIA technology are satisfactory.

  4. Biomolecular environment, quantification, and intracellular interaction of multifunctional magnetic SERS nanoprobes.

    Science.gov (United States)

    Büchner, Tina; Drescher, Daniela; Merk, Virginia; Traub, Heike; Guttmann, Peter; Werner, Stephan; Jakubowski, Norbert; Schneider, Gerd; Kneipp, Janina

    2016-08-15

    Multifunctional composite nanoprobes consisting of iron oxide nanoparticles linked to silver and gold nanoparticles, Ag-Magnetite and Au-Magnetite, respectively, were introduced by endocytic uptake into cultured fibroblast cells. The cells containing the non-toxic nanoprobes were shown to be displaceable in an external magnetic field and can be manipulated in microfluidic channels. The distribution of the composite nanostructures that are contained in the endosomal system is discussed on the basis of surface-enhanced Raman scattering (SERS) mapping, quantitative laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) micromapping, and cryo soft X-ray tomography (cryo soft-XRT). Cryo soft-XRT of intact, vitrified cells reveals that the composite nanoprobes form intra-endosomal aggregates. The nanoprobes provide SERS signals from the biomolecular composition of their surface in the endosomal environment. The SERS data indicate the high stability of the nanoprobes and of their plasmonic properties in the harsh environment of endosomes and lysosomes. The spectra point at the molecular composition at the surface of the Ag-Magnetite and Au-Magnetite nanostructures that is very similar to that of other composite structures, but different from the composition of pure silver and gold SERS nanoprobes used for intracellular investigations. As shown by the LA-ICP-MS data, the uptake efficiency of the magnetite composites is approximately two to three times higher than that of the pure gold and silver nanoparticles. PMID:27353290

  5. A coarse-grained model for the simulations of biomolecular interactions in cellular environments

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao, E-mail: yinghao.wu@einstein.yu.edu [Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461 (United States)

    2014-02-07

    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.

  6. Biomolecular Nano-Flow-Sensor to Measure Near-Surface Flow

    Directory of Open Access Journals (Sweden)

    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

  7. Nanoscale Biomolecular Detection Limit for Gold Nanoparticles Based on Near-Infrared Response

    Directory of Open Access Journals (Sweden)

    Mario D’Acunto

    2012-01-01

    Full Text Available Gold nanoparticles have been widely used during the past few years in various technical and biomedical applications. In particular, the resonance optical properties of nanometer-sized particles have been employed to design biochips and biosensors used as analytical tools. The optical properties of nonfunctionalized gold nanoparticles and core-gold nanoshells play a crucial role for the design of biosensors where gold surface is used as a sensing component. Gold nanoparticles exhibit excellent optical tunability at visible and near-infrared frequencies leading to sharp peaks in their spectral extinction. In this paper, we study how the optical properties of gold nanoparticles and core-gold nanoshells are changed as a function of different sizes, shapes, composition, and biomolecular coating with characteristic shifts towards the near-infrared region. We show that the optical tenability can be carefully tailored for particle sizes falling in the range 100–150 nm. The results should improve the design of sensors working at the detection limit.

  8. 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.

  9. Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids.

    Science.gov (United States)

    Tessier, Matthew B; Demarco, Mari L; Yongye, Austin B; Woods, Robert J

    2008-01-01

    GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials.In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein-lipid complexes and proteins in biologically relevant membrane-like environments. PMID:22247593

  10. Bio-objectifying European bodies: standardisation of biobanks in the Biobanking and Biomolecular Resources Research Infrastructure.

    Science.gov (United States)

    Tamminen, Sakari

    2015-01-01

    The article traces the genealogy of the Minimum Information About Biobank Data Sharing model, created in the European Biobanking and Biomolecular Resources Research Infrastructure to facilitate collaboration among biobanks and to foster the exchange of biological samples and data. This information model is aimed at the identification of biobanks; unification of databases; and objectification of the information, samples, and related studies - to create a completely new 'bio-object infrastructure' within the EU. The paper discusses key challenges in creating a 'universal' information model of such a kind, the most important technical translations of European research policy needed for a standardised model for biobank information, and how this model creates new bio-objects. The author claims that this amounts to redefinition of biobanks and technical governance over virtually bio-objectified European populations. It is argued here that old governance models based on the nation-state need radical reconsideration so that we are prepared for a new and changing situation wherein bodies of information that lack organs flow from one database to another with a click of a mouse. PMID:26626620

  11. Indirect readout in protein-peptide recognition: a different story from classical biomolecular recognition.

    Science.gov (United States)

    Yu, Hua; Zhou, Peng; Deng, Maolin; Shang, Zhicai

    2014-07-28

    Protein-peptide interactions are prevalent and play essential roles in many living activities. Peptides recognize their protein partners by direct nonbonded interactions and indirect adjustment of conformations. Although processes of protein-peptide recognition have been comprehensively studied in both sequences and structures recently, flexibility of peptides and the configuration entropy penalty in recognition did not get enough attention. In this study, 20 protein-peptide complexes and their corresponding unbound peptides were investigated by molecular dynamics simulations. Energy analysis revealed that configurational entropy penalty introduced by restriction of the degrees of freedom of peptides in indirect readout process of protein-peptide recognition is significant. Configurational entropy penalty has become the main content of the indirect readout energy in protein-peptide recognition instead of deformation energy which is the main source of the indirect readout energy in classical biomolecular recognition phenomena, such as protein-DNA binding. These results provide us a better understanding of protein-peptide recognition and give us some implications in peptide ligand design.

  12. Magneto-optical relaxation measurements for the characterization of biomolecular interactions

    International Nuclear Information System (INIS)

    Measurements of the magneto-optical relaxation of ferrofluids (MORFF) were applied as a novel homogeneous immunoassay for the investigation of biomolecular interactions. The technique is based on magnetic nanoparticles (MNP) functionalized with antibodies. The relaxation time of the optical birefringence that occurs when a pulsed magnetic field is applied to the nanoparticle suspension depends on the particle size. This enables the detection of particle aggregates formed after the addition of the antigen coupling partner. MORFF size measurements on the original ferrofluid and its fractions obtained by magnetic fractionation are comparable with results from other methods such as atomic force microscopy and photon correlation spectroscopy. In kinetic studies, the binding properties of five antigens and their polyclonal antibodies were investigated: human immunoglobulin G (hIgG), human immunoglobulin M (hIgM), human Eotaxin (hEotaxin), human carcinoembryonic antigen (hCEA), and human insulin (hInsulin). The enlargement of the relaxation time observed during the coupling experiments is expressed in terms of a size distribution function, which includes MNP monomers as well as aggregates. The kinetic process can be described by a model of stepwise polymerization. The kinetic parameters obtained are compared to results of surface plasmon resonance measurements

  13. Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.

    Science.gov (United States)

    Moradi, Mahmoud; Tajkhorshid, Emad

    2014-07-01

    Characterizing large-scale structural transitions in biomolecular systems poses major technical challenges to both experimental and computational approaches. On the computational side, efficient sampling of the configuration space along the transition pathway remains the most daunting challenge. Recognizing this issue, we introduce a knowledge-based computational approach toward describing large-scale conformational transitions using (i) nonequilibrium, driven simulations combined with work measurements and (ii) free energy calculations using empirically optimized biasing protocols. The first part is based on designing mechanistically relevant, system-specific reaction coordinates whose usefulness and applicability in inducing the transition of interest are examined using knowledge-based, qualitative assessments along with nonequilirbrium work measurements which provide an empirical framework for optimizing the biasing protocol. The second part employs the optimized biasing protocol resulting from the first part to initiate free energy calculations and characterize the transition quantitatively. Using a biasing protocol fine-tuned to a particular transition not only improves the accuracy of the resulting free energies but also speeds up the convergence. The efficiency of the sampling will be assessed by employing dimensionality reduction techniques to help detect possible flaws and provide potential improvements in the design of the biasing protocol. Structural transition of a membrane transporter will be used as an example to illustrate the workings of the proposed approach.

  14. Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads

    Science.gov (United States)

    Stone, John E.; Hallock, Michael J.; Phillips, James C.; Peterson, Joseph R.; Luthey-Schulten, Zaida; Schulten, Klaus

    2016-01-01

    Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis of cellular processes on biologically-relevant timescales. A critical challenge facing the development of future exascale supercomputer systems is the development of new computing hardware and associated scientific applications that dramatically improve upon the energy efficiency of existing solutions, while providing increased simulation, analysis, and visualization performance. Mobile computing platforms have recently become powerful enough to support interactive molecular visualization tasks that were previously only possible on laptops and workstations, creating future opportunities for their convenient use for meetings, remote collaboration, and as head mounted displays for immersive stereoscopic viewing. We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-on-chip multi-core CPUs with high-performance massively parallel GPUs. We present low-cost power monitoring instrumentation that provides sufficient temporal resolution to evaluate the power consumption of individual CPU algorithms and GPU kernels. We compare the performance and energy efficiency of scientific applications running on emerging platforms with results obtained on traditional platforms, identify hardware and algorithmic performance bottlenecks that affect the usability of these platforms, and describe avenues for improving both the hardware and applications in pursuit of the needs of molecular modeling tasks on mobile devices and future exascale computers.

  15. An Atomic Force Microscope with Dual Actuation Capability for Biomolecular Experiments

    Science.gov (United States)

    Sevim, Semih; Shamsudhin, Naveen; Ozer, Sevil; Feng, Luying; Fakhraee, Arielle; Ergeneman, Olgaç; Pané, Salvador; Nelson, Bradley J.; Torun, Hamdi

    2016-06-01

    We report a modular atomic force microscope (AFM) design for biomolecular experiments. The AFM head uses readily available components and incorporates deflection-based optics and a piezotube-based cantilever actuator. Jetted-polymers have been used in the mechanical assembly, which allows rapid manufacturing. In addition, a FeCo-tipped electromagnet provides high-force cantilever actuation with vertical magnetic fields up to 0.55 T. Magnetic field calibration has been performed with a micro-hall sensor, which corresponds well with results from finite element magnetostatics simulations. An integrated force resolution of 1.82 and 2.98 pN, in air and in DI water, respectively was achieved in 1 kHz bandwidth with commercially available cantilevers made of Silicon Nitride. The controller and user interface are implemented on modular hardware to ensure scalability. The AFM can be operated in different modes, such as molecular pulling or force-clamp, by actuating the cantilever with the available actuators. The electromagnetic and piezoelectric actuation capabilities have been demonstrated in unbinding experiments of the biotin-streptavidin complex.

  16. A new source for quantum optics with biomolecules and biomolecular clusters

    Science.gov (United States)

    Marksteiner, Markus; Haslinger, Philipp; Ulbricht, Hendrik; Arndt, Markus

    2008-03-01

    We present recent progress towards matter wave experiments with amino acids, polypeptides and large biomolecular clusters. All successful experiments on macromolecule interferometry so far, with fullerenes, fullerene derivates and large perfluoroalkyl-functionalized azobenzenes used effusive beam sources. The combination of Stark deflectometry with quantum interferometry also allowed us to create a new device for precisely measuring electric susceptibilities of large molecules in the gas phase. In order to apply quantum interference to molecules of biological interest, we have now implemented a pulsed laser desorption source. The combination of UV laser desorption into an intense noble gas jet and single-photon ionization by a VUV excimer laser (157nm) allows us to observe intense neutral jets of amino acids (e.g. Tryptophan), nucleotides (e.g. Guanin) and polypeptides ranging from tri-peptides to Gramicidin. Remarkably, we also found a new method for producing large neutral amino acid clusters, such as for instance Trp30, with masses exceeding 6000 amu: the addition of alkaline Earth salts in the desorption process leads to the inclusion of at least one metal atom per complex and is sufficient to catalyze the cluster formation process.

  17. Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes

    Science.gov (United States)

    Forney, Michael W.; Janosi, Lorant; Kosztin, Ioan

    2008-11-01

    Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics (MD) simulations. A practical approach to this inherently multiscale problem is to model the system as a fictitious overdamped Brownian particle that diffuses along the RC in the presence of an effective potential of mean force (PMF) due to the rest of the system. By employing the recently proposed FR method [I. Kosztin , J. Chem. Phys. 124, 064106 (2006)], which requires only a small number of fast nonequilibrium MD simulations of the system in both forward and time reversed directions along the RC, we reconstruct the PMF: (1) of deca-alanine as a function of its end-to-end distance, and (2) that guides the motion of potassium ions through the gramicidin A channel. In both cases the computed PMFs are found to be in good agreement with previous results obtained by different methods. Our approach appears to be about one order of magnitude faster than the other PMF calculation methods and, in addition, it also provides the position-dependent diffusion coefficient along the RC. Thus, the obtained PMF and diffusion coefficient can be used in an overdamped Brownian model to estimate important characteristics of the studied systems, e.g., the mean folding time of the stretched deca-alanine and the mean diffusion time of the potassium ion through gramicidin A.

  18. Calculating free energy profiles in biomolecular systems from fast non-equilibrium processes

    CERN Document Server

    Forney, Michael; Kosztin, Ioan

    2008-01-01

    Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics (MD) simulations. A practical approach to this inherently multiscale problem is to model the system as a fictitious overdamped Brownian particle that diffuses along the RC in the presence of an effective potential of mean force (PMF) due to the rest of the system. By employing the recently proposed FR method [I. Kosztin et al., J. of Chem. Phys. 124, 064106 (2006)], which requires only a small number of fast nonequilibrium MD simulations of the system in both forward and time reversed directions along the RC, we reconstruct the PMF: (1) of deca-alanine as a function of its end-to-end distance, and (2) that guides the motion of potassium ions through the gramicidin A channel. In both cases the computed PMFs are found to be in good agreement with previous results obtained by ...

  19. Drug Transport Microdevice Mimicking an Idealized Nanoscale Bio-molecular Motor

    Institute of Scientific and Technical Information of China (English)

    Jae Hwan Lee; Ramana M. Pidaparti

    2011-01-01

    Molecular motors are nature's nano-devices and the essential agents of movement that are an integral part of many living organisms.The supramolecular motor,called Nuclear Pore Complex (NPC),controls the transport of all cellular material between the cytoplasm and the nucleus that occurs naturally in biological cells of many organisms.In order to understand the design characteristics of the NPC,we developed a microdevice for drug/fluidic transport mimicking the coarse-grained representation of the NPC geometry through computational fluid dynamic analysis and optimization.Specifically,the role of the central plug in active fluidic/particle transport and passive transport (without central plug) was investigated.Results of flow rate,pressure and velocity profiles obtained from the models indicate that the central plug plays a major role in transport through this biomolecular machine.The results of this investigation show that fluidic transport and flow passages are important factors in designing NPC based nano- and micro-devices for drug delivery.

  20. Computer Aided Solvent Selection and Design Framework

    DEFF Research Database (Denmark)

    Mitrofanov, Igor; Conte, Elisa; Abildskov, Jens;

    Solvents are widely used as a reaction medium, as a reactant or as carrier at some stages of the manufacturing chain in products from the chemical, fine chemical, pharmaceutical, food, and agrochemical industries. Solvent are either required for processing after which they are removed...... is to develop a systematic framework and implement it as software for selection and design of solvents for many applications including organic synthesis, complex reaction systems and solvent-based separations. The solvent selection framework is based on a combination of knowledge from industrial practice...... for each reaction: 1. Problem identification. Finding an objective for given system, identifying actual functions of the solvent. 2. Search criteria definition. The solvent functions that satisfy the operational needs of the process are defined in terms of a set of search criteria (R-indices), defined...

  1. Entropy-enthalpy Compensation of Biomolecular Systems in Aqueous Phase: a Dry Perspective.

    Science.gov (United States)

    Movileanu, Liviu; Schiff, Eric A

    2013-01-01

    We survey thermodynamic measurements on processes involving biological macromolecules in aqueous solution, which illustrate well the ubiquitous phenomenon of entropy-enthalpy compensation. The processes include protein folding/unfolding and ligand binding/unbinding, with compensation temperatures varying by about 50 K around an average near 293 K. We show that incorporating both near-exact entropy-enthalpy compensation (due to solvent relaxation) and multi-excitation entropy (from vibrational quanta) leads to a compensation temperature in water of about 230 K. We illustrate a general procedure for subtracting solvent and environment-related terms to determine the bare Gibbs free energy changes of chemical processes.

  2. Economic analysis of thermal solvent processes

    International Nuclear Information System (INIS)

    Vapour extraction (VAPEX) uses horizontal well pairs and a gaseous solvent to mobilize the oil. Hybrid solvent processes inject a light hydrocarbon solvent in addition to sufficient amounts of steam to vaporize the solvent. This paper reviewed various laboratory model experiments that evaluated VAPEX and solvent-based processes for the recovery of heavy oil or bitumen. The project compared a VAPEX process, a thermal solvent reflux process and a hybrid-solvent SAGD process using scaled laboratory models. Several experimental models were used. The first high-pressure thermal solvent experiment was conducted with a laboratory model designed to scale a 20 m thick Burnt Lake reservoir. Propane was used as the solvent. The second sequence of experiments scaled a range of processes from VAPEX to hybrid solvents for an Athabasca bitumen reservoir using a sealed can type of model confined by a gaseous overburden with propane as the solvent. The third experiment was a hybrid solvent experiment in which propane and steam were injected simultaneously into the injector well. The final experiment was a propane-steam hybrid experiment at a higher steam injection rate. The aim of the study was to evaluate the processes, build a database of experimental performance and to determine whether any single process had a significant economic advantage. It was concluded that the lowest cost process for Athabasca bitumen was the thermal solvent hybrid process followed by low pressure SAGD. The thermal solvent experiment using hot propane injection recovered heavy oil at costs competitive to SAGD. Many of the experiments suggested a process life longer than 15 years, as the high viscosity of Athabasca bitumen and the resulting low diffusivity resulted in a slower oil recovery process. 5 refs., 3 tabs., 16 figs

  3. Advanced integrated solvent extraction systems

    Energy Technology Data Exchange (ETDEWEB)

    Horwitz, E.P.; Dietz, M.L.; Leonard, R.A. [Argonne National Lab., IL (United States)

    1997-10-01

    Advanced integrated solvent extraction systems are a series of novel solvent extraction (SX) processes that will remove and recover all of the major radioisotopes from acidic-dissolved sludge or other acidic high-level wastes. The major focus of this effort during the last 2 years has been the development of a combined cesium-strontium extraction/recovery process, the Combined CSEX-SREX Process. The Combined CSEX-SREX Process relies on a mixture of a strontium-selective macrocyclic polyether and a novel cesium-selective extractant based on dibenzo 18-crown-6. The process offers several potential advantages over possible alternatives in a chemical processing scheme for high-level waste treatment. First, if the process is applied as the first step in chemical pretreatment, the radiation level for all subsequent processing steps (e.g., transuranic extraction/recovery, or TRUEX) will be significantly reduced. Thus, less costly shielding would be required. The second advantage of the Combined CSEX-SREX Process is that the recovered Cs-Sr fraction is non-transuranic, and therefore will decay to low-level waste after only a few hundred years. Finally, combining individual processes into a single process will reduce the amount of equipment required to pretreat the waste and therefore reduce the size and cost of the waste processing facility. In an ongoing collaboration with Lockheed Martin Idaho Technology Company (LMITCO), the authors have successfully tested various segments of the Advanced Integrated Solvent Extraction Systems. Eichrom Industries, Inc. (Darien, IL) synthesizes and markets the Sr extractant and can supply the Cs extractant on a limited basis. Plans are under way to perform a test of the Combined CSEX-SREX Process with real waste at LMITCO in the near future.

  4. Event Detection and Sub-state Discovery from Bio-molecular Simulations Using Higher-Order Statistics: Application To Enzyme Adenylate Kinase

    Science.gov (United States)

    Ramanathan, Arvind; Savol, Andrej J.; Agarwal, Pratul K.; Chennubhotla, Chakra S.

    2012-01-01

    Biomolecular simulations at milli-second and longer timescales can provide vital insights into functional mechanisms. Since post-simulation analyses of such large trajectory data-sets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are progressing. Recently, we have introduced a novel computational technique, quasi-anharmonic analysis (QAA) (PLoS One 6(1): e15827), for partitioning the conformational landscape into a hierarchy of functionally relevant sub-states. The unique capabilities of QAA are enabled by exploiting anharmonicity in the form of fourth-order statistics for characterizing atomic fluctuations. In this paper, we extend QAA for analyzing long time-scale simulations online. In particular, we present HOST4MD - a higher-order statistical toolbox for molecular dynamics simulations, which (1) identifies key dynamical events as simulations are in progress, (2) explores potential sub-states and (3) identifies conformational transitions that enable the protein to access those sub-states. We demonstrate HOST4MD on micro-second time-scale simulations of the enzyme adenylate kinase in its apo state. HOST4MD identifies several conformational events in these simulations, revealing how the intrinsic coupling between the three sub-domains (LID, CORE and NMP) changes during the simulations. Further, it also identifies an inherent asymmetry in the opening/closing of the two binding sites. We anticipate HOST4MD will provide a powerful and extensible framework for detecting biophysically relevant conformational coordinates from long time-scale simulations. PMID:22733562

  5. Green Solvents for Precision Cleaning

    Science.gov (United States)

    Grandelli, Heather; Maloney, Phillip; DeVor, Robert; Surma, Jan; Hintze, Paul

    2013-01-01

    Aerospace machinery used in liquid oxygen (LOX) fuel systems must be precision cleaned to achieve a very low level of non-volatile residue (solvent-replacement is non-flammable, environmentally benign, non-corrosive, inexpensive, effective and evaporates completely, leaving no residue. Highlighted is a green precision cleaning process, which is contaminant removal using supercritical carbon dioxide as the environmentally benign solvent. In this process, the contaminant is dissolved in carbon dioxide, and the parts are recovered at the end of the cleaning process completely dry and ready for use. Typical contaminants of aerospace components include hydrocarbon greases, hydraulic fluids, silicone fluids and greases, fluorocarbon fluids and greases and fingerprint oil. Metallic aerospace components range from small nuts and bolts to much larger parts, such as butterfly valves 18 in diameter. A fluorinated grease, Krytox, is investigated as a model contaminant in these preliminary studies, and aluminum coupons are employed as a model aerospace component. Preliminary studies are presented in which the experimental parameters are optimized for removal of Krytox from aluminum coupons in a stirred-batch process. The experimental conditions investigated are temperature, pressure, exposure time and impeller speed. Temperatures of 308 - 423 K, pressures in the range of 8.3 - 41.4 MPa, exposure times between 5 - 60 min and impeller speeds of 0 - 1000 rpm were investigated. Preliminary results showed up to 86 cleaning efficiency with the moderate processing conditions of 323 K, 13.8 MPa, 30 min and 750 rpm.

  6. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments

    Science.gov (United States)

    Doster, W.; Nakagawa, H.; Appavou, M. S.

    2013-07-01

    Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and/or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at Td from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature Tg. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature Td.

  7. Morbillivirus infection in cetaceans stranded along the Italian coastline: pathological, immunohistochemical and biomolecular findings.

    Science.gov (United States)

    Di Guardo, Giovanni; Di Francesco, Cristina Esmeralda; Eleni, Claudia; Cocumelli, Cristiano; Scholl, Francesco; Casalone, Cristina; Peletto, Simone; Mignone, Walter; Tittarelli, Cristiana; Di Nocera, Fabio; Leonardi, Leonardo; Fernández, Antonio; Marcer, Federica; Mazzariol, Sandro

    2013-02-01

    Morbilliviruses are recognized as biological agents highly impacting the health and conservation status of free-ranging cetaceans worldwide, as clearly exemplified by the two Dolphin Morbillivirus (DMV) epidemics of 1990-1992 and 2006-2008 among Mediterranean striped dolphins (Stenella coeruleoalba). After these two epidemics, morbilliviral infection (MI) cases with peculiar neurobiological features were reported in striped dolphins stranded along the Spanish coastline. Affected cetaceans showed a subacute-to-chronic, non-suppurative encephalitis, with brain lesions strongly resembling those found in human "subacute sclerosing panencephalitis" and "old dog encephalitis". Brain was the only tissue in which morbilliviral antigen and/or genome could be detected. Beside a case of morbilliviral encephalitis in a striped dolphin's calf stranded in 2009, we observed 5 additional MI cases in 2 striped dolphins, 1 bottlenose dolphin (Tursiops truncatus) and 2 fin whales (Balaenoptera physalus), all stranded in 2011 along the Italian coastline. Noteworthy, 3 of these animals (2 striped dolphins and 1 bottlenose dolphin) showed immunohistochemical (IHC) and/or biomolecular (PCR) evidence of morbilliviral antigen and/or genome exclusively in their brain, with 1 striped dolphin and 1 bottlenose dolphin also exhibiting a non-suppurative encephalitis. Furthermore, simultaneous IHC and PCR evidence of a Toxoplasma gondii coinfection was obtained in 1 fin whale. The above results are consistent with those reported in striped dolphins after the two MI epidemics of 1990-92 and 2006-2008, with evidence of morbilliviral antigen and/or genome being found exclusively in the brain tissue from affected animals.

  8. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments

    Energy Technology Data Exchange (ETDEWEB)

    Doster, W. [Physik-Department, Technische Universität München, D-85748 Garching (Germany); Nakagawa, H. [Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching (Germany); Japan Atomic Energy Agency, Quantum Beam Science Directorate, Tokai, Ibaraki 319-1195 (Japan); Appavou, M. S. [Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching (Germany)

    2013-07-28

    Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and/or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at T{sub d} from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature T{sub g}. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature T{sub d}.

  9. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments

    International Nuclear Information System (INIS)

    Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and/or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at Td from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature Tg. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature Td

  10. Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

    Science.gov (United States)

    Yoo, Jejoong; Wilson, James; Aksimentiev, Aleksei

    2016-10-01

    Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA-DNA interactions. In the simulations performed using the two standard models, Ca(2+) ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2 and CaCl2 solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca(2+) ions in the simulations of Ca(2+) -mediated DNA-DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca(2+) to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca(2+) model, we introduce a custom model of a hydrated Ca(2+) ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca(2+) can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752-763, 2016. PMID:27144470

  11. Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues.

    Directory of Open Access Journals (Sweden)

    Alexander V Ratushny

    2011-06-01

    Full Text Available When living systems detect changes in their external environment their response must be measured to balance the need to react appropriately with the need to remain stable, ignoring insignificant signals. Because this is a fundamental challenge of all biological systems that execute programs in response to stimuli, we developed a generalized time-frequency analysis (TFA framework to systematically explore the dynamical properties of biomolecular networks. Using TFA, we focused on two well-characterized yeast gene regulatory networks responsive to carbon-source shifts and a mammalian innate immune regulatory network responsive to lipopolysaccharides (LPS. The networks are comprised of two different basic architectures. Dual positive and negative feedback loops make up the yeast galactose network; whereas overlapping positive and negative feed-forward loops are common to the yeast fatty-acid response network and the LPS-induced network of macrophages. TFA revealed remarkably distinct network behaviors in terms of trade-offs in responsiveness and noise suppression that are appropriately tuned to each biological response. The wild type galactose network was found to be highly responsive while the oleate network has greater noise suppression ability. The LPS network appeared more balanced, exhibiting less bias toward noise suppression or responsiveness. Exploration of the network parameter space exposed dramatic differences in system behaviors for each network. These studies highlight fundamental structural and dynamical principles that underlie each network, reveal constrained parameters of positive and negative feedback and feed-forward strengths that tune the networks appropriately for their respective biological roles, and demonstrate the general utility of the TFA approach for systems and synthetic biology.

  12. Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions.

    Science.gov (United States)

    Carter, Megan; Voth, Andrea Regier; Scholfield, Matthew R; Rummel, Brittany; Sowers, Lawrence C; Ho, P Shing

    2013-07-23

    Interest in noncovalent interactions involving halogens, particularly halogen bonds (X-bonds), has grown dramatically in the past decade, propelled by the use of X-bonding in molecular engineering and drug design. However, it is clear that a complete analysis of the structure-energy relationship must be established in biological systems to fully exploit X-bonds for biomolecular engineering. We present here the first comprehensive experimental study to correlate geometries with their stabilizing potentials for fluorine (F), chlorine (Cl), bromine (Br), or iodine (I) X-bonds in a biological context. For these studies, we determine the single-crystal structures of DNA Holliday junctions containing halogenated uracil bases that compete X-bonds against classic hydrogen bonds (H-bonds), estimate the enthalpic energies of the competing interactions in the crystal system through crystallographic titrations, and compare the enthalpic and entropic energies of bromine and iodine X-bonds in solution by differential scanning calorimetry. The culmination of these studies demonstrates that enthalpic stabilization of X-bonds increases with increasing polarizability from F to Cl to Br to I, which is consistent with the σ-hole theory of X-bonding. Furthermore, an increase in the X-bonding potential is seen to direct the interaction toward a more ideal geometry. However, the entropic contributions to the total free energies must also be considered to determine how each halogen potentially contributes to the overall stability of the interaction. We find that bromine has the optimal balance between enthalpic and entropic energy components, resulting in the lowest free energy for X-bonding in this DNA system. The X-bond formed by iodine is more enthalpically stable, but this comes with an entropic cost, which we attribute to crowding effects. Thus, the overall free energy of an X-bonding interaction balances the stabilizing electrostatic effects of the σ-hole against the competing

  13. Biomolecularly capped uniformly sized nanocrystalline materials: glutathione-capped ZnS nanocrystals

    Science.gov (United States)

    Torres-Martínez, Claudia L.; Nguyen, Liem; Kho, Richard; Bae, Weon; Bozhilov, Krassimir; Klimov, Victor; Mehra, Rajesh K.

    1999-09-01

    Micro-organisms such as bacteria and yeasts form CdS to detoxify toxic cadmium ions. Frequently, CdS particles formed in yeasts and bacteria were found to be associated with specific biomolecules. It was later determined that these biomolecules were present at the surface of CdS. This coating caused a restriction in the growth of CdS particles and resulted in the formation of nanometre-sized semiconductors (NCs) that exhibited typical quantum confinement properties. Glutathione and related phytochelatin peptides were shown to be the biomolecules that capped CdS nanocrystallites synthesized by yeasts Candida glabrata and Schizosaccharomyces pombe. Although early studies showed the existence of specific biochemical pathways for the synthesis of biomolecularly capped CdS NCs, these NCs could be formed in vitro under appropriate conditions. We have recently shown that cysteine and cysteine-containing peptides such as glutathione and phytochelatins can be used in vitro to dictate the formation of discrete sizes of CdS and ZnS nanocrystals. We have evolved protocols for the synthesis of ZnS or CdS nanocrystals within a narrow size distribution range. These procedures involve three steps: (1) formation of metallo-complexes of cysteine or cysteine-containing peptides, (2) introduction of stoichiometric amounts of inorganic sulfide into the metallo-complexes to initiate the formation of nanocrystallites and finally (3) size-selective precipitation of NCs with ethanol in the presence of Na+. The resulting NCs were characterized by optical spectroscopy, high-resolution transmission electron microscopy (HRTEM), x-ray diffraction and electron diffraction. HRTEM showed that the diameter of the ZnS-glutathione nanocrystals was 3.45+/-0.5 nm. X-ray diffraction and electron diffraction analyses indicated ZnS-glutathione to be hexagonal. Photocatalytic studies suggest that glutathione-capped ZnS nanocrystals prepared by our procedure are highly efficient in degrading a test model

  14. Remediation of Contaminated Soils by Solvent Flushing

    OpenAIRE

    Augustijn, Denie C.M.; Jessup, Ron E.; Rao, P. Suresh C.; Wood, A. Lynn

    1994-01-01

    Solvent flushing is a potential technique for remediating a waste disposal/spill site contaminated with organic chemicals. This technique involves the injection of a solvent mixture (e.g., water plus alcohols) that enhances contaminant solubility, reduces the retardation factor, and increases the release rates of the contaminants. A simulation model is developed to predict contaminant elution curves during solvent flushing for the case of one‐dimensional, steady flow through a contaminated me...

  15. Thermally activated solvent bonding of polymers

    OpenAIRE

    Ng, S H; Tjeung, R. T.; Z. F. Wang; Lu, A. C. W.; Rodriguez, I.; de Rooij, Nicolaas F.

    2010-01-01

    We present a thermally activated solvent bonding technique for the formation of embedded microstructures in polymer. It is based on the temperature dependent solubility of polymer in a liquid that is not a solvent at room temperature. With thermal activation, the liquid is transformed into a solvent of the polymer, creating a bonding capability through segmental or chain interdiffusion at the bonding interface. The technique has advantages over the more commonly used thermal bonding due to it...

  16. Modeling of salt solubilities in mixed solvents

    OpenAIRE

    Chiavone Filho O.; Rasmussen P.

    2000-01-01

    A method to correlate and predict salt solubilities in mixed solvents using a UNIQUAC+Debye-Hückel model is developed. The UNIQUAC equation is applied in a form with temperature-dependent parameters. The Debye-Hückel model is extended to mixed solvents by properly evaluating the dielectric constants and the liquid densities of the solvent media. To normalize the activity coefficients, the symmetric convention is adopted. Thermochemical properties of the salt are used to estimate the solubilit...

  17. OCCUPATIONAL SOLVENT EXPOSURE ASSOCIATED WITH DEVELOPMENTAL TOXICITY

    Directory of Open Access Journals (Sweden)

    Alina-Costina LUCA

    2016-05-01

    Full Text Available Organic solvent is a broad term that applies to many classes of chemicals. The solvent (benzene, toluene etc. aspects of occupational exposure are reviewed via the examination of the use, occurrence, and disposition as well as population’s potential of risk. The general public can be exposed to solvent in ambient air as a result of its occurrence in paint process. Solvents are primarily irritants to the skin and mucous membranes and have narcotic properties at high concentrations. Published epidemiological data identified various types of birth defects in certain occupations.

  18. Extractive Distillation with Salt in Solvent

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Extractive distillation with salt in solvent is a new process for producing anhydrous ethanol by combining the principle of "salt effect" and some traditional extractive distillation methods. Compared with the common extractive distillation the performance of solvent is improved, the recycling amount of solvent is reduced to 1/4-1/5, and the number of theoretical plates is reduced to 1/3. Energy consumption and cost of equipment are also reduced and continuous production is realized. High efficiency and low solvent wastage make this technique feasible.

  19. Modeling of salt solubilities in mixed solvents

    Directory of Open Access Journals (Sweden)

    O. Chiavone Filho

    2000-06-01

    Full Text Available A method to correlate and predict salt solubilities in mixed solvents using a UNIQUAC+Debye-Hückel model is developed. The UNIQUAC equation is applied in a form with temperature-dependent parameters. The Debye-Hückel model is extended to mixed solvents by properly evaluating the dielectric constants and the liquid densities of the solvent media. To normalize the activity coefficients, the symmetric convention is adopted. Thermochemical properties of the salt are used to estimate the solubility product. It is shown that the proposed procedure can describe with good accuracy a series of salt solubility measurements in aqueous organic solvent mixtures.

  20. A first principle particle mesh method for solution SAXS of large bio-molecular systems

    Science.gov (United States)

    Marchi, Massimo

    2016-07-01

    This paper will show that the solution small angle X-ray scattering (SAXS) intensity of globular and membrane proteins can be efficiently and accurately computed from molecular dynamics trajectories using 3D fast Fourier transforms (FFTs). A suitable particle meshing interpolation, similar to the one used in smooth particle mesh Ewald for electrostatic energies and forces, was combined with a uniform solvent density FFT padding scheme to obtain a convenient SAXS spectral resolution. The CPU time scaling of the method, as a function of system size, is highly favorable and its application to large systems such as solutions of solvated membrane proteins is computationally undemanding. Differently from other approaches, all contributions from the simulation cell are included. This means that the subtraction of the buffer from the solution scattering intensity is straightforward and devoid of artifact due to ad hoc definitions of proximal and distal solvent intensity contributions.

  1. Single polymer chains in poor solvent: using the bond fluctuation method with explicit solvent.

    Science.gov (United States)

    Jentzsch, Christoph; Werner, Marco; Sommer, Jens-Uwe

    2013-03-01

    We use the bond fluctuation model with explicit solvent to study single polymer chains under poor solvent conditions. Static and dynamic properties of the bond fluctuation model with explicit solvent are compared with the implicit solvent model, and the Θ-temperatures are determined for both solvent models. We show that even in the very poor solvent regime, dynamics is not frozen for the explicit solvent model. We investigate some aspects of the structure of a single collapsed globule and show that rather large chain lengths are necessary to reach the scaling regime of a dense sphere. The force-extension curve of a single polymer chain under poor solvent conditions in the fixed end-to-end distance ensemble is analyzed. We find that the transition of the tadpole conformation to the stretched chain conformation is rather smooth because of fluctuation effects, which is in agreement with recent experimental results. PMID:23485321

  2. Evaluation of kinetic constants of biomolecular interaction on optical surface plasmon resonance sensor with Newton Iteration Method

    Science.gov (United States)

    Zhao, Yuanyuan; Jiang, Guoliang; Hu, Jiandong; Hu, Fengjiang; Wei, Jianguang; Shi, Liang

    2010-10-01

    In the immunology, there are two important types of biomolecular interaction: antigens-antibodies and receptors-ligands. Monitoring the response rate and affinity of biomolecular interaction can help analyze the protein function, drug discover, genomics and proteomics research. Moreover the association rate constant and dissociation rate constant of receptors-ligands are the important parameters for the study of signal transmission between cells. Recent advances in bioanalyzer instruments have greatly simplified the measurement of the kinetics of molecular interactions. Non-destructive and real-time monitoring the response to evaluate the parameters between antigens and antibodies can be performed by using optical surface plasmon resonance (SPR) biosensor technology. This technology provides a quantitative analysis that is carried out rapidly with label-free high-throughput detection using the binding curves of antigens-antibodies. Consequently, the kinetic parameters of interaction between antigens and antibodies can be obtained. This article presents a low cost integrated SPR-based bioanalyzer (HPSPR-6000) designed by ourselves. This bioanalyzer is mainly composed of a biosensor TSPR1K23, a touch-screen monitor, a microprocessor PIC24F128, a microflow cell with three channels, a clamp and a photoelectric conversion device. To obtain the kinetic parameters, sensorgrams may be modeled using one of several binding models provided with BIAevaluation software 3.0, SensiQ or Autolab. This allows calculation of the association rate constant (ka) and the dissociation rate constant (kd). The ratio of ka to kd can be used to estimate the equilibrium constant. Another kind is the analysis software OriginPro, which can process the obtained data by nonlinear fitting and then get some correlative parameters, but it can't be embedded into the bioanalyzer, so the bioanalyzer don't support the use of OriginPro. This paper proposes a novel method to evaluate the kinetic parameters

  3. A radiochemical technique for the establishment of a solvent-independent scale of ion activities in amphiprotic solvents

    International Nuclear Information System (INIS)

    The radiochemical determination of solubilities of hardly soluble compounds of silver (Ph4BAg, AgCl), by means of Ag-110m in amphiprotic solutions is used for setting-up a solvent-independent scale of ion activities based on the concept of the media effect. The media effects of the salts are calculated from the solubility data of the Ag compounds in question. The splitting into the media effects of single ions takes place with the extrathermodynamic assumption of the same media effects for large ions, such as Ph4B- = Ph4As-. A standardized ion activity scale in connection with the activity coefficients for the solvent in question can be established with water as the basic state of the chemical potential. As the sum of the media effects of the single ions gives the media effect of the salt concerned, which is easily obtained from data which are experimentally accessible (solubility, vapour pressure, ion exchange ect.), this method leads to single ion activities of a large number of ions in a multitude of solvents. (orig./LH)

  4. Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters

    Science.gov (United States)

    Nott, Timothy J.; Craggs, Timothy D.; Baldwin, Andrew J.

    2016-06-01

    Membraneless organelles are cellular compartments made from drops of liquid protein inside a cell. These compartments assemble via the phase separation of disordered regions of proteins in response to changes in the cellular environment and the cell cycle. Here we demonstrate that the solvent environment within the interior of these cellular bodies behaves more like an organic solvent than like water. One of the most-stable biological structures known, the DNA double helix, can be melted once inside the liquid droplet, and simultaneously structures formed from regulatory single-stranded nucleic acids are stabilized. Moreover, proteins are shown to have a wide range of absorption or exclusion from these bodies, and can act as importers for otherwise-excluded nucleic acids, which suggests the existence of a protein-mediated trafficking system. A common strategy in organic chemistry is to utilize different solvents to influence the behaviour of molecules and reactions. These results reveal that cells have also evolved this capability by exploiting the interiors of membraneless organelles.

  5. BioMart Central Portal--unified access to biological data.

    Science.gov (United States)

    Haider, Syed; Ballester, Benoit; Smedley, Damian; Zhang, Junjun; Rice, Peter; Kasprzyk, Arek

    2009-07-01

    BioMart Central Portal (www.biomart.org) offers a one-stop shop solution to access a wide array of biological databases. These include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase and PRIDE; for a complete list, visit, http://www.biomart.org/biomart/martview. Moreover, the web server features seamless data federation making cross querying of these data sources in a user friendly and unified way. The web server not only provides access through a web interface (MartView), it also supports programmatic access through a Perl API as well as RESTful and SOAP oriented web services. The website is free and open to all users and there is no login requirement.

  6. REMEDIATION OF CONTAMINATED SOILS BY SOLVENT FLUSHING

    Science.gov (United States)

    Solvent flushing is a potential technique for remediating a waste disposal/spill site contaminated with organic chemicals. This technique involves the injection of a solvent mixture (e.g., water plus alcohols) that enhances contaminant solubility, reduces the retardation factor, ...

  7. REMEDIATING PESTICIDE CONTAMINATED SOILS USING SOLVENT EXTRACTION

    Science.gov (United States)

    Bench-scale solvent extraction studies were performed on soil samples obtained from a Superfund site contaminated with high levels of p,p'-DDT, p,p'-DDD,, p,p'-DDE and toxaphene. The effectiveness of the solvent extraction process was assessed using methanol and 2-propanol as sol...

  8. Modeling of Salt Solubilities in Mixed Solvents

    DEFF Research Database (Denmark)

    Chiavone-Filho, O.; Rasmussen, Peter

    2000-01-01

    A method to correlate and predict salt solubilities in mixed solvents using a UNIQUAC+Debye-Huckel model is developed. The UNIQUAC equation is applied in a form with temperature-dependent parameters. The Debye-Huckel model is extended to mixed solvents by properly evaluating the dielectric consta...

  9. Structuring of polymer solutions upon solvent evaporation

    NARCIS (Netherlands)

    Schaefer, C.; van der Schoot, P.; Michels, J. J.

    2015-01-01

    The morphology of solution-cast, phase-separated polymers becomes finer with increasing solvent evaporation rate. We address this observation theoretically for a model polymer where demixing is induced by steady solvent evaporation. In contrast to what is the case for a classical, thermal quench inv

  10. Improved Supercritical-Solvent Extraction of Coal

    Science.gov (United States)

    Compton, L.

    1982-01-01

    Raw coal upgraded by supercritical-solvent extraction system that uses two materials instead of one. System achieved extraction yields of 20 to 49 weight percent. Single-solvent yields are about 25 weight percent. Experimental results show extraction yields may be timedependent. Observed decreases in weight of coal agreed well with increases in ash content of residue.

  11. Supercritical-Multiple-Solvent Extraction From Coal

    Science.gov (United States)

    Corcoran, W.; Fong, W.; Pichaichanarong, P.; Chan, P.; Lawson, D.

    1983-01-01

    Large and small molecules dissolve different constituents. Experimental apparatus used to test supercritical extraction of hydrogen rich compounds from coal in various organic solvents. In decreasing order of importance, relevant process parameters were found to be temperature, solvent type, pressure, and residence time.

  12. Molecular Thermodynamic Modeling of Mixed Solvent Solubility

    DEFF Research Database (Denmark)

    Ellegaard, Martin Dela; Abildskov, Jens; O’Connell, John P.

    2010-01-01

    A method based on statistical mechanical fluctuation solution theory for composition derivatives of activity coefficients is employed for estimating dilute solubilities of 11 solid pharmaceutical solutes in nearly 70 mixed aqueous and nonaqueous solvent systems. The solvent mixtures range from ne...

  13. Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

    Science.gov (United States)

    Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu

    2011-10-01

    A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.

  14. Organic solvent regeneration of granular activated carbon

    Science.gov (United States)

    Cross, W. H.; Suidan, M. T.; Roller, M. A.; Kim, B. R.; Gould, J. P.

    1982-09-01

    The use of activated carbon for the treatment of industrial waste-streams was shown to be an effective treatment. The high costs associated with the replacement or thermal regeneration of the carbon have prohibited the economic feasibility of this process. The in situ solvent regeneration of activated carbon by means of organic solvent extraction was suggested as an economically alternative to thermal regeneration. The important aspects of the solvent regeneration process include: the physical and chemical characteristics of the adsorbent, the pore size distribution and energy of adsorption associated with the activated carbon; the degree of solubility of the adsorbate in the organic solvent; the miscibility of the organic solvent in water; and the temperature at which the generation is performed.

  15. The chemistry of nonaqueous solvents v.4 solution phenomena and aprotic solvents

    CERN Document Server

    Lagowski, J J

    1976-01-01

    The Chemistry of Nonaqueous Solvents, Volume IV: Solution Phenomena and Aprotic Solvents focuses on the chemistry of nonaqueous solvents, with emphasis on solution phenomena and aprotic solvents such as tetramethylurea, inorganic acid chlorides, cyclic carbonates, and sulfolane. This book is organized into seven chapters and begins with an overview of the theory of electrical conductivity and elementary experimental considerations, along with some of the interesting research on nonaqueous solvents. It then turns to a discussion on hydrogen bonding phenomena in nonaqueous systems as probed

  16. Unraveling the biomolecular snapshots of mitosis in healthy and cancer cells using plasmonically-enhanced Raman spectroscopy.

    Science.gov (United States)

    Panikkanvalappil, Sajanlal R; Hira, Steven M; Mahmoud, Mahmoud A; El-Sayed, Mostafa A

    2014-11-12

    Owing to the dynamic and complex nature of mitosis, precise and timely executions of biomolecular events are critical for high fidelity cell division. In this context, visualization of such complex events at the molecular level can provide vital information on the biomolecular processes in abnormal cells. Here, we explored the plasmonically enhanced light scattering properties of functionalized gold nanocubes (AuNCs) together with surface-enhanced Raman spectroscopy (SERS) to unravel the complex and dynamic biological processes involved in mitosis of healthy and cancerous cells from its molecular perspectives. By monitoring various stages of mitosis using SERS, we noticed that relatively high rate of conversion of mitotic proteins from their α-helix structure to β-sheet conformation is likely in the cancer cells during meta-, ana-, and telophases. Unique biochemical modifications to the lipid and amino acid moieties, associated with the observed protein conformational modifications, were also identified. However, in healthy cells, the existence of proteins in their β conformation was momentary and was largely in the α-helix form. The role of abnormal conformational modifications of mitotic proteins on the development of anomalous mitotic activities was further confirmed by looking at plasmonic nanoparticle-induced cytokinesis failure in cancer cells. Our findings illustrate the vast possibilities of SERS in real-time tracking of complex, subtle, and momentary modifications of biomolecules in live cells, which could provide new insights to the role of protein conformation dynamics during mitosis on the development of cancer and many other diseases.

  17. A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network

    Directory of Open Access Journals (Sweden)

    Tsuji Shingo

    2012-09-01

    Full Text Available Abstract Background In the functional genomics analysis domain, various methodologies are available for interpreting the results produced by high-throughput biological experiments. These methods commonly use a list of genes as an analysis input, and most of them produce a more complicated list of genes or pathways as the results of the analysis. Although there are several network-based methods, which detect key nodes in the network, the results tend to include well-studied, major hub genes. Results To mine the molecules that have biological meaning but to fewer degrees than major hubs, we propose, in this study, a new network-based method for selecting these hidden key molecules based on virtual information flows circulating among the input list of genes. The human biomolecular network was constructed from the Pathway Commons database, and a calculation method based on betweenness centrality was newly developed. We validated the method with the ErbB pathway and applied it to practical cancer research data. We were able to confirm that the output genes, despite having fewer edges than major hubs, have biological meanings that were able to be invoked by the input list of genes. Conclusions The developed method, named NetHiKe (Network-based Hidden Key molecule miner, was able to detect potential key molecules by utilizing the human biomolecular network as a knowledge base. Thus, it is hoped that this method will enhance the progress of biological data analysis in the whole-genome research era.

  18. Real-time and label-free detection of biomolecular interactions by oblique-incidence reflectivity difference method

    Science.gov (United States)

    Wang, Xu; Lu, Heng; Dai, Jun; Wen, Juan; Yuan, Kun; Lü, Hui-Bin; Jin, Kui-Juan; Zhou, Yue-Liang; Yang, Guo-Zhen

    2011-01-01

    We successfully conduct the label-free and real-time detection of the interactions between epoxy groups and rabbit IgG and 5' CTT CAG GTC ATG AGC CTG AT 3' oligonucleotide, and between the hybridization of 5' CTT CAG GTC ATG AGC CTG AT 3' and its complementary 3' GAA GTC CAG TAC TCG GAC TA 5' oligonucleotide, by the oblique-incidence reflectivity difference (OI-RD) method. The dynamic curves of OI-RD signals, corresponding to the kinetic processes of biomolecular combination or hybridization, are acquired. In our case, the combination of epoxy groups with rabbit IgG and 5' CTT CAG GTC ATG AGC CTG AT 3' oligonucleotide need almost one and a half hours and about two hundred seconds, respectively; and the hybridization of the two oligonucleotides needs about five hundred seconds. The experimental results show that the OI-RD is a promising method for the real-time and label-free detection of biomolecular interactions.

  19. PARIS II: Computer Aided Solvent Design for Pollution Prevention

    Science.gov (United States)

    This product is a summary of U.S. EPA researchers' work developing the solvent substitution software tool PARIS II (Program for Assisting the Replacement of Industrial Solvents, version 2.0). PARIS II finds less toxic solvents or solvent mixtures to replace more toxic solvents co...

  20. Predicting the Solubility of Pharmaceutical Cocrystals in Solvent/Anti-Solvent Mixtures.

    Science.gov (United States)

    Lange, Linda; Heisel, Stefan; Sadowski, Gabriele

    2016-01-01

    In this work, the solubilities of pharmaceutical cocrystals in solvent/anti-solvent systems were predicted using PC-SAFT in order to increase the efficiency of cocrystal formation processes. Modeling results and experimental data were compared for the cocrystal system nicotinamide/succinic acid (2:1) in the solvent/anti-solvent mixtures ethanol/water, ethanol/acetonitrile and ethanol/ethyl acetate at 298.15 K and in the ethanol/ethyl acetate mixture also at 310.15 K. The solubility of the investigated cocrystal slightly increased when adding small amounts of anti-solvent to the solvent, but drastically decreased for high anti-solvent amounts. Furthermore, the solubilities of nicotinamide, succinic acid and the cocrystal in the considered solvent/anti-solvent mixtures showed strong deviations from ideal-solution behavior. However, by accounting for the thermodynamic non-ideality of the components, PC-SAFT is able to predict the solubilities in all above-mentioned solvent/anti-solvent systems in good agreement with the experimental data. PMID:27164075

  1. Predicting the Solubility of Pharmaceutical Cocrystals in Solvent/Anti-Solvent Mixtures

    Directory of Open Access Journals (Sweden)

    Linda Lange

    2016-05-01

    Full Text Available In this work, the solubilities of pharmaceutical cocrystals in solvent/anti-solvent systems were predicted using PC-SAFT in order to increase the efficiency of cocrystal formation processes. Modeling results and experimental data were compared for the cocrystal system nicotinamide/succinic acid (2:1 in the solvent/anti-solvent mixtures ethanol/water, ethanol/acetonitrile and ethanol/ethyl acetate at 298.15 K and in the ethanol/ethyl acetate mixture also at 310.15 K. The solubility of the investigated cocrystal slightly increased when adding small amounts of anti-solvent to the solvent, but drastically decreased for high anti-solvent amounts. Furthermore, the solubilities of nicotinamide, succinic acid and the cocrystal in the considered solvent/anti-solvent mixtures showed strong deviations from ideal-solution behavior. However, by accounting for the thermodynamic non-ideality of the components, PC-SAFT is able to predict the solubilities in all above-mentioned solvent/anti-solvent systems in good agreement with the experimental data.

  2. PSE For Solvent Applications: A Generic Computer-aided Solvent Selection and Design Framework

    DEFF Research Database (Denmark)

    Mitrofanov, Igor; Sin, Gürkan; Gani, Rafiqul

    industry (API solubility), solvents i! ! n formulations and as cleaning agents. The template is expected to guide the average user through the essential and desirable steps in solvent selection and design. The expert may also use the general interface and create their own template for the types of solvent......Solvents are widely used across a number of industries in many applications such as separation agents, reaction mediums, cleaning agents and product carriers. Selection of optimal solvents in these applications is mostly based on previous experiences and experimental trial and error. A process...... related problems they usually solve. The solvents database currently contains information about more than 1000 organic solvents and their properties -including environmental and transportation - and about 1000 ionic liquids useful for extraction-based separation processes. Property models library include...

  3. Computer-aided tool for solvent selection in pharmaceutical processes: Solvent swap

    DEFF Research Database (Denmark)

    Papadakis, Emmanouil; K. Tula, Anjan; Gernaey, Krist V.;

    swap solvents is developed and is used to retrieve information for the most commonly used solvent candidates typically found in the pharmaceutical industry. The selection is verified by simulation. The framework for the solvent selection and solvent swap is part of an integrated computer......-aided framework with the objective to assist the pharmaceutical industry in gaining better process understanding. A software interface to improve the usability of the tool has been created also.......In the pharmaceutical processes, solvents have a multipurpose role since different solvents can be used in different stages (such as chemical reactions, separations and purification) in the multistage active pharmaceutical ingredients (APIs) production process. The solvent swap and selection tasks...

  4. Intermolecular interaction of thiosemicarbazone derivatives to solvents and a potential Aedes aegypti target

    Science.gov (United States)

    da Silva, João Bosco P.; Hallwass, Fernando; da Silva, Aluizio G.; Moreira, Diogo Rodrigo; Ramos, Mozart N.; Espíndola, José Wanderlan P.; de Oliveira, Ana Daura T.; Brondani, Dalci José; Leite, Ana Cristina L.; Merz, Kenneth M.

    2015-08-01

    DFT calculations were used to access information about structure, energy and electronic properties of series of phenyl- and phenoxymethyl-(thio)semicarbazone derivatives with demonstrated activity against the larvae of Aedes aegypti in stage L4. The way as the thiosemicarbazone derivatives can interact with solvents like DMSO and water were analyzed from the comparison between calculated and experimental 1H NMR chemical shifts. The evidences of thiosemicarbazone derivatives making H-bond interaction to solvent have provide us insights on how they can interact with a potential A. aegypti's biological target, the Sterol Carrier Protein-2.

  5. Production and detection of neutral molecular beams : from single amino acids to biomolecular complexes

    International Nuclear Information System (INIS)

    biomolecular complexes. The largest observed complex is a gramicidin tetramer with a mass of 7,536amu. Furthermore, desorption of tryptophan together with alkaline earth salts, such as calcium-carbonate results in the formation of two different kinds of massive tryptophan clusters: Tryptophan clusters containing a single calcium atom with a mass of up to 6,800amu and also pure clusters with a mass of up to 7,100amu are observed. The inclusion of a metal atom into tryptophan clusters is observed also for strontium, barium ,sodium and copper. The cluster formation is studied additionally for other amino acids such as phenylalanine, the tripeptide tyrosine-tryptophan-glycine and the nucleotide guanine. The cluster formation between two different molecular species was observed after the simultaneous desorption of gramicidin and tryptophan and resulted in the attachment of tryptophan molecules to a single gramicidin. An alternative detection method to photo-ionization is examined by testing a superconducting single photon detector (SSPD) for its ability to detect individual neutral molecules. The sensitivity of the nanostructured SSPD seems not to be limited to small molecules. The superconducting detector is able to record velocity distributions of neutral insulin (∼5,700amu), myoglobin(∼17 kDa) and hemoglobin (∼66 kDa) beams. A check if the intact molecules leave the source is missing due to the lack of alternative detection methods for these molecules. The working principle of the SSPD relies on the fact, that an impinging particle leads to a breakdown of superconductivity. Further developments of the SSPD appear possible and promising in order to increase the mass range of detected neutral organic molecules, which cannot be detected in photo-ionization. The source is developed in order to fulfil the criteria needed for a combination with a Talbot-Lau interferometer. Interference of biomolecules is, beside the prove of the wave-particle duality, interesting for the

  6. Non-Markovian and Non-Perturbative Entanglement Dynamics of Biomolecular Excitons

    Institute of Scientific and Technical Information of China (English)

    LIU Zhi-Qiang; LIANG Xian-Ting

    2011-01-01

    @@ We investigate the entanglement dynamics of two coupled chromophore pairs embedded in a protein-solvent environment.The non-Markovian and non-perturbative hierarchical expansion technique is used in the solution of the quantum dynamics.The spectral distribution function of the bath is set with the Drude-Lorentz form.It is shown that the evolutions of the entanglement described by the measures of negativity and concurrence are in agreement with each other.They decay to zero in a short time and the sudden death and sudden birth can be observed in the process of the evolutions of the entanglement.

  7. Toward Extreme Biophysics: Deciphering the Infrared Response of Biomolecular Solutions at High Pressures.

    Science.gov (United States)

    Imoto, Sho; Kibies, Patrick; Rosin, Christopher; Winter, Roland; Kast, Stefan M; Marx, Dominik

    2016-08-01

    Biophysics under extreme conditions is the fundamental platform for scrutinizing life in unusual habitats, such as those in the deep sea or continental subsurfaces, but also for putative extraterrestrial organisms. Therefore, an important thermodynamic variable to explore is pressure. It is shown that the combination of infrared spectroscopy with simulation is an exquisite approach for unraveling the intricate pressure response of the solvation pattern of TMAO in water, which is expected to be transferable to biomolecules in their native solvent. Pressure-enhanced hydrogen bonding was found for TMAO in water. TMAO is a molecule known to stabilize proteins against pressure-induced denaturation in deep-sea organisms. PMID:27351995

  8. Environmental Impacts on Nuclear Reprocessing Solvents

    Science.gov (United States)

    Gillens, A. R.; Fessenden, J. E.

    2009-12-01

    Nuclear tests have been employed ever since the first nuclear explosion in Alamogordo, NM during the mid-1940s. Nuclear weapons pose a threat to civil society and result in extensive biological (medical) damages. For this reason, treaties banning nuclear tests and weapons have been employed since the 1960s to cease proliferation of weapons. However, as nuclear tests continue in secrecy and actinides, such as plutonium and uranium, are eligible for theft, nuclear forensics is needed to prevent weapons proliferation. In this study, solvents [tributyl phosphate (TBP), dodecane, decanol] used in reprocessing spent nuclear fuel are analyzed using an isotope ratio mass spectrometer, which provides indisputable evidence in identifying the operation in which solvents were used. Solvent samples are observed under variable conditions in the laboratory for different time periods. It is assumed that their carbon isotope values (δ13C) will become more positive (shift heavy) with time. It is found that the solvents are hygroscopic. TBP leaves the most robust signature compared to the other solvents studied and the isotope values for all solvents under all conditions become more positive with time. This study serves as primary research in understanding how solvents behave under variable conditions in the laboratory and how this could be translated to the environment in fate and transport studies.

  9. Organic Solvent Tolerant Lipases and Applications

    Directory of Open Access Journals (Sweden)

    Shivika Sharma

    2014-01-01

    Full Text Available Lipases are a group of enzymes naturally endowed with the property of performing reactions in aqueous as well as organic solvents. The esterification reactions using lipase(s could be performed in water-restricted organic media as organic solvent(s not only improve(s the solubility of substrate and reactant in reaction mixture but also permit(s the reaction in the reverse direction, and often it is easy to recover the product in organic phase in two-phase equilibrium systems. The use of organic solvent tolerant lipase in organic media has exhibited many advantages: increased activity and stability, regiospecificity and stereoselectivity, higher solubility of substrate, ease of products recovery, and ability to shift the reaction equilibrium toward synthetic direction. Therefore the search for organic solvent tolerant enzymes has been an extensive area of research. A variety of fatty acid esters are now being produced commercially using immobilized lipase in nonaqueous solvents. This review describes the organic tolerance and industrial application of lipases. The main emphasis is to study the nature of organic solvent tolerant lipases. Also, the potential industrial applications that make lipases the biocatalysts of choice for the present and future have been presented.

  10. Predicting the activity coefficients of free-solvent for concentrated globular protein solutions using independently determined physical parameters.

    Directory of Open Access Journals (Sweden)

    Devin W McBride

    Full Text Available The activity coefficient is largely considered an empirical parameter that was traditionally introduced to correct the non-ideality observed in thermodynamic systems such as osmotic pressure. Here, the activity coefficient of free-solvent is related to physically realistic parameters and a mathematical expression is developed to directly predict the activity coefficients of free-solvent, for aqueous protein solutions up to near-saturation concentrations. The model is based on the free-solvent model, which has previously been shown to provide excellent prediction of the osmotic pressure of concentrated and crowded globular proteins in aqueous solutions up to near-saturation concentrations. Thus, this model uses only the independently determined, physically realizable quantities: mole fraction, solvent accessible surface area, and ion binding, in its prediction. Predictions are presented for the activity coefficients of free-solvent for near-saturated protein solutions containing either bovine serum albumin or hemoglobin. As a verification step, the predictability of the model for the activity coefficient of sucrose solutions was evaluated. The predicted activity coefficients of free-solvent are compared to the calculated activity coefficients of free-solvent based on osmotic pressure data. It is observed that the predicted activity coefficients are increasingly dependent on the solute-solvent parameters as the protein concentration increases to near-saturation concentrations.

  11. Predicting the activity coefficients of free-solvent for concentrated globular protein solutions using independently determined physical parameters.

    Science.gov (United States)

    McBride, Devin W; Rodgers, Victor G J

    2013-01-01

    The activity coefficient is largely considered an empirical parameter that was traditionally introduced to correct the non-ideality observed in thermodynamic systems such as osmotic pressure. Here, the activity coefficient of free-solvent is related to physically realistic parameters and a mathematical expression is developed to directly predict the activity coefficients of free-solvent, for aqueous protein solutions up to near-saturation concentrations. The model is based on the free-solvent model, which has previously been shown to provide excellent prediction of the osmotic pressure of concentrated and crowded globular proteins in aqueous solutions up to near-saturation concentrations. Thus, this model uses only the independently determined, physically realizable quantities: mole fraction, solvent accessible surface area, and ion binding, in its prediction. Predictions are presented for the activity coefficients of free-solvent for near-saturated protein solutions containing either bovine serum albumin or hemoglobin. As a verification step, the predictability of the model for the activity coefficient of sucrose solutions was evaluated. The predicted activity coefficients of free-solvent are compared to the calculated activity coefficients of free-solvent based on osmotic pressure data. It is observed that the predicted activity coefficients are increasingly dependent on the solute-solvent parameters as the protein concentration increases to near-saturation concentrations.

  12. TRUEX process solvent cleanup with solid sorbents

    Energy Technology Data Exchange (ETDEWEB)

    Tse, Pui-Kwan; Reichley-Yinger, L.; Vandegrift, G.F.

    1989-01-01

    Solid sorbents, alumina, silica gel, and Amberlyst A-26 have been tested for the cleanup of degraded TRUEX-NPH solvent. A sodium carbonate scrub alone does not completely remove acidic degradation products from highly degraded solvent and cannot restore the stripping performance of the solvent. By following the carbonate scrub with either neutral alumina or Amberlyst A-26 anion exchange resin, the performance of the TRUEX-NPH is substantially restored. The degraded TRUEX-NPH was characterized before and after treatment by supercritical fluid chromatography. Its performance was evaluated by americium distribution ratios, phase-separation times, and lauric acid distribution coefficients. 17 refs., 2 figs., 5 tabs.

  13. Genomic and Genetic Approaches to Solvent Tolerance

    Energy Technology Data Exchange (ETDEWEB)

    Eleftherios T. Papoutsakis

    2005-06-10

    The proposed research is to understand and exploit the molecular basis that determines tolerance of the industrially important anaerobic clostridia to solvents. Furthermore, we aim to develop general genomic and metabolic engineering strategies for understanding the molecular basis of tolerance to chemicals and for developing tolerant strains. Our hypothesis is that the molecular basis of what makes bacterial cells able to withstand high solvent concentrations can be used to metabolically engineer cells so that they can tolerate higher concentrations of solvents and related chemicals.

  14. Chemical reactions in solvents and melts

    CERN Document Server

    Charlot, G

    1969-01-01

    Chemical Reactions in Solvents and Melts discusses the use of organic and inorganic compounds as well as of melts as solvents. This book examines the applications in organic and inorganic chemistry as well as in electrochemistry. Organized into two parts encompassing 15 chapters, this book begins with an overview of the general properties and the different types of reactions, including acid-base reactions, complex formation reactions, and oxidation-reduction reactions. This text then describes the properties of inert and active solvents. Other chapters consider the proton transfer reactions in

  15. Solvent Handbook Database System user's manual

    International Nuclear Information System (INIS)

    Industrial solvents and cleaners are used in maintenance facilities to remove wax, grease, oil, carbon, machining fluids, solder fluxes, mold release, and various other contaminants from parts, and to prepare the surface of various metals. However, because of growing environmental and worker-safety concerns, government regulations have already excluded the use of some chemicals and have restricted the use of halogenated hydrocarbons because they affect the ozone layer and may cause cancer. The Solvent Handbook Database System lets you view information on solvents and cleaners, including test results on cleaning performance, air emissions, recycling and recovery, corrosion, and non-metals compatibility. Company and product safety information is also available

  16. Full scale solvent extraction remedial results

    International Nuclear Information System (INIS)

    Sevenson Extraction Technology, Inc. has completed the development of the Soil Restoration Unit (initially developed by Terra-Kleen Corporation), a mobile, totally enclosed solvent extraction treatment facility for the removal of organic contaminated media is greater by a closed loop, counter current process that recycles all solvents. The solvents used are selected for the individual site dependant upon the contaminants, such as PCB's, oil, etc. and the soil conditions. A mixture of up to fourteen non-toxic solvents can be used for complicated sites. The full scale unit has been used to treat one superfund site, the Traband Site in Tulsa, Oklahoma, and is currently treating another superfund site, the Pinette's Salvage Yard Site in Washburn, Maine. The full scale Soil Restoration Unit has also been used at a non-superfund site, as part of a TSCA Research and Development permit. The results from these sites will be discussed in brief herein, and in more detail in the full paper

  17. Solvent-Free Synthesis of New Coumarins

    Directory of Open Access Journals (Sweden)

    Redah I. Al-Bayati

    2012-01-01

    Full Text Available A solvent-free synthesis of five series of coumarin derivatives using microwave assistant is presented herein. The synthesized compounds are fully characterized by UV-VIS, FT-IR, and NMR spectroscopy.

  18. Solvent Extraction Developments in Southern Africa

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The largest solvent-extraction plant in the world at the time, the Nchanga Copper Operation, was in Zambia. The first commercial process using solvent extraction for the refining of the platinum-group metals was in South Africa. More recently, the Southern African region has seen the implementation of solvent extraction for other base metals, precious metals, and specialty metals. These include the world firsts of primary production of zinc at Skorpion Zinc in Namibia and the large-scale refining of gold by Harmony Gold in South Africa. Several other flowsheets that use solvent-extraction technology are currently under commissioning, development, or feasibility study for implementation in this part of the world, including those for the recovery of copper, cobalt, nickel, tantalum, and niobium.

  19. Computer-Aided Solvent Screening for Biocatalysis

    DEFF Research Database (Denmark)

    Abildskov, Jens; Leeuwen, M.B. van; Boeriu, C.G.;

    2013-01-01

    constrained properties related to chemical reaction equilibrium, substrate and product solubility, water solubility, boiling points, toxicity and others. Two examples are provided, covering the screening of solvents for lipase-catalyzed transesterification of octanol and inulin with vinyl laurate...

  20. [Shoe factory workers, solvents and health].

    Science.gov (United States)

    Foà, Vito; Martinotti, Irene

    2012-01-01

    Exposure to organic solvents in footwear manufacturing industry came from the glues used adhering the shoe parts to each other. Benzene was the first solvent used in shoe factories until the evidence of its capacity to cause leukaemia. Then, the demonstration that exposure to n-hexane was related to distal polyneuropathy limited the use of this substance. After that, results of neurotoxicological studies conducted on workers exposed to different mixtures of organic solvents make necessary prevention measure directed to a progressive reduction of air dispersion of these chemicals. Today exposure to solvents in workplaces is regulated by health based exposure limit values that should warranty absence of central nervous system effects. One of the most important rules of occupational medicine is verify that these exposure levels are really health protective also for workers with increased susceptibility. PMID:22697025

  1. Implicit solvent methods for free energy estimation.

    Science.gov (United States)

    Decherchi, Sergio; Masetti, Matteo; Vyalov, Ivan; Rocchia, Walter

    2015-02-16

    Solvation is a fundamental contribution in many biological processes and especially in molecular binding. Its estimation can be performed by means of several computational approaches. The aim of this review is to give an overview of existing theories and methods to estimate solvent effects giving a specific focus on the category of implicit solvent models and their use in Molecular Dynamics. In many of these models, the solvent is considered as a continuum homogenous medium, while the solute can be represented at the atomic detail and at different levels of theory. Despite their degree of approximation, implicit methods are still widely employed due to their trade-off between accuracy and efficiency. Their derivation is rooted in the statistical mechanics and integral equations disciplines, some of the related details being provided here. Finally, methods that combine implicit solvent models and molecular dynamics simulation, are briefly described. PMID:25193298

  2. Method of stripping metals from organic solvents

    Science.gov (United States)

    Todd, Terry A.; Law, Jack D.; Herbst, R. Scott; Romanovskiy, Valeriy N.; Smirnov, Igor V.; Babain, Vasily A.; Esimantovski, Vyatcheslav M.

    2009-02-24

    A new method to strip metals from organic solvents in a manner that allows for the recycle of the stripping agent. The method utilizes carbonate solutions of organic amines with complexants, in low concentrations, to strip metals from organic solvents. The method allows for the distillation and reuse of organic amines. The concentrated metal/complexant fraction from distillation is more amenable to immobilization than solutions resulting from current practice.

  3. Hydrogen recovery by novel solvent systems

    Energy Technology Data Exchange (ETDEWEB)

    Shinnar, R.; Ludmer, Z.; Ullmann, A.

    1991-08-01

    The objective of this work is to develop a novel method for purification of hydrogen from coal-derived synthesis gas. The study involved a search for suitable mixtures of solvents for their ability to separate hydrogen from the coal derived gas stream in significant concentration near their critical point of miscibility. The properties of solvent pairs identified were investigated in more detail to provide data necessary for economic evaluation and process development.

  4. Solvent management in a reprocessing plant

    International Nuclear Information System (INIS)

    Solvent management in large capacity reprocessing plant is studied to limit production of organic wastes. Chemical processing increases life time of solvent. Low pressure distillation allows the recycling of TBP and diluent at a low activity level. Besides heavy degradation products are eliminated. For the safety the flash point of distillated diluent increases slightly. Tests on an industrial scale started in 1985 and since more than 500 cubic meters were treated

  5. Single molecules in soft matter : a study of biomolecular conformation, heterogeneity and plasmon enhanced fluorescence

    NARCIS (Netherlands)

    Yuan, Haifeng

    2013-01-01

    We study the dynamics of single molecules and individual gold nanorods in glycerol at variable temperatures. We demonstrate temperature-cycle microscopy on FRET-labeled polyproline and double-stranded DNA molecules to access micro-second dynamics of single molecules, and reveal the influences of dye

  6. Solvent dependent photophysical properties of dimethoxy curcumin

    Science.gov (United States)

    Barik, Atanu; Indira Priyadarsini, K.

    2013-03-01

    Dimethoxy curcumin (DMC) is a methylated derivative of curcumin. In order to know the effect of ring substitution on photophysical properties of curcumin, steady state absorption and fluorescence spectra of DMC were recorded in organic solvents with different polarity and compared with those of curcumin. The absorption and fluorescence spectra of DMC, like curcumin, are strongly dependent on solvent polarity and the maxima of DMC showed red shift with increase in solvent polarity function (Δf), but the above effect is prominently observed in case of fluorescence maxima. From the dependence of Stokes' shift on solvent polarity function the difference between the excited state and ground state dipole moment was estimated as 4.9 D. Fluorescence quantum yield (ϕf) and fluorescence lifetime (τf) of DMC were also measured in different solvents at room temperature. The results indicated that with increasing solvent polarity, ϕf increased linearly, which has been accounted for the decrease in non-radiative rate by intersystem crossing (ISC) processes.

  7. Recycling of solvent used in a solvent extraction of petroleum hydrocarbons contaminated soil.

    OpenAIRE

    Wu, Guozhong; Li, XinGang; Coulon, Frederic; LI Hong; Lian, Jingyan; Sui, Hong

    2011-01-01

    The application of water washing technology for recycling an organic composite solvent consisting of hexane and pentane (4:1; TU-A solvent) was investigated for extracting total petroleum hydrocarbons (TPH) from contaminated soil. The effects of water volume, water temperature, washing time and initial concentration of solvent were evaluated using orthogonal experiments followed by single factor experiments. Our results showed that the water volume was a statistically signif...

  8. CHEMICAL STABILITY OF POLYPHENYLENE SULFIDE IN THE NEXT GENERATION SOLVENT FOR CAUSTIC-SIDE SOLVENT EXTRACTION

    Energy Technology Data Exchange (ETDEWEB)

    Fondeur, F.; Fink, S.

    2011-12-08

    The Office of Waste Processing, within the Office of Technology Innovation and Development, is funding the development of an enhanced solvent for deployment at the Savannah River Site for removal of cesium from High Level Waste. For simplicity, this solvent is referred to as the Next Generation Solvent (NGS). The technical effort is collaboration between Oak Ridge National Laboratory (ORNL), Savannah River National Laboratory (SRNL), and Argonne National Laboratory. The initial deployment target envisioned for the technology was within the Modular Caustic-Side Solvent Extraction Unit (MCU). Deployment of a new chemical within an existing facility requires verification that the chemical components are compatible with the installed equipment. In the instance of a new organic solvent, the primary focus is on compatibility of the solvent with polyphenylene sulfide (PPS), the polymer used in the coalescers within MCU. This report provides the data from exposing PPS polymer to NGS. The test was conducted over a three month period. PPS is remarkably stable in the presence of the next generation solvent. Testing showed no indication of swelling or significant leaching. Preferential sorption of the Modifier on PPS was observed but the same behavior occurs with the baseline solvent. Therefore, PPS coalescers exposed to the NGS are expected to perform comparably to those in contact with the baseline solvent.

  9. Influence of solute-solvent coordination on the orientational relaxation of ion assemblies in polar solvents

    Science.gov (United States)

    Ji, Minbiao; Hartsock, Robert W.; Sung, Zheng; Gaffney, Kelly J.

    2012-01-01

    We have investigated the rotational dynamics of lithium thiocyanate (LiNCS) dissolved in various polar solvents with time and polarization resolved vibrational spectroscopy. LiNCS forms multiple distinct ionic structures in solution that can be distinguished with the CN stretch vibrational frequency of the different ionic assemblies. By varying the solvent and the LiNCS concentration, the number and type of ionic structures present in solution can be controlled. Control of the ionic structure provides control over the volume, shape, and dipole moment of the solute, critical parameters for hydrodynamic and dielectric continuum models of friction. The use of solutes with sizes comparable to or smaller than the solvent molecules also helps amplify the sensitivity of the measurement to the short-ranged solute-solvent interaction. The measured orientational relaxation dynamics show many clear and distinct deviations from simple hydrodynamic behavior. All ionic structures in all solvents exhibit multi-exponential relaxation dynamics that do not scale with the solute volume. For Lewis base solvents such as benzonitrile, dimethyl carbonate, and ethyl acetate, the observed dynamics strongly show the effect of solute-solvent complex formation. For the weak Lewis base solvent nitromethane, we see no evidence for solute-solvent complex formation, but still see strong deviation from the predictions of simple hydrodynamic theory.

  10. The use of environmentally sustainable bio-derived solvents in solvent extraction applications-A review

    Institute of Scientific and Technical Information of China (English)

    Zheng Li; Kathryn H. Smith; Geoffrey W. Stevens

    2016-01-01

    Replacement of volatile organic compounds (VOCs) by greener or more environmental y sustainable solvents is becoming increasingly important due to the increasing health and environmental concerns as wel as economic pressures associated with VOCs. Solvents that are derived from biomass, namely bio-derived solvents, are a type of green solvent that have attracted intensive investigations in recent years because of their advantages over con-ventional VOCs, such as low toxicity, biodegradability and renewability. This review aims to summarize the use of bio-derived solvents in solvent extraction applications, with special emphasis given to utilization of biodiesels and terpenes. Compared with the conventional VOCs, the overall performance of these bio-derived solvents is comparable in terms of extraction yields and selectivity for natural product extraction and no difference was found for metal extraction. To date most researchers have focused on laboratory scale thermodynamics studies. Future work is required to develop and test new bio-derived solvents and understand the kinetic performance as well as solvent extraction pilot plant studies.

  11. Influence of Energy on Solvent Diffusion in Polymer/Solvent Systems

    Institute of Scientific and Technical Information of China (English)

    HUHuijun; JIANGWenhua; 等

    2002-01-01

    The Vrentas-Duda free-volume theory has been extensively used to correlate or predict the solvent diffusion coefficient of a polymer/solvent system.The energy term in the free volume diffusion equation is difficult to estimate,so the energy term was usually neglected in previous predictive versions of the free volume diffusion coefficient equation.Recent studies show that the energy effect is very important even above the glass transition temperature of the system. In this paper, a new evaluation method of the energy term is proposed,that is the diffusion energy at different solvent concentrations is assumed to be a linear function of the solvent diffusion energy in pure solvents and that in polymers under the condition that the solvent in infinite dilution.By taking consideration of the influence of energy on the solvent diffustion,the prediction of solvent diffusion coefficient was preformed for three polymer/solvent systems over a wide range of concentrations and temperatures.The results show an improvement on the predictive capability of the free volume diffusion theory.

  12. PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems.

    Science.gov (United States)

    Torras, Juan; Roberts, Benjamin P; Seabra, Gustavo M; Trickey, Samuel B

    2015-01-01

    PUPIL (Program for User Package Interfacing and Linking) implements a distinctive multi-scale approach to hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. Originally developed to interface different external programs for multi-scale simulation with applications in the materials sciences, PUPIL is finding increasing use in the study of complex biological systems. Advanced MD techniques from the external packages can be applied readily to a hybrid QM/MM treatment in which the forces and energy for the QM region can be computed by any of the QM methods available in any of the other external packages. Here, we give a survey of PUPIL design philosophy, main features, and key implementation decisions, with an orientation to biomolecular simulation. We discuss recently implemented features which enable highly realistic simulations of complex biological systems which have more than one active site that must be treated concurrently. Examples are given.

  13. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications

    Directory of Open Access Journals (Sweden)

    Arjun Verma

    2016-07-01

    Full Text Available We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.

  14. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications.

    Science.gov (United States)

    Verma, Arjun; Fratto, Brian E; Privman, Vladimir; Katz, Evgeny

    2016-07-05

    We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s) as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.

  15. Diffusion Monte Carlo applied to weak interactions - hydrogen bonding and aromatic stacking in (bio-)molecular model systems

    Science.gov (United States)

    Fuchs, M.; Ireta, J.; Scheffler, M.; Filippi, C.

    2006-03-01

    Dispersion (Van der Waals) forces are important in many molecular phenomena such as self-assembly of molecular crystals or peptide folding. Calculating this nonlocal correlation effect requires accurate electronic structure methods. Usual density-functional theory with generalized gradient functionals (GGA-DFT) fails unless empirical corrections are added that still need extensive validation. Quantum chemical methods like MP2 and coupled cluster are more accurate, yet limited to rather small systems by their unfavorable computational scaling. Diffusion Monte Carlo (DMC) can provide accurate molecular total energies and remains feasible also for larger systems. Here we apply the fixed-node DMC method to (bio-)molecular model systems where dispersion forces are significant: (dimethyl-) formamide and benzene dimers, and adenine-thymine DNA base pairs. Our DMC binding energies agree well with data from coupled cluster (CCSD(T)), in particular for stacked geometries where GGA-DFT fails qualitatively and MP2 predicts too strong binding.

  16. 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...

  17. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications.

    Science.gov (United States)

    Verma, Arjun; Fratto, Brian E; Privman, Vladimir; Katz, Evgeny

    2016-01-01

    We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s) as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed. PMID:27399702

  18. Stability of the Caustic-Side Solvent Extraction (CSSX) Process Solvent: Effect of High Nitrite on Solvent Nitration

    Energy Technology Data Exchange (ETDEWEB)

    Bonnesen, P.V.

    2002-06-26

    The purpose of this investigation was to determine whether nitrated organic compounds could be formed during operation of the Caustic-Side Solvent Extraction (CSSX) process, and whether such compounds would present a safety concern. The CSSX process was developed to remove cesium from alkaline high-level salt waste stored at the US Department of Energy Savannah River Site (SRS). The solvent is composed of the cesium extractant calix[4]arene-bis-(4-tert-octylbenzo-crown-6) (BOBCalixC6), a fluorinated alcohol phase modifier, tri-n-octylamine (TOA), and an isoparaffinic diluent (Iospar{reg_sign}). During the CSSX process, the solvent is expected to be exposed to high concentrations of nitrate and nitrite dissolved in the alkaline waste feed. The solvent will also be exposed to dilute (50 mM) nitric acid solutions containing low concentrations of nitrite during scrubbing, followed by stripping with 1 mM nitric acid. The solvent is expected to last for one year of plant operation, and the temperatures the solvent may experience during the process could range from as low as 15 C to as high as 35 C. Excursions from standard process conditions could result in the solvent experiencing higher temperatures, as well as concentrations of nitrate, nitrite, and most importantly nitric acid, that exceed normal operating conditions. Accordingly, conditions may exist where nitration reactions involving the solvent components, possibly leading to other chemical reactions stemming from nitration reactions, could occur. To model such nitration reactions, the solvent was exposed to the types of nitrate- and nitrite-containing solutions that might be expected to be encountered during the process (even under off-normal conditions), as a function of time, temperature, and concentration of nitrate, nitrite, and nitric acid. The experiments conducted as part of this report were designed to examine the more specific effect that high nitrite concentrations could have on forming nitrated

  19. CERN Access Cards and Access Authorisations

    CERN Multimedia

    2003-01-01

    From the 01/05/2003, all problems relating to access cards and refusal of access to any zone, building or experiment within CERN must be addressed to the Centrale de Surveillance des Accès (CSA building 120) on 78877 or send an e-mail to Access.Surveillance@cern.ch. The responsibles for CERN access control have put into place a procedure with the CSA, Service Enregistrement and the Technical Control Room, to make sure that all problems get resolved in a proper and timely manner.

  20. Toluene promotes lid 2 interfacial activation of cold active solvent tolerant lipase from Pseudomonas fluorescens strain AMS8.

    Science.gov (United States)

    Yaacob, Norhayati; Mohamad Ali, Mohd Shukuri; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Raja Abdul; Leow, Adam Thean Chor

    2016-07-01

    The utilization of cold active lipases in organic solvents proves an excellent approach for chiral synthesis and modification of fats and oil due to the inherent flexibility of lipases under low water conditions. In order to verify whether this lipase can function as a valuable synthetic catalyst, the mechanism concerning activation of the lid and interacting solvent residues in the presence of organic solvent must be well understood. A new alkaline cold-adapted lipase, AMS8, from Pseudomonas fluorescens was studied for its structural adaptation and flexibility prior to its exposure to non-polar, polar aprotic and protic solvents. Solvents such as ethanol, toluene, DMSO and 2-propanol showed to have good interactions with active sites. Asparagine (Asn) and tyrosine (Tyr) were key residues attracted to solvents because they could form hydrogen bonds. Unlike in other solvents, Phe-18, Tyr-236 and Tyr-318 were predicted to have aromatic-aromatic side-chain interactions with toluene. Non-polar solvent also was found to possess highest energy binding compared to polar solvents. Due to this circumstance, the interaction of toluene and AMS8 lipase was primarily based on hydrophobicity and molecular recognition. The molecular dynamic simulation showed that lid 2 (residues 148-167) was very flexible in toluene and Ca(2+). As a result, lid 2 moves away from the catalytic areas, leaving an opening for better substrate accessibility which promotes protein activation. Only a single lid (lid 2) showed the movement following interactions with toluene, although AMS8 lipase displayed double lids. The secondary conformation of AMS8 lipase that was affected by toluene observed a reduction of helical strands and increased coil structure. Overall, this work shows that cold active lipase, AMS8 exhibits distinguish interfacial activation and stability in the presence of polar and non-polar solvents. PMID:27474867

  1. Accessibility and sensory experiences

    DEFF Research Database (Denmark)

    Ryhl, Camilla

    2010-01-01

    This article introduces a new design concept; sensory accessibility. While acknowledging the importance of sensory experiences in architectural quality, as well as the importance of accommodating user needs the concept combines three equally important factors; architecture, the senses...... and accessibility. Sensory accessibility accommodates aspects of a sensory disability and describes architectural design requirements needed to ensure access to architectural experiences. In the context of architecture accessibility has become a design concept of its own. It is generally described as ensuring...

  2. Local Phase Separation of Co-solvents Enhances Pretreatment of Biomass for Bioenergy Applications.

    Science.gov (United States)

    Mostofian, Barmak; Cai, Charles M; Smith, Micholas Dean; Petridis, Loukas; Cheng, Xiaolin; Wyman, Charles E; Smith, Jeremy C

    2016-08-31

    Pretreatment facilitates more complete deconstruction of plant biomass to enable more economic production of lignocellulosic biofuels and byproducts. Various co-solvent pretreatments have demonstrated advantages relative to aqueous-only methods by enhancing lignin removal to allow unfettered access to cellulose. However, there is a limited mechanistic understanding of the interactions between the co-solvents and cellulose that impedes further improvement of such pretreatment methods. Recently, tetrahydrofuran (THF) has been identified as a highly effective co-solvent for the pretreatment and fractionation of biomass. To elucidate the mechanism of the THF-water interactions with cellulose, we pair simulation and experimental data demonstrating that enhanced solubilization of cellulose can be achieved by the THF-water co-solvent system at equivolume mixtures and moderate temperatures (≤445 K). The simulations show that THF and water spontaneously phase separate on the local surface of a cellulose fiber, owing to hydrogen bonding of water molecules with the hydrophilic cellulose faces and stacking of THF molecules on the hydrophobic faces. Furthermore, a single fully solvated cellulose chain is shown to be preferentially bound by water molecules in the THF-water mixture. In light of these findings, co-solvent reactions were performed on microcrystalline cellulose and maple wood to show that THF significantly enhanced cellulose deconstruction and lignocellulose solubilization at simulation conditions, enabling a highly versatile and efficient biomass pretreatment and fractionation method.

  3. Local Phase Separation of Co-solvents Enhances Pretreatment of Biomass for Bioenergy Applications.

    Science.gov (United States)

    Mostofian, Barmak; Cai, Charles M; Smith, Micholas Dean; Petridis, Loukas; Cheng, Xiaolin; Wyman, Charles E; Smith, Jeremy C

    2016-08-31

    Pretreatment facilitates more complete deconstruction of plant biomass to enable more economic production of lignocellulosic biofuels and byproducts. Various co-solvent pretreatments have demonstrated advantages relative to aqueous-only methods by enhancing lignin removal to allow unfettered access to cellulose. However, there is a limited mechanistic understanding of the interactions between the co-solvents and cellulose that impedes further improvement of such pretreatment methods. Recently, tetrahydrofuran (THF) has been identified as a highly effective co-solvent for the pretreatment and fractionation of biomass. To elucidate the mechanism of the THF-water interactions with cellulose, we pair simulation and experimental data demonstrating that enhanced solubilization of cellulose can be achieved by the THF-water co-solvent system at equivolume mixtures and moderate temperatures (≤445 K). The simulations show that THF and water spontaneously phase separate on the local surface of a cellulose fiber, owing to hydrogen bonding of water molecules with the hydrophilic cellulose faces and stacking of THF molecules on the hydrophobic faces. Furthermore, a single fully solvated cellulose chain is shown to be preferentially bound by water molecules in the THF-water mixture. In light of these findings, co-solvent reactions were performed on microcrystalline cellulose and maple wood to show that THF significantly enhanced cellulose deconstruction and lignocellulose solubilization at simulation conditions, enabling a highly versatile and efficient biomass pretreatment and fractionation method. PMID:27482599

  4. The orientation of solvent-dipoles at the surface of the pure solvent

    NARCIS (Netherlands)

    Nedermeijer-Denessen, H.J.M.; Ligny, C.L. de

    1975-01-01

    A method is described for the assessment of the preferential orientation of solvent-dipoles at the surface of the solvent from the surface potential χ and its temperature coefficient, dχ/dT. The method is based on the model of Levine et al. of the Stern inner region at the mercury-water interface in

  5. Chlorinated solvent replacements recycle/recovery review report

    Energy Technology Data Exchange (ETDEWEB)

    Beal, M.; Hsu, D.; McAtee, R.E.; Weidner, J.R. (EG and G Idaho, Inc., Idaho Falls, ID (United States)); Berg, L.; McCandless, F.P.; Waltari, S.; Peterson, C. (Montana State Univ., Bozeman, MT (United States). Dept. of Chemical Engineering)

    1992-08-01

    This report is a literature review of waste solvents recycle/recovery methods and shows the results of solvent separations using membrane and distillation technologies. The experimental solvent recovery methods were conducted on solvent replacements for chlorinated solvents at Montana State University. The literature review covers waste solvents separation using distillation, membranes decantation, filtration, carbon adsorption, solvent extraction, and other vapor-phase separation techniques. The results of this study identify solvent distillation methods as the most common separation technique. The alternative separation methods typically supplement distillation. The study shows the need for industries to identify waste solvent disposal methods and investigate the economics of waste solvent recycling as a possible waste reduction method.

  6. Recommended methods for purification of solvents and tests for impurities

    CERN Document Server

    Coetzee, J F

    1982-01-01

    Recommended Methods for Purification of Solvents and Tests for Impurities is a compilation of recommended procedures for purification of solvents and tests for solvent impurities. Ten solvents are covered: acetonitrile, sulfolane, propylene carbonate, dimethyl sulfoxide, dimethylformamide, hexamethylphosphoramide, pyridine, ethylenediamine, N-methylacetamide, and N-methylpropionamide. This book is comprised of 12 chapters and opens with an introduction to general aspects of impurity effects. The rationale for the selection of solvent is explained, and the relative reactivities of solutes in di

  7. Professional Access 2013 programming

    CERN Document Server

    Hennig, Teresa; Hepworth, George; Yudovich, Dagi (Doug)

    2013-01-01

    Authoritative and comprehensive coverage for building Access 2013 Solutions Access, the most popular database system in the world, just opened a new frontier in the Cloud. Access 2013 provides significant new features for building robust line-of-business solutions for web, client and integrated environments.  This book was written by a team of Microsoft Access MVPs, with consulting and editing by Access experts, MVPs and members of the Microsoft Access team. It gives you the information and examples to expand your areas of expertise and immediately start to develop and upgrade projects. Exp

  8. Alternative Solvents through Green Chemistry Project

    Science.gov (United States)

    Hintze, Paul E.; Quinn, Jacqueline

    2014-01-01

    Components in the aerospace industry must perform with accuracy and precision under extreme conditions, and surface contamination can be detrimental to the desired performance, especially in cases when the components come into contact with strong oxidizers such as liquid oxygen. Therefore, precision cleaning is an important part of a components preparation prior to utilization in aerospace applications. Current cleaning technologies employ a variety of cleaning agents, many of which are halogenated solvents that are either toxic or cause environmental damage. Thus, this project seeks to identify alternative precision cleaning solvents and technologies, including use of less harmful cleaning solvents, ultrasonic and megasonic agitation, low-pressure plasma cleaning techniques, and supercritical carbon dioxide extraction. Please review all data content found in the Public Data tab located at: https:techport.nasa.govview11697public

  9. Hazardous Solvent Substitution Data System tutorial

    International Nuclear Information System (INIS)

    This manual is the tutorial for the Hazardous Solvent Substitution Data System (HSSDS), an online, comprehensive system of information on alternatives to hazardous solvents and related subjects. The HSSDS data base contains product information, material safety data sheets, toxicity reports, usage reports, biodegradable data, product chemical element lists, and background information on solvents. HSSDS use TOPIC reg-sign to search for information based on a query defined by the user. TOPIC provides a full text retrieval of unstructured source documents. In this tutorial, a series of lessons is provided that guides the user through basic steps common to most queries performed with HSSDS. Instructions are provided for both window-based and character-based applications

  10. Thermal Characterization of Nanofluids with Different Solvents

    Science.gov (United States)

    Jiménez-Pérez, J. L.; Cruz-Orea, A.; Sánchez-Ramírez, J. F.; Sánchez-Sinencio, F.; Martínez-Pérez, L.; López Muñoz, G. A.

    2009-08-01

    Thermal lens spectrometry (TLS) and photopyroelectric (PPE) techniques were used to obtain the thermal diffusivity and effusivity of different nanofluid samples. The thermal effusivity of these samples was obtained by the PPE technique in a front detection configuration. In the case of the determination of the thermal diffusivity, TLS was used for the different solvents in the presence of gold nanoparticles (nanofluids). In this technique, an Ar+ laser and intensity stabilized He-Ne laser were used as the heating source and probe beam, respectively. The experimental results showed that thermal diffusivity values of the studied solvents (water, ethanol, and ethylene glycol) were enhanced by the presence of gold nanoparticles. Comparisons with literature values show good agreement with pure solvents. These techniques are applicable for all kind of liquid samples, including semitransparent ones.

  11. 300 Area solvent evaporator closure plan

    International Nuclear Information System (INIS)

    This document describes activities for the closure of a dangerous waste treatment tank facility, owned and operated by the US Department of Energy-Richland Operations Office (DOE-RL) and co-operated by the Westinghouse Hanford Company (Westinghouse Hanford). This tank treatment facility is the 300 Area Solvent Evaporator (300 ASE), which was located in the 300 Area of the Hanford Site from 1975 to 1986, and was managed for the DOE-RL by UNC Nuclear Industries, Incorporated. The 300 ASE evaporator unit was a modified load lugger (dumpster) in which solvent wastes were evaporated, and the adjacent 333 East Concrete Pad, where 55-gallon barrels of waste solvents were temporarily stored while awaiting liquid transfers into the evaporator. 26 refs., 14 figs., 6 tabs

  12. Solvent-resistant microporous polymide membranes

    Science.gov (United States)

    Miller, Warren K.; McCray, Scott B.; Friesen, Dwayne T.

    1998-01-01

    An asymmetric microporous membrane with exceptional solvent resistance and highly desirable permeability is disclosed. The membrane is made by a solution-casting or solution-spinning process from a copolyamic acid comprising the condensation reaction product in a solvent of at least three reactants selected from certain diamines and dianhydrides and post-treated to imidize and in some cases cross-link the copolyamic acid. The membrane is useful as an uncoated membrane for ultrafiltration, microfiltration, and membrane contactor applications, or may be used as a support for a permselective coating to form a composite membrane useful in gas separations, reverse osmosis, nanofiltration, pervaporation, or vapor permeation.

  13. Thermal extraction of bamboo with various solvents

    OpenAIRE

    Kim, Junghee

    2010-01-01

    This thesis is to describe the potential of improvement by liquefaction with various solvents in pyrolysis in terms of conversion of bamboo to gas and liquid and quality of the bio-oils and residues produced. Fluidised sand bath and pressure gauge reactor were used for pyrolysis. The reactor was coupled with bamboo and a solvent and after 1 hour of pyrolysis and liquefaction at 410°C, the gas produced was collected in gas bag. To extract compounds uniformly from the chemically decomposed...

  14. Physical Access Control Database

    Data.gov (United States)

    Department of Transportation — This data set contains the personnel access card data (photo, name, activation/expiration dates, card number, and access level) as well as data about turnstiles and...

  15. Application of isothermal titration calorimetry for characterizing thermodynamic parameters of biomolecular interactions: peptide self-assembly and protein adsorption case studies.

    Science.gov (United States)

    Kabiri, Maryam; Unsworth, Larry D

    2014-10-13

    The complex nature of macromolecular interactions usually makes it very hard to identify the molecular-level mechanisms that ultimately dictate the result of these interactions. This is especially evident in the case of biological systems, where the complex interaction of molecules in various situations may be responsible for driving biomolecular interactions themselves but also has a broader effect at the cell and/or tissue level. This review will endeavor to further the understanding of biomolecular interactions utilizing the isothermal titration calorimetry (ITC) technique for thermodynamic characterization of two extremely important biomaterial systems, viz., peptide self-assembly and nonfouling polymer-modified surfaces. The advantages and shortcomings of this technique will be presented along with a thorough review of the recent application of ITC to these two areas. Furthermore, the controversies associated with the enthalpy-entropy compensation effect as well as thermodynamic equilibrium state for such interactions will be discussed.

  16. Access Customized Forms

    OpenAIRE

    Cosma Emil; Jeflea Victor

    2010-01-01

    By using Word, Excel or PowerPoint one can automate routine operations using the VBA language (Visual Basic for Applications). This language is also used in Access, allowing access to data stored in tables or queries. Thus, Access and VBA resources can be used together. Access is designed for programming forms and reports (among other things), so there won’t be found any of the VBA editor’s specific forms.

  17. 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

    The 1st Nano-IBCT Conference entitled 'Radiation Damage in Biomolecular Systems: Nanoscale Insights into Ion Beam Cancer Therapy' was held in Caen, France, in October 2011. The Meeting was organised in the framework of the COST Action MP1002 (Nano-IBCT) which was launched in December 2010 (http://fias.uni-frankfurt.de/nano-ibct). This action aims to promote the understanding of mechanisms and processes underlying the radiation damage of biomolecular systems at the molecular and nanoscopic level and to use the findings to improve the strategy of Ion Beam Cancer Therapy. In the hope of achieving this, participants from different disciplines were invited to represent the fields of physics, biology, medicine and chemistry, and also included those from industry and the operators of hadron therapy centres. Ion beam therapy offers the possibility of excellent dose localization for treatment of malignant tumours, minimizing radiation damage in normal healthy tissue, while maximizing cell killing within the tumour. Several ion beam cancer therapy clinical centres are now operating in Europe and elsewhere. However, the full potential of such therapy can only be exploited by better understanding the physical, chemical and biological mechanisms that lead to cell death under ion irradiation. Considering a range of spatio-temporal scales, the proposed action therefore aims to combine the unique experimental and theoretical expertise available within Europe to acquire greater insight at the nanoscopic and molecular level into radiation damage induced by ion impact. Success in this endeavour will be both an important scientific breakthrough and give great impetus to the practical improvement of this innovative therapeutic technique. Ion therapy potentially provides an important advance in cancer therapy and the COST action MP1002 will be very significant in ensuring Europe's leadership in this field, providing the scientific background, required data and mechanistic insight which

  18. Next Generation Solvent Performance in the Modular Caustic Side Solvent Extraction Process - 15495

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Tara E. [Savannah River Remediation, LLC., Aiken, SC (United States); Scherman, Carl [Savannah River Remediation, LLC., Aiken, SC (United States); Martin, David [Savannah River Remediation, LLC., Aiken, SC (United States); Suggs, Patricia [Savannah River Site (SRS), Aiken, SC (United States)

    2015-01-14

    Changes to the Modular Caustic Side Solvent Extraction Unit (MCU) flow-sheet were implemented in the facility. Implementation included changing the scrub and strip chemicals and concentrations, modifying the O/A ratios for the strip, scrub, and extraction contactor banks, and blending the current BoBCalixC6 extractant-based solvent in MCU with clean MaxCalix extractant-based solvent. During the successful demonstration period, the MCU process was subject to rigorous oversight to ensure hydraulic stability and chemical/radionuclide analysis of the key process tanks (caustic wash tank, solvent hold tank, strip effluent hold tank, and decontaminated salt solution hold tank) to evaluate solvent carryover to downstream facilities and the effectiveness of cesium removal from the liquid salt waste. Results indicated the extraction of cesium was significantly more effective with an average Decontamination Factor (DF) of 1,129 (range was 107 to 1,824) and that stripping was effective. The contactor hydraulic performance was stable and satisfactory, as indicated by contactor vibration, contactor rotational speed, and flow stability; all of which remained at or near target values. Furthermore, the Solvent Hold Tank (SHT) level and specific gravity was as expected, indicating that solvent integrity and organic hydraulic stability were maintained. The coalescer performances were in the range of processing results under the BOBCalixC6 flow sheet, indicating negligible adverse impact of NGS deployment. After the Demonstration period, MCU began processing via routine operations. Results to date reiterate the enhanced cesium extraction and stripping capability of the Next Generation Solvent (NGS) flow sheet. This paper presents process performance results of the NGS Demonstration and continued operations of MCU utilizing the blended BobCalixC6-MaxCalix solvent under the NGS flowsheet.

  19. Event Detection and Sub-state Discovery from Bio-molecular Simulations Using Higher-Order Statistics: Application To Enzyme Adenylate Kinase

    OpenAIRE

    Ramanathan, Arvind; Savol, Andrej J.; Agarwal, Pratul K.; Chennubhotla, Chakra S.

    2012-01-01

    Biomolecular simulations at milli-second and longer timescales can provide vital insights into functional mechanisms. Since post-simulation analyses of such large trajectory data-sets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are progressing. Recently, we have introduced a novel computational technique, quasi-anharmonic analysis (QAA)...

  20. Open Access Alternatives

    Science.gov (United States)

    Tenopir, Carol

    2004-01-01

    Open access publishing is a hot topic today. But open access publishing can have many different definitions, and pros and cons vary with the definitions. Open access publishing is especially attractive to companies and small colleges or universities that are likely to have many more readers than authors. A downside is that a membership fee sounds…

  1. Organic solvent nanofiltration: prospects and application

    International Nuclear Information System (INIS)

    The key lines of research in a new field of the membrane science and technology, viz., organic solvent nanofiltration, are considered. The prospects for its use in chemical, petrochemical and food industries are discussed. Attention is focused on membranes developed for this method.

  2. Organic solvent nanofiltration: prospects and application

    Energy Technology Data Exchange (ETDEWEB)

    Volkov, A V; Korneeva, G A; Tereshchenko, Gennadii F [A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow (Russian Federation)

    2008-11-30

    The key lines of research in a new field of the membrane science and technology, viz., organic solvent nanofiltration, are considered. The prospects for its use in chemical, petrochemical and food industries are discussed. Attention is focused on membranes developed for this method.

  3. Mixed Solvent Reactive Recrystallization of Sodium Carbonate

    NARCIS (Netherlands)

    Gaertner, R.S.

    2005-01-01

    Investigation of the reactive recrystallization of trona (sodium sesquicarbonate) and sodium bicarbonate to sodium carbonate (soda) in a mixed solvent led to the design of several alternative, less energy consumptive, economically very attractive process routes for the production of soda from all pr

  4. Ferrier reaction in a deep eutectic solvent.

    Science.gov (United States)

    Rokade, Sunil M; Bhate, Prakash M

    2015-10-13

    A mild and efficient synthesis of 2,3-unsaturated sugar derivatives has been achieved by conducting the Ferrier reaction in a deep eutectic solvent (DES). A wide range of alcohols including primary, secondary, benzylic, and sugar-derived primary alcohols can be used. Advantages include good yields, shorter reaction times and recyclability of DES. PMID:26279523

  5. Structure and Solvent Properties of Microemulsions

    Science.gov (United States)

    Katz, Civia A.; Calzola, Zachary J.; Mbindyo, Jeremiah K. N.

    2008-01-01

    A microscale laboratory experiment to investigate the formation and utility of microemulsions is described. Microemulsions are technologically important fluids that can reduce the use of toxic organic solvents. In the experiment, students prepare a microemulsion and compare the solubility of sudan III dye in the microemulsion and in dodecane. They…

  6. Solvent-Free Synthesis of Chalcones

    Science.gov (United States)

    Palleros, Daniel R.

    2004-01-01

    The synthesis of twenty different chalcones in the absence of solvent is presented. The results indicated that out of the twenty different chalcones investigated seventeen can be obtained in a matter of minutes by mixing the corresponding benzaldehyde and acetophenone in the presence of solid NaOH in a mortar with pestle.

  7. 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.

  8. 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)

    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

  9. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure

    Science.gov (United States)

    Prilusky, Jaime; Hodis, Eran; Sussman, Joel L.

    Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other structures. Proteopedia ( http://www.proteopedia.org ) presents 3D biomolecule structures in a broadly accessible manner to a diverse scientific audience through easy-to-use molecular visualization tools integrated into a wiki environment that anyone with a user account can edit. We describe recent advances in the web resource in the areas of content and software. In terms of content, we describe a large growth in user-added content as well as improvements in automatically-generated content for all PDB entry pages in the resource. In terms of software, we describe new features ranging from the capability to create pages hidden from public view to the capability to export pages for offline viewing. New software features also include an improved file-handling system and availability of biological assemblies of protein structures alongside their asymmetric units.

  10. AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis

    Directory of Open Access Journals (Sweden)

    Burger Gertraud

    2003-12-01

    Full Text Available Abstract Background Sequence data analyses such as gene identification, structure modeling or phylogenetic tree inference involve a variety of bioinformatics software tools. Due to the heterogeneity of bioinformatics tools in usage and data requirements, scientists spend much effort on technical issues including data format, storage and management of input and output, and memorization of numerous parameters and multi-step analysis procedures. Results In this paper, we present the design and implementation of AnaBench, an interactive, Web-based bioinformatics Analysis workBench allowing streamlined data analysis. Our philosophy was to minimize the technical effort not only for the scientist who uses this environment to analyze data, but also for the administrator who manages and maintains the workbench. With new bioinformatics tools published daily, AnaBench permits easy incorporation of additional tools. This flexibility is achieved by employing a three-tier distributed architecture and recent technologies including CORBA middleware, Java, JDBC, and JSP. A CORBA server permits transparent access to a workbench management database, which stores information about the users, their data, as well as the description of all bioinformatics applications that can be launched from the workbench. Conclusion AnaBench is an efficient and intuitive interactive bioinformatics environment, which offers scientists application-driven, data-driven and protocol-driven analysis approaches. The prototype of AnaBench, managed by a team at the Université de Montréal, is accessible on-line at: http://malawimonas.bcm.umontreal.ca:8091/anabench. Please contact the authors for details about setting up a local-network AnaBench site elsewhere.

  11. Pro Access 2010 Development

    CERN Document Server

    Collins, Mark

    2011-01-01

    Pro Access 2010 Development is a fundamental resource for developing business applications that take advantage of the features of Access 2010 and the many sources of data available to your business. In this book, you'll learn how to build database applications, create Web-based databases, develop macros and Visual Basic for Applications (VBA) tools for Access applications, integrate Access with SharePoint and other business systems, and much more. Using a practical, hands-on approach, this book will take you through all the facets of developing Access-based solutions, such as data modeling, co

  12. Access 2013 for dummies

    CERN Document Server

    Ulrich Fuller, Laurie

    2013-01-01

    The easy guide to Microsoft Access returns with updates on the latest version! Microsoft Access allows you to store, organize, view, analyze, and share data; the new Access 2013 release enables you to build even more powerful, custom database solutions that integrate with the web and enterprise data sources. Access 2013 For Dummies covers all the new features of the latest version of Accessand serves as an ideal reference, combining the latest Access features with the basics of building usable databases. You'll learn how to create an app from the Welcome screen, get support

  13. Android Access Control Extension

    Directory of Open Access Journals (Sweden)

    Anton Baláž

    2015-12-01

    Full Text Available The main objective of this work is to analyze and extend security model of mobile devices running on Android OS. Provided security extension is a Linux kernel security module that allows the system administrator to restrict program's capabilities with per-program profiles. Profiles can allow capabilities like network access, raw socket access, and the permission to read, write, or execute files on matching paths. Module supplements the traditional Android capability access control model by providing mandatory access control (MAC based on path. This extension increases security of access to system objects in a device and allows creating security sandboxes per application.

  14. Effect of solvent structure on election reactivity

    International Nuclear Information System (INIS)

    The reactivity of solvated electrons (es-) with efficient (nitrobenzene, acetone) and inefficient (phenol, toluene) scavengers is affected greatly by the solvent composition in 2-propanol/water mixed solvents. 2-Propanol is the only secondary alcohol that is completely miscible with water. The variation of the nitrobenzene rate constant k2 with solvent composition displays four viscosity zones, as in primary and tertiary alcohol/water mixtures. In zone (c), where the Stokes-Smoluchowski equation applies, the nitrobenzene k2 values in the secondary alcohol/water mixtures are situated between those in the primary and tertiary alcohols, due to the relative values of the dielectric permittivity ε. The charge-dipole attraction energy varies at ε-1. The two water-rich zones (c) and (d) are characterized by a large change of viscosity η and a small change in es- solvation energy (trap depth) Er; here k2 for all the scavengers correlates with the inverse of the viscosity. In the two alcohol-rich zones (a) and (b) the change of η is small but that of Er is large; here k2 of inefficient scavengers correlates with the inverse of Er, due to the difficulty of electron transfer out of deeper traps. Activation energies E2 and entropies ΔS2(double dagger) also show composition zone behaviour. The value of ΔS2(double dagger) is more negative for less efficient scavengers; E2 varies less and does not correlate with reactivity of Er. Electron transfer from solvent to inefficient scavenger is driven by solvent rearrangement around the reaction center, reflected in ΔS2(double dagger)

  15. Solvent density mode instability in non-polar solutions

    Indian Academy of Sciences (India)

    Susmita Kar; Ranjit Biswas; J Chakrabarti

    2008-08-01

    We analyse the origin of the multiple long time scales associated with the long time decay observed in non-polar solvation dynamics by linear stability analysis of solvent density modes where the effects of compressibility and solvent structure are systematically incorporated. The coupling of the solute–solvent interactions at both ground and excited states of the solute with the compressibility and solvent structure is found to have important effects on the time scales. The present theory suggests that the relatively longer time constant is controlled by the solvent compressibility, while the solvent structure at the nearest-neighbour length scale dominates the shorter time constant.

  16. Urban Railway Accessibility

    Institute of Scientific and Technical Information of China (English)

    GUAN Hongzhi; YIN Yuanfei; YAN Hai; HAN Yan; QIN Huanmei

    2007-01-01

    Effective use of urban rapid railway systems requires that the railway systems be effectively connected with other transportation modes so that they are accessible. This paper uses the logit model and data to analyze the factors influencing railway access choices in a railway choice access model. The results indicate that access time, access cost, and access distance are factors significantly affecting railway access choices. The user's income significantly affects the probability of choosing to walk rather than to take a taxi,but is not related to choosing buses or bicycles. Vehicle ownership significantly affects the probability of choosing a taxi, but is not significantly related to the other modes. The conclusions provide an analysis tool for urban railway planning and construction.

  17. Open Access @ DTU

    DEFF Research Database (Denmark)

    Ekstrøm, Jeannette

    Open Access is high on the agenda in Denmark and internationally. Denmark has announced a national strategy for Open Access that aims to achieve Open Access to 80% in 2017 and 100% in 2022 to peer review research articles. All public Danish funders as well as H2020 requires that all peer review...... articles that is an outcome of their funding will be Open Access. Uploading your full texts (your final author manuscript after review ) to DTU Orbit is a fundamental part of providing Open Access to your research. We are here to answer all your questions with regards to Open Access and related topics...... such as copyright, DTU Orbit, Open Access journals, APCs, Vouchers etc....

  18. pH and solvent H/D isotope effects on the thermodynamics and kinetics of electron transfer for electrode-immobilized native and urea-unfolded stellacyanin.

    Science.gov (United States)

    Ranieri, Antonio; Battistuzzi, Gianantonio; Borsari, Marco; Bortolotti, Carlo Augusto; Di Rocco, Giulia; Sola, Marco

    2012-10-23

    The thermodynamics of Cu(II) to Cu(I) reduction and the kinetics of the electron transfer (ET) process for Rhus vernicifera stellacyanin (STC) immobilized on a decane-1-thiol coated gold electrode have been measured through cyclic voltammetry at varying pH and temperature, in the presence of urea and in D(2)O. Immobilized STC undergoes a limited conformational change that mainly results in an enhanced exposure of one or both copper binding histidines to solvent which slightly stabilizes the cupric state and increases histidine basicity. The large immobilization-induced increase in the pK(a) for the acid transition (from 4.5 to 6.3) makes this electrode-SAM-protein construct an attractive candidate as a biomolecular ET switch operating near neutral pH in molecular electronics. Such a potential interest is increased by the robustness of this interface against chemical unfolding as it undergoes only moderate changes in the reduction thermodynamics and in the ET rate in the presence of up to 8 M urea. The sensitivity of these parameters to solvent H/D isotope effects testifies to the role of protein solvation as effector of the thermodynamics and kinetics of ET.

  19. Solvent/Non-Solvent Sintering: A Novel Route to Create Porous Microsphere Scaffolds For Tissue Regeneration

    OpenAIRE

    Justin L Brown; Nair, Lakshmi S.; Laurencin, Cato T.

    2008-01-01

    Solvent/non-solvent sintering creates porous polymeric microsphere scaffolds suitable for tissue engineering purposes with control over the resulting porosity, average pore diameter and mechanical properties. Five different biodegradable biocompatible polyphosphazenes exhibiting glass transition temperatures from −8°C to 41oC and poly(lactide-co-glycolide), (PLAGA) a degradable polymer used in a number of biomedical settings, were examined to study the versatility of the process and benchmark...

  20. Environmental Light and Its Relationship with Electromagnetic Resonances of Biomolecular Interactions, as Predicted by the Resonant Recognition Model

    Science.gov (United States)

    Cosic, Irena; Cosic, Drasko; Lazar, Katarina

    2016-01-01

    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. PMID:27367714

  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. Environmental Light and Its Relationship with Electromagnetic Resonances of Biomolecular Interactions, as Predicted by the Resonant Recognition Model.

    Science.gov (United States)

    Cosic, Irena; Cosic, Drasko; Lazar, Katarina

    2016-01-01

    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. PMID:27367714

  3. Tailored surface-enhanced Raman nanopillar arrays fabricated by laser-assisted replication for biomolecular detection using organic semiconductor lasers.

    Science.gov (United States)

    Liu, Xin; Lebedkin, Sergei; Besser, Heino; Pfleging, Wilhelm; Prinz, Stephan; Wissmann, Markus; Schwab, Patrick M; Nazarenko, Irina; Guttmann, Markus; Kappes, Manfred M; Lemmer, Uli

    2015-01-27

    Organic semiconductor distributed feedback (DFB) lasers are of interest as external or chip-integrated excitation sources in the visible spectral range for miniaturized Raman-on-chip biomolecular detection systems. However, the inherently limited excitation power of such lasers as well as oftentimes low analyte concentrations requires efficient Raman detection schemes. We present an approach using surface-enhanced Raman scattering (SERS) substrates, which has the potential to significantly improve the sensitivity of on-chip Raman detection systems. Instead of lithographically fabricated Au/Ag-coated periodic nanostructures on Si/SiO2 wafers, which can provide large SERS enhancements but are expensive and time-consuming to fabricate, we use low-cost and large-area SERS substrates made via laser-assisted nanoreplication. These substrates comprise gold-coated cyclic olefin copolymer (COC) nanopillar arrays, which show an estimated SERS enhancement factor of up to ∼ 10(7). The effect of the nanopillar diameter (60-260 nm) and interpillar spacing (10-190 nm) on the local electromagnetic field enhancement is studied by finite-difference-time-domain (FDTD) modeling. The favorable SERS detection capability of this setup is verified by using rhodamine 6G and adenosine as analytes and an organic semiconductor DFB laser with an emission wavelength of 631.4 nm as the external fiber-coupled excitation source.

  4. Solvent mimicry with methylene carbene to probe protein topography.

    Science.gov (United States)

    Gómez, Gabriela Elena; Monti, José Luis E; Mundo, Mariana Rocío; Delfino, José María

    2015-10-01

    The solvent accessible surface area (SASA) of the polypeptide chain plays a key role in protein folding, conformational change, and interaction. This fundamental biophysical parameter is elusive in experimental measurement. Our approach to this problem relies on the reaction of the minimal photochemical reagent diazirine (DZN) with polypeptides. This reagent (i) exerts solvent mimicry because its size is comparable to water and (ii) shows scant chemical selectivity because it generates extremely reactive methylene carbene. Methylation gives rise to the EM (extent of modification) signal, which is useful for scrutinizing the conformational change triggered by Ca(2+) binding to calmodulin (CaM). The increased EM observed for the full protein is dominated by the enhanced exposure of hydrophobic area in Ca(2+)-CaM. Fragmentation allowed us to quantify the methylene incorporation at specific sites. Peptide 91-106 reveals a major reorganization around the calcium 151 binding site, resulting in local ordering and a greater exposure of the hydrophobic surface. Additionally, this technique shows a high sensitivity to probe recognition between CaM and melittin (Mel). The large decrease in EM indicates the occlusion of a significant hydrophobic area upon complexation. Protection from labeling reveals a larger involvement of the N-terminal and central regions of CaM in this interaction. Despite its smaller size, Mel's differential exposure can also be quantified. Moreover, MS/MS fragmentation realizes the goal of extending the resolution of labeled sites at the amino acid level. Overall, DZN labeling emerges as a useful footprinting method capable of shedding light on physiological conformational changes and interactions. PMID:26348271

  5. Access Governance for Biobanks: The Case of the BioSHaRE-EU Cohorts.

    Science.gov (United States)

    Kaye, Jane; Briceño Moraia, Linda; Mitchell, Colin; Bell, Jessica; Bovenberg, Jasper Adriaan; Tassé, Anne-Marie; Knoppers, Bartha Maria

    2016-06-01

    Currently, researchers have to apply separately to individual biobanks if they want to carry out studies that use samples and data from multiple biobanks. This article analyzes the access governance arrangements of the original five biobank members of the Biobank Standardisation and Harmonisation for Research Excellence in the European Union (BioSHaRE-EU) project in Finland, Germany, the Netherlands, Norway, and the United Kingdom to identify similarities and differences in policies and procedures, and consider the potential for internal policy "harmonization." Our analysis found differences in the range of researchers and organizations eligible to access biobanks; application processes; requirements for Research Ethics Committee approval; and terms of Material Transfer Agreements relating to ownership and commercialization. However, the main elements of access are the same across biobanks; access will be granted to bona fide researchers conducting research in the public interest, and all biobanks will consider the scientific merit of the proposed use and it's compatibility with the biobank's objectives. These findings suggest potential areas for harmonization across biobanks. This could be achieved through a single centralized application to a number of biobanks or a system of mutual recognition that places a presumption in favor of access to one biobank if already approved by another member of the same consortium. Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortia (BBMRI-ERIC), a European consortium of biobanks and bioresources with its own ethical, legal, and social implications (ELSI) common service, could provide a platform by developing guidelines for harmonized internal processes.

  6. Evaluation of binary solvent mixtures for efficient monoacylglycerol production by continuous enzymatic glycerolysis.

    Science.gov (United States)

    Damstrup, Marianne L; Abildskov, Jens; Kiil, Søren; Jensen, Anker D; Sparsø, Flemming V; Xu, Xuebing

    2006-09-20

    This study was aimed at evaluating different binary solvent mixtures for efficient industrial monoacylglycerol (MAG) production by enzymatic glycerolysis. Of all investigated cases, the binary mixture of tert-butanol:tert-pentanol (TB:TP) 80:20 vol % was the most suitable organic medium for continuous enzymatic glycerolysis, ensuring high MAG formation in a short time, reasonable solvent price, and easy handling during distillation/condensation processing. A minimum solvent dosage of 44-54 wt % of the reaction mixture was necessary to achieve high MAG yields of 47-56 wt %, within 20 min. The melting and boiling points of the TB:TP mixture were estimated to be 7 and 85 degrees C, respectively, using thermodynamic models. These predictions were in good agreement with experimentally determined values. In spite of the high reaction efficiency in the binary TB:TP system, the mixture of glycerol and sunflower oil (containing 97.1% triacylglycerol) yielded surprisingly a liquid/liquid phase split behavior even at high temperatures (>80 degrees C). This in contrast to thermodynamic model calculations suggested full miscibility in all proportions. These findings suggest that enhanced reaction efficiency in organic solvent also depends upon aspects other than the system homogeneity such as reduced viscosity, reduced mass transfer limitations, and the accessibility of the substrate to the active site of the enzyme. PMID:16968070

  7. [Cloning and expression of organic solvent tolerant lipase gene from Staphylococcus saprophyticus M36].

    Science.gov (United States)

    Tang, Yanchong; Lu, Yaping; Lü, Fengxia; Bie, Xiaomei; Guo, Yao; Lu, Zhaoxin

    2009-12-01

    Lipases are important biocatalysts that are widely used in food processing and bio-diesel production. However, organic solvents could inactivate some lipases during applications. Therefore, the efficient cloning and expression of the organic solvent-tolerant lipase is important to its application. In this work, we first found out an organic solvent-tolerant lipase from Staphylococcus saprophyticus M36 and amplified the 741 bp Lipase gene lip3 (GenBank Accession No. FJ979867), by PCR, which encoded a 31.6 kD polypeptide of 247 amino acid residues. But the lipase shared 83% identity with tentative lip3 gene of Staphylococcus saprophyticus (GenBank Accession No. AP008934). We connected the gene with expression vector pET-DsbA, transformed it into Escherichia coli BL21 (DE3), and obtained the recombinant pET-DsbA-lip3. With the induction by 0.4 mmol/L of isopropyl beta-D-thiogalactopyranoside at pH 8.0, OD600 1.0, 25 degrees C for 12 h, the lipase activity reached up to 25.8 U/mL. The lipase expressed was stable in the presence of methanol, n-hexane, and isooctane, n-heptane.

  8. Selection and evaluation of alternative solvents for caprolactam extraction

    NARCIS (Netherlands)

    Delden, van Mathijs L.; Kuipers, Norbert J.M.; Haan, de André B.

    2006-01-01

    Because of the strict legislation for currently applied solvents in the industrial extraction of caprolactam, being benzene, toluene and chlorinated hydrocarbons, a need exists for alternative, environmentally benign solvents. An experimental screening procedure consisting of several steps was used

  9. Method for Predicting Solubilities of Solids in Mixed Solvents

    DEFF Research Database (Denmark)

    Ellegaard, Martin Dela; Abildskov, Jens; O'Connell, J. P.

    2009-01-01

    A method is presented for predicting solubilities of solid solutes in mixed solvents, based on excess Henry's law constants. The basis is statistical mechanical fluctuation solution theory for composition derivatives of solute/solvent infinite dilution activity coefficients. Suitable approximations...

  10. Organic Solvent Tropical Report [SEC 1 and 2

    Energy Technology Data Exchange (ETDEWEB)

    COWLEY, W.L.

    2000-06-21

    This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an unmitigated organic solvent fire is within risk evaluation guidelines.

  11. Effect of solvents on propylene epoxidation over TS-1 catalyst

    Institute of Scientific and Technical Information of China (English)

    Yulong WU; Qingshan LIU; Xueli SU; Zhentao MI

    2008-01-01

    Solvents have an important effect on the epoxidation of propylene catalyzed by TS-1. The experimental results show that, in different solvents, the catalytic activity of epoxidation is in the following order: methanol > 2-propanol > 2-butanol > acetoni-trile > acetone > tetrahydrofuran. Based on the reaction mechanism, the effects of solvents on the epoxidation were studied from eight aspects, which included the electronic effect, the steric effect, the polarity of solvent, the effect of solvent on sorption and diffusion of reactant, the oxidation of alcohol, the etherification of PO, the deactivation of TS-1 and the solubility of propylene in the solvents. The electronic effect, steric effect and the polarity of solvent were considered to be the main aspects. This work may provide theoretical guidance for choosing solvents for these kinds of reactions and also may serve as basis for further industrialization.

  12. Occupational exposure to chlorinated and petroleum solvents and mycosis fungoides

    DEFF Research Database (Denmark)

    Morales-Suárez-Varela, Maria M; Olsen, Jørn; Villeneuve, Sara;

    2013-01-01

    To evaluate the potential association between occupational exposure to chlorinated and petroleum solvents and mycosis fungoides (MF).......To evaluate the potential association between occupational exposure to chlorinated and petroleum solvents and mycosis fungoides (MF)....

  13. A solvent/non-solvent system for achieving solution-processed multilayer organic light-emitting devices

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Yue; Wu, Zhaoxin, E-mail: zhaoxinwu@mail.xjtu.edu.cn; He, Lin; Jiao, Bo; Hou, Xun

    2015-08-31

    We developed a solvent/non-solvent system to fabricate the multilayer organic light-emitting devices (OLEDs) based on poly(N-vinylcarbazole) (PVK) by solution-process. This solvent system consists of both the solvent and non-solvent of PVK, in which fluorescent small molecules could be fully dissolved and directly spin-coated on top of the PVK layer; it could effectively avoid the redissolution of PVK during the spin-coating process of small molecules emitting layer. In the further investigation of this system, we also demonstrated the three-component solvent system, and found out that the third component, a less volatile solvent of PVK, was crucial for preparing a smoother interface between PVK and emitting layer. Compared with OLEDs through the vacuum deposition, the devices fabricated by solution-process from the solvent/non-solvent system showed comparable efficiency, which indicate that the solvent/non-solvent system can be used as an alternative process to prepare the polymer and small molecule multilayer devices through all-solution-process. - Highlights: • We fabricate the multilayer OLEDs by solution-process using a novel system. • We develop a solvent/non-solvent system of polymer (PVK) to avoid redissolution. • Small molecules could be fully dissolved and directly spin-coated on PVK layer. • The devices fabricated by the system and vacuum deposition show comparable efficiency.

  14. A solvent/non-solvent system for achieving solution-processed multilayer organic light-emitting devices

    International Nuclear Information System (INIS)

    We developed a solvent/non-solvent system to fabricate the multilayer organic light-emitting devices (OLEDs) based on poly(N-vinylcarbazole) (PVK) by solution-process. This solvent system consists of both the solvent and non-solvent of PVK, in which fluorescent small molecules could be fully dissolved and directly spin-coated on top of the PVK layer; it could effectively avoid the redissolution of PVK during the spin-coating process of small molecules emitting layer. In the further investigation of this system, we also demonstrated the three-component solvent system, and found out that the third component, a less volatile solvent of PVK, was crucial for preparing a smoother interface between PVK and emitting layer. Compared with OLEDs through the vacuum deposition, the devices fabricated by solution-process from the solvent/non-solvent system showed comparable efficiency, which indicate that the solvent/non-solvent system can be used as an alternative process to prepare the polymer and small molecule multilayer devices through all-solution-process. - Highlights: • We fabricate the multilayer OLEDs by solution-process using a novel system. • We develop a solvent/non-solvent system of polymer (PVK) to avoid redissolution. • Small molecules could be fully dissolved and directly spin-coated on PVK layer. • The devices fabricated by the system and vacuum deposition show comparable efficiency

  15. Migrants' access to healthcare

    DEFF Research Database (Denmark)

    Norredam, Marie

    2011-01-01

    There are strong pragmatic and moral reasons for receiving societies to address access to healthcare for migrants. Receiving societies have a pragmatic interest in sustaining migrants' health to facilitate integration; they also have a moral obligation to ensure migrants' access to healthcare...... according to international human rights principles. The intention of this thesis is to increase the understanding of migrants' access to healthcare by exploring two study aims: 1) Are there differences in migrants' access to healthcare compared to that of non-migrants? (substudy I and II); and 2) Why...... are there possible differences in migrants' access to healthcare compared to that of non-migrants? (substudy III and IV). The thesis builds on different methodological approaches using both register-based retrospective cohort design, cross-sectional design and survey methods. Two different measures of access were...

  16. Re-Refining of Waste Lubricating Oil by Solvent Extraction

    OpenAIRE

    Hassan Ali Durrani; Muhammed Ibrahim Panhwar; Rafique Akthar Kazi

    2011-01-01

    Re-refining of waste lubricating oil by solvent extraction is one of the potential techniques. The advantages of solvent extraction technique practically offers from environmental and economic points of view have received due attention. In this paper selection of composite solvent and technique to upgrade the used lubricant oil into base oil has been made. The composite solvent 2-propanol, 1-butanol and butanone have two alcohols that make a binary system reasonably effective. ...

  17. Method for Predicting Solubilities of Solids in Mixed Solvents

    OpenAIRE

    Ellegaard, Martin Dela; Abildskov, Jens; O'Connell, J P

    2009-01-01

    A method is presented for predicting solubilities of solid solutes in mixed solvents, based on excess Henry's law constants. The basis is statistical mechanical fluctuation solution theory for composition derivatives of solute/solvent infinite dilution activity coefficients. Suitable approximations are made for a single parameter characterizing solute/solvent interactions. Comparisons with available data show that the method is successful in describing a variety of observed mixed solvent solu...

  18. Alternative solvents for post combustion carbon capture

    Directory of Open Access Journals (Sweden)

    Udara S. P. R. Arachchige, Morten C. Melaaen

    2013-01-01

    Full Text Available The process model of post combustion chemical absorption is developed in Aspen Plus for both coal and gas fired power plant flue gas treating. The re-boiler energy requirement is considered as the most important factor to be optimized. Two types of solvents, mono-ethylamine (MEA and di-ethylamine (DEA, are used to implement the model for three different efficiencies. The re-boiler energy requirement for regeneration process is calculated. Temperature and concentration profiles in absorption column are analyzed to understand the model behavior. Re-boiler energy requirement is considerably lower for DEA than MEA as well as impact of corrosion also less in DEA. Therefore, DEA can be recommended as a better solvent for post combustion process for carbon capture plants in fossil fuel fired power industries.

  19. Alternative solvents for post combustion carbon capture

    Energy Technology Data Exchange (ETDEWEB)

    Arachchige, Udara S.P.R. [Telemark University College, Porsgrunn (Norway); Melaaen, Morten C. [Telemark University College, Porsgrunn (Norway); Tel-Tek, Porsgrunn (Norway)

    2013-07-01

    The process model of post combustion chemical absorption is developed in Aspen Plus for both coal and gas fired power plant flue gas treating. The re-boiler energy requirement is considered as the most important factor to be optimized. Two types of solvents, mono-ethylamine (MEA) and di-ethylamine (DEA), are used to implement the model for three different efficiencies. The re-boiler energy requirement for regeneration process is calculated. Temperature and concentration profiles in absorption column are analyzed to understand the model behavior. Re-boiler energy requirement is considerably lower for DEA than MEA as well as impact of corrosion also less in DEA. Therefore, DEA can be recommended as a better solvent for post combustion process for carbon capture plants in fossil fuel fired power industries.

  20. Critical bubble radius in solvent sublation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The complex compound of dithizone-Co(Ⅱ) was separated and concentrated from the aqueous phase to n-octanol by solvent sublation. From the analysis of the coalescence behavior of bubbles on water-organic interface, the conception of critical bubble radius was proposed, and the value of the critical bubble radius in the water-octanol system was obtained: 1.196 × 10-3 m. The simulation of the mathematical model using CBR and experimental data is completed with perfect results, and the simulation of the mathematical model using CBR is very different with the classic one. The analytical results proved that the critical bubble radius should be adequately considered in mathematical model of solvent sublation.

  1. Gamma Ray Radiolysis of the FPEX Solvent

    Energy Technology Data Exchange (ETDEWEB)

    B. J. Mincher; S. P. Mezyk; D. R. Peterman

    2006-09-01

    Slide presentation. FPEX contains a calixarene for Cs extraction, a crown ether for Sr extraction, Cs7SB modifier, and TOA to aid in stripping, in Isopar L diluent. The radiation stability FPEX must be evaluated prior to process use. Radiolytic degradation of species in solution are due to reaction with the direct radiolysis products of the diluent. In Isopar L, the reactive species produced include e-, •H and alkane radicals, resulting in a reducing environment. However, in nitric acid, oxidizing hydroxyl (•OH) and nitro (•NO2) radicals dominate system chemistry. Thus, the nature of diluent and the presence of radical scavengers affect the results of irradiation. We report the preliminary results of a new program to investigate the radiolysis of FPEX using the 60Co irradiation of FPEX neat solvent, acid pre-equilibrated solvent and mixed aerated phases. The Cs and Sr distribution ratios were used as metrics.

  2. Structuring of polymer solutions upon solvent evaporation

    Science.gov (United States)

    Schaefer, C.; van der Schoot, P.; Michels, J. J.

    2015-02-01

    The morphology of solution-cast, phase-separated polymers becomes finer with increasing solvent evaporation rate. We address this observation theoretically for a model polymer where demixing is induced by steady solvent evaporation. In contrast to what is the case for a classical, thermal quench involving immiscible blends, the spinodal instability initially develops slowly and the associated length scale is not time invariant but decreases with time as t-1 /2. After a time lag, phase separation accelerates. Time lag and characteristic length exhibit power-law behavior as a function of the evaporation rate with exponents of -2 /3 and -1 /6 . Interestingly, at later stages the spinodal structure disappears completely while a second length scale develops. The associated structure coarsens but does not follow the usual Lifshitz-Slyozov-Wagner kinetics.

  3. GREENER REACTIONS UNDER SOLVENT FREE CONDITIONS

    Directory of Open Access Journals (Sweden)

    Hiren M. Marvaniya

    2011-06-01

    Full Text Available The toxicity and volatile nature of many organic solvents, particularly chlorinated hydrocarbons that are widely used in huge amounts for organic reactions have posed a serious threat to the environment. Thus, design of solventless catalytic reaction has received tremendous attention in recent times in the area of green synthesis. A solvent-free or solid state reaction may be carried out using the reactants alone or incorporating them in clays, zeolites, silica, alumina or other matrices to achieve high degree of stereoselectivity in the products, to reduce byproducts, to maximize rate of reaction. We illustrate the environmentally benign approach to 1,2-Oxazine-2- oxides, Michael addition, Wohl–Ziegler reaction, Acylation, Heck reaction, Tishchenko reaction, Diels– Alder reaction, Reformatsky and Luche Reaction, Oxidative coupling Reaction, Synthesis of chalcones, Synthesis of Dihydropyrimidinones

  4. Simulation of annealed polyelectrolytes in poor solvents

    International Nuclear Information System (INIS)

    We present (semi-)grand canonical Monte Carlo simulations on annealed polyelectrolytes in poor solvent. Increasing the chemical potential of the charges, which is equal to the pH of the solution except for a trivial additive constant, in rather poor solvents, we find the first-order phase transition between a weakly charged globule and a highly charged extended chain predicted by theory. In the close-to-Q -point regime, we investigate under which conditions pearl-necklace structures are stable. Most of the pearl-necklace parameters are found to obey the scaling relations predicted for quenched polyelectrolytes. However, similarly to the behavior known for this class of polyelectrolytes we obtain large fluctuations in pearl number and size. In agreement with theoretical predictions we find a non-uniform charge distribution between pearls and strings

  5. Effect of water droplet in solvent sublation

    Institute of Scientific and Technical Information of China (English)

    Peng Yu Bi; Hui Ru Dong; Nan Nan Wang

    2008-01-01

    Aqueous phase layer around bubble and water droplet are two additional processes in solvent sublation. In the dynamic processof mass transfer, they are always neglected, but they are very important in the investigation of thermodynamic equilibrium. In thispaper, the effect of water droplet in solvent sublation was discussed in detail, and the previous mathematical model of solventsubaltion was improved. Matlab 6.5 was used to simulate the process of water droplets, and the comparison between the previoushypothesis and the improvement in this paper showed the superiority, especially in the investigation of thermodynamic equilibrium.Moreover, the separation and concentration of the complex compound dithizone-Co(Ⅱ) from aqueous phase to n-octanol by solventsublation also proved the improved mathematical model was reasonable.2008 Hui Ru Dong. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.

  6. Functionalization of graphene using deep eutectic solvents

    Science.gov (United States)

    Hayyan, Maan; Abo-Hamad, Ali; AlSaadi, Mohammed AbdulHakim; Hashim, Mohd Ali

    2015-08-01

    Deep eutectic solvents (DESs) have received attention in various applications because of their distinctive properties. In this work, DESs were used as functionalizing agents for graphene due to their potential to introduce new functional groups and cause other surface modifications. Eighteen different types of ammonium- and phosphonium-salt-based DESs were prepared and characterized by FTIR. The graphene was characterized by FTIR, STA, Raman spectroscopy, XRD, SEM, and TEM. Additional experiments were performed to study the dispersion behavior of the functionalized graphene in different solvents. The DESs exhibited both reduction and functionalization effects on DES-treated graphene. Dispersion stability was investigated and then characterized by UV-vis spectroscopy and zeta potential. DES-modified graphene can be used in many applications, such as drug delivery, wastewater treatment, catalysts, composite materials, nanofluids, and biosensors. To the best of our knowledge, this is the first investigation on the use of DESs for graphene functionalization.

  7. Myoglobin solvent structure at different temperatures

    Energy Technology Data Exchange (ETDEWEB)

    Daniels, B.V.; Korszun, Z.R. [Brookhaven National Laboratory, Upton, NY (United States); Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)

    1994-12-31

    The structure of the solvent surrounding myoglobin crystals has been analyzed using neutron diffraction data, and the results indicate that the water around the protein is not disordered, but rather lies in well-defined hydration shells. We have analyzed the structure of the solvent surrounding the protein by collecting neutron diffraction data at four different temperatures, namely, 80, 130, 180, and 240K. Relative Wilson Statistics applied to low resolution data showed evidence of a phase transition in the region of 180K. A plot of the liquidity factor, B{sub sn}, versus distance from the protein surface begins with a high plateau near the surface of the protein and drops to two minima at distances from the protein surface of about 2.35{Angstrom} and 3.85{Angstrom}. Two distinct hydration shells are observed. Both hydration shells are observed to expand as the temperature is increased.

  8. Access Data Analysis Cookbook

    CERN Document Server

    Bluttman, Ken

    2008-01-01

    This book offers practical recipes to solve a variety of common problems that users have with extracting Access data and performing calculations on it. Whether you use Access 2007 or an earlier version, this book will teach you new methods to query data, different ways to move data in and out of Access, how to calculate answers to financial and investment issues, how to jump beyond SQL by manipulating data with VBA, and more.

  9. Usability and accessibility curricula

    OpenAIRE

    Luján Mora, Sergio; Cachero Castro, Cristina

    2012-01-01

    Presentation of existing curricula connected with usability and accessibility at the University of Alicante for the Leonardo da Vinci project "GUI Usability and Accessibility: Exchanging Knowledge and Experiences" (Grenoble, France, 27 November 2012). Presentación del currículo actual relacionado con la usabilidad y la accesibilidad en la Universidad de Alicante para el proyecto Leonardo da Vinci "GUI Usability and Accessibility: Exchanging Knowledge and Experiences" (Grenoble, Francia, 27...

  10. Solvent-resistant elastomeric microfluidic devices and applications

    Science.gov (United States)

    van Dam, Robert Michael

    Microfluidics is increasingly being used in many areas of biotechnology and chemistry to achieve reduced reagent volumes, improved performance, integration, and parallelism, among other advantages. Though early devices were based on rigid materials such as glass and silicon, elastomeric materials such as polydiznethylsiloxane (PDMS) are rapidly emerging as a ubiquitous platform for applications in biotechnology. This is due, in part, to simpler fabrication procedures and to the ability to integrate mechanical microvalves at vastly greater densities. For many applications in the areas of chemical synthesis and analysis, however, PDMS cannot replace glass and silicon due to its incompatibility with many solvents and reagents. Such areas could benefit tremendously from the development of an elastomeric microfluidic device technology that combines the advantages of PDMS with the property of solvent resistance. Simplified fabrication could increase the accessibility of microfluidics, and the possibility of dense valve integration could lead to significant advances in device sophistication. Applications could be more rapidly developed by design re-use due to the independence of mechanical valves on fluid properties (unlike electrokinetic pumping), and the property of permeability could enable novel fluidic functions for accessing a broader range of reactions than is possible in glass and silicon. The first half of this thesis describes our strategies and efforts to develop this new enabling technology. Several approaches are presented in Chapter 3, and two particularly successful ones, based on new elastomers (FNB and PFPE), are described in Chapters 4 and 5. Chapter 6 describes a novel method of fabricating devices from 3D molds that could expand the range of useful clastomers. The second half of this thesis discusses microfluidic combinatorial synthesis and high throughput screening-applications that take particular advantage of the ability to integrate thousands of

  11. Indentation of polydimethylsiloxane submerged in organic solvents

    OpenAIRE

    Hu, Yuhang; Chen, Xin; Whitesides, George McClelland; Vlassak, Joost J.; Suo, Zhigang

    2011-01-01

    This work uses a method based on indentation to characterize a polydimethylsiloxane (PDMS) elastomer submerged in an organic solvent (decane, heptane, pentane, or cyclohexane). An indenter is pressed into a disk of a swollen elastomer to a fixed depth, and the force on the indenter is recorded as a function of time. By examining how the relaxation time scales with the radius of contact, one can differentiate the poroelastic behavior from the viscoelastic behavior. By matching the relaxation c...

  12. Solvent extraction of Southern US tar sands

    Energy Technology Data Exchange (ETDEWEB)

    Penney, W.R.

    1990-01-01

    The Department of Chemical Engineering at the University of Arkansas, in association with Diversified Petroleum Recovery, Inc. (DPR) of Little Rock, Arkansas, has been developing a solvent extraction process for the recovery of bitumen from tar sands for the past five years. The unique feature of the process is that the bitumen is recovered from the solvent by contacting with a co-solvent, which causes the bitumen to precipitate. The overall purpose of this project is to study both the technical and economic feasibility of applying this technology for recovery of bitumen from tar sands by (1) investigating the socioeconmic factors which affect (a) plant siting and (b) the market value of recovered bitumen; (2) operating a process demonstration unit at the rate of 1 lb/hr recovered bitumen while producing clean sand and recyclable solvents; and (3) determine the economic conditions which will make a bitumen recovery project economical. DPR has analyzed the historical trends of domestic production, consumption, discoveries and reserves of crude oil. They have started an investigation of the volatility in the price of crude oil and of gasoline prices and of the differential between gasoline and crude oil. DPR continues to analyze the geographical movement and demand for asphalt products. Utah does not appear economically attractive as a site for a bitumen from tar sands asphalt plant. Oklahoma sites are now being studied. This report also contains the quarterly progress report from a University of Nevada study to determine bitumen composition, oxygen uptake rates, and viscosities of Alabama and Utah bitumens. Both reports have been indexed separately for inclusion on the data base.

  13. Solvent enhanced bioremediation of weathered oil contamination

    International Nuclear Information System (INIS)

    This paper describes a novel bioremediation process for the treatment of oil spills on land. The method was developed specifically to deal with long term oil contamination where the volatile fractions have evaporated leaving the more recalcitrant fractions. A model system of sand and Kuwaiti crude oil was used to test the system. A combined treatment which introduced an additional solvent component was found to enhance mobility and availability of oil, enhancing bioremediation. (author)

  14. Mycosis fungoides progression and chronic solvent exposure

    OpenAIRE

    Nikkels, Arjen; Quatresooz, Pascale; Delvenne, Philippe; Balsat, A.; Pierard, Gérald

    2004-01-01

    The effect of repeated exposure to specific chemicals on the initiation or progression of mycosis fungoides (MF) remains unsettled. A patient with low-grade patch stage MF progressively developed MF plaques restricted to his arms, and a tumour on his right thigh. These areas were subject to repeated exposure to solvents. His thigh was indeed in close contact with his trousers pocket where he used to store a wiping rag drenched into white spirit and cellulosic thinner. Immunophenotyping these ...

  15. Mixed Solvent Reactive Recrystallization of Sodium Carbonate

    OpenAIRE

    Gaertner, R.S.

    2005-01-01

    Investigation of the reactive recrystallization of trona (sodium sesquicarbonate) and sodium bicarbonate to sodium carbonate (soda) in a mixed solvent led to the design of several alternative, less energy consumptive, economically very attractive process routes for the production of soda from all principal sodium carbonate sources. The kinetics of the recrystallization as well as of the superimposed chemical reaction, the decomposition of the bicarbonate ion, have been measured, a thermodynam...

  16. Functionalization of graphene using deep eutectic solvents

    OpenAIRE

    Hayyan, Maan; Abo-Hamad, Ali; AlSaadi, Mohammed AbdulHakim; Hashim, Mohd Ali

    2015-01-01

    Deep eutectic solvents (DESs) have received attention in various applications because of their distinctive properties. In this work, DESs were used as functionalizing agents for graphene due to their potential to introduce new functional groups and cause other surface modifications. Eighteen different types of ammonium- and phosphonium-salt-based DESs were prepared and characterized by FTIR. The graphene was characterized by FTIR, STA, Raman spectroscopy, XRD, SEM, and TEM. Additional experim...

  17. Shrinkage in propellant Manufactured by Solvent Process

    Directory of Open Access Journals (Sweden)

    K.M. Agrawal

    1991-04-01

    Full Text Available The propellant manufacturers select the dimensions of die-pin for extrusion of dough by trial and error method based on their experience. This paper presents a general equation applicable for any propellant composition processed by solvent process, in any shape, i.e., cord, monotubular or the multitubular. To illustrate the relationship, calculation for outer radius for a few typical single-base propellants is given.

  18. Physiology of solvent tolerance in Pseudomonas putida S12

    NARCIS (Netherlands)

    Isken, S.

    2000-01-01

    Hydrophobic organic solvents, like toluene, are toxic for living organisms. This toxicity is an important drawback in the environmental biotechnology as well as in the application of solvents in the production of fine chemicals by whole-cell biotransformations. The effects of organic solvents on mic

  19. Catalytic coal liquefaction with treated solvent and SRC recycle

    Science.gov (United States)

    Garg, Diwakar; Givens, Edwin N.; Schweighardt, Frank K.

    1986-01-01

    A process for the solvent refining of coal to distillable, pentane soluble products using a dephenolated and denitrogenated recycle solvent and a recycled, pentane-insoluble, solvent-refined coal material, which process provides enhanced oil-make in the conversion of coal.

  20. Web Accessibility and Guidelines

    Science.gov (United States)

    Harper, Simon; Yesilada, Yeliz

    Access to, and movement around, complex online environments, of which the World Wide Web (Web) is the most popular example, has long been considered an important and major issue in the Web design and usability field. The commonly used slang phrase ‘surfing the Web’ implies rapid and free access, pointing to its importance among designers and users alike. It has also been long established that this potentially complex and difficult access is further complicated, and becomes neither rapid nor free, if the user is disabled. There are millions of people who have disabilities that affect their use of the Web. Web accessibility aims to help these people to perceive, understand, navigate, and interact with, as well as contribute to, the Web, and thereby the society in general. This accessibility is, in part, facilitated by the Web Content Accessibility Guidelines (WCAG) currently moving from version one to two. These guidelines are intended to encourage designers to make sure their sites conform to specifications, and in that conformance enable the assistive technologies of disabled users to better interact with the page content. In this way, it was hoped that accessibility could be supported. While this is in part true, guidelines do not solve all problems and the new WCAG version two guidelines are surrounded by controversy and intrigue. This chapter aims to establish the published literature related to Web accessibility and Web accessibility guidelines, and discuss limitations of the current guidelines and future directions.

  1. OGIS Access System

    Data.gov (United States)

    National Archives and Records Administration — The OGIS Access System (OAS) provides case management, stakeholder collaboration, and public communications activities including a web presence via a web portal.

  2. Solvent-assisted polymer micro-molding

    Institute of Scientific and Technical Information of China (English)

    HAN LuLu; ZHOU Jing; GONG Xiao; GAO ChangYou

    2009-01-01

    The micro-molding technology has played an important role in fabrication of polymer micro-patterns and development of functional devices.In such a process,suitable solvent can swell or dissolve the polymer films to decrease their glass transition temperature (Tg) and viscosity and thereby improve flowing ability.Consequently,it is easy to obtain the 2D and 3D patterns with high fidelity by the solvent-assisted micro-molding.Compared with the high temperature molding,this technology overcomes some shortcomings such as shrinking after cooling,degradation at high temperature,difficulty in processing some functional materials having high Tg,etc.It can be applied to making patterns not only on polymer monolayers but also on polyelectrolyte multilayers.Moreover,the compressioninduced patterns on the multilayers are chemically homogenous but physically heterogeneous.In this review,the controlling factors on the pattern quality are also discussed,including materials of the mold,solvent,pressure,temperature and pattern density.

  3. Dynamics of solvent-free grafted nanoparticles

    KAUST Repository

    Chremos, Alexandros

    2012-01-01

    The diffusivity and structural relaxation characteristics of oligomer-grafted nanoparticles have been investigated with simulations of a previously proposed coarse-grained model at atmospheric pressure. Solvent-free, polymer-grafted nanoparticles as well as grafted nanoparticles in a melt were compared to a reference system of bare (ungrafted) particles in a melt. Whereas longer chains lead to a larger hydrodynamic radius and lower relative diffusivity for grafted particles in a melt, bulk solvent-free nanoparticles with longer chains have higher relative diffusivities than their short chain counterparts. Solvent-free nanoparticles with short chains undergo a glass transition as indicated by a vanishing diffusivity, diverging structural relaxation time and the formation of body-centered-cubic-like order. Nanoparticles with longer chains exhibit a more gradual increase in the structural relaxation time with decreasing temperature and concomitantly increasing particle volume fraction. The diffusivity of the long chain nanoparticles exhibits a minimum at an intermediate temperature and volume fraction where the polymer brushes of neighboring particles overlap, but must stretch to fill the interparticle space. © 2012 American Institute of Physics.

  4. 10.6% Certified Colloidal Quantum Dot Solar Cells via Solvent-Polarity-Engineered Halide Passivation.

    Science.gov (United States)

    Lan, Xinzheng; Voznyy, Oleksandr; García de Arquer, F Pelayo; Liu, Mengxia; Xu, Jixian; Proppe, Andrew H; Walters, Grant; Fan, Fengjia; Tan, Hairen; Liu, Min; Yang, Zhenyu; Hoogland, Sjoerd; Sargent, Edward H

    2016-07-13

    Colloidal quantum dot (CQD) solar cells are solution-processed photovoltaics with broad spectral absorption tunability. Major advances in their efficiency have been made via improved CQD surface passivation and device architectures with enhanced charge carrier collection. Herein, we demonstrate a new strategy to improve further the passivation of CQDs starting from the solution phase. A cosolvent system is employed to tune the solvent polarity in order to achieve the solvation of methylammonium iodide (MAI) and the dispersion of hydrophobic PbS CQDs simultaneously in a homogeneous phase, otherwise not achieved in a single solvent. This process enables MAI to access the CQDs to confer improved passivation. This, in turn, allows for efficient charge extraction from a thicker photoactive layer device, leading to a certified solar cell power conversion efficiency of 10.6%, a new certified record in CQD photovoltaics. PMID:27351104

  5. Sequential accelerated solvent extraction of polycyclic aromatic hydrocarbons with different solvents: performance and implication.

    Science.gov (United States)

    Ma, Xiaoxuan; Ran, Yong; Gong, Jian; Chen, Diyun

    2010-01-01

    Sixteen USEPA priority polycyclic aromatic hydrocarbons (PAHs) extracted by Soxhlet extraction (S-PAHs) with dichloromethane and routine accelerated solvent extraction (A-PAHs) with 1:1 toluene/methanol, respectively, were investigated in 24 soil samples from two cities in the center of the Pearl River Delta, South China. Polycyclic aromatic hydrocarbons, methylphenanthrene and perylene, in two soils, two sediments, and an immature oil shale were also sequentially extracted by accelerated solvent extraction (ASE) with each of four different organic solvents for three times. The A-PAHs' concentrations are 2.41 times the S-PAHs' concentrations. For sequential three ASEs, PAHs in the first extract account for 56 to 67% of their total concentrations in the sequential three extractions and toluene displays the best extraction performance among the four solvents. Diagnostic ratios of PAHs in Soxhlet extraction, routine ASE, and sequential ASE with each solvent for a given sample are very similar, suggesting their identical petrogenic and pyrogenic sources in the soils and sediments. But the PAH ratios for the shale have an obvious petrogenic origin. The perylene/5-ring PAH ratios indicate a diagenetic source, especially in the shale and sediments. The correlation analysis shows that A-PAHs/S-PAHs is better associated with the contents of total organic carbon (TOC) than those of black carbon (BC). The above results indicate the significant petrogenic origin of PAHs and the important effect of organic matter on their extraction and distribution in the investigated field soils/sediments. PMID:21284305

  6. A generic method for assignment of reliability scores applied to solvent accessibility predictions

    DEFF Research Database (Denmark)

    Petersen, Bent; Petersen, Thomas Nordahl; Andersen, Pernille;

    2009-01-01

    score with the individual predictions. However, our implementation of reliability scores in the form of a Z-score is shown to be the more informative measure for discriminating good predictions from bad ones in the entire range from completely buried to fully exposed amino acids. This is evident when......Estimation of the reliability of specific real value predictions is nontrivial and the efficacy of this is often questionable. It is important to know if you can trust a given prediction and therefore the best methods associate a prediction with a reliability score or index. For discrete...... qualitative predictions, the reliability is conventionally estimated as the difference between output scores of selected classes. Such an approach is not feasible for methods that predict a biological feature as a single real value rather than a classification. As a solution to this challenge, we have...

  7. A solvent evaporation route towards fabrication of hierarchically porous ZSM-11 with highly accessible mesopores

    DEFF Research Database (Denmark)

    Song, Wen; Liu, Zhiting; Liu, Liping;

    2015-01-01

    from hierarchical ZSM-11 have been conducted to characterize the textural properties of the material. Ammonia temperature-programmed-desorption (NH3-TPD) measurements and infrared spectra using probe molecules such as pyridine (Py-IR) and 2,4,6-collidine (Coll-IR) have been collected to investigate...

  8. Coded Random Access

    DEFF Research Database (Denmark)

    Paolini, Enrico; Stefanovic, Cedomir; Liva, Gianluigi;

    2015-01-01

    as waste. However, if the common receiver (e.g., base station) is capable to store the collision slots and use them in a transmission recovery process based on successive interference cancellation, the design space for access protocols is radically expanded. We present the paradigm of coded random access...

  9. Market Access and Welfare

    DEFF Research Database (Denmark)

    Raimondos-Møller, Pascalis; Woodland, Alan D.

    2015-01-01

    Well known tariff reform rules that are guaranteed to increase welfare will not necessarily increase market access, while rules that are guaranteed to increase market access will not necessarily increase welfare. The present paper proposes a new set of tariff reforms that can achieve both...

  10. Intellectual Access to Images.

    Science.gov (United States)

    Chen, Hsin-Liang; Rasmussen, Edie M.

    1999-01-01

    The increased availability of digital images is accompanied by a need for solutions to the problems inherent in indexing them for retrieval. Problems in image description and access are discussed, with a perspective on traditional and new solutions. Recent developments in intellectual access to images are surveyed and contrasted with…

  11. The Open Access Divide

    Directory of Open Access Journals (Sweden)

    Jingfeng Xia

    2013-10-01

    Full Text Available This paper is an attempt to review various aspects of the open access divide regarding the difference between those academics who support free sharing of data and scholarly output and those academics who do not. It provides a structured description by adopting the Ws doctrines emphasizing such questions as who, what, when, where and why for information-gathering. Using measurable variables to define a common expression of the open access divide, this study collects aggregated data from existing open access as well as non-open access publications including journal articles and extensive reports. The definition of the open access divide is integrated into the discussion of scholarship on a larger scale.

  12. Nonhazardous solvent composition and method for cleaning metal surfaces

    International Nuclear Information System (INIS)

    A solvent composition for displacing greasy and oily contaminants as well as water and/or aqueous residue from metallic surfaces, especially surfaces of radioactive materials so that such surfaces can be wiped clean of the displaced contaminants, water and/or aqueous residue. The solvent composition consists essentially of a blend of nonpolar aliphatic hydrocarbon solvent having a minimum flash point of about 140 F and 2 to 25 volume percent of a polar solvent having a flash point sufficiently high so as to provide the solvent composition with a minimum flash point of at least 140 F. The solvent composition is nonhazardous so that when it is used to clean the surfaces of radioactive materials the waste in the form of paper or cloth wipes, lab coats and the like used in the cleaning operation is not considered to be mixed waste composed of a hazardous solvent and a radioactive material

  13. Protease activation in glycerol-based deep eutectic solvents

    Science.gov (United States)

    Zhao, Hua; Baker, Gary A.; Holmes, Shaletha

    2011-01-01

    Deep eutectic solvents (DESs) consisting of mixtures of a choline salt (chloride or acetate form) and glycerol are prepared as easily accessible, biodegradable, and inexpensive alternatives to conventional aprotic cation-anion paired ionic liquids. These DES systems display excellent fluidity coupled with thermal stability to nearly 200 °C. In this work, the transesterification activities of cross-linked proteases (subtilisin and α-chymotrypsin), immobilized on chitosan, were individually examined in these novel DESs. In the 1:2 molar ratio mixture of choline chloride/glycerol containing 3% (v/v) water, cross-linked subtilisin exhibited an excellent activity (2.9 μmo l min−1 g−1) in conjunction with a selectivity of 98% in the transesterification reaction of N-acetyl-L-phenylalanine ethyl ester with 1-propanol. These highly encouraging results advocate more extensive exploration of DESs in protease-mediated biotransformations of additional polar substrates and use of DESs in biocatalysis more generally. PMID:21909232

  14. Next Generation Solvent (NGS): Development for Caustic-Side Solvent Extraction of Cesium

    International Nuclear Information System (INIS)

    This report summarizes the FY 2010 and 2011 accomplishments at Oak Ridge National Laboratory (ORNL) in developing the Next Generation Caustic-Side Solvent Extraction (NG-CSSX) process, referred to commonly as the Next Generation Solvent (NGS), under funding from the U.S. Department of Energy, Office of Environmental Management (DOE-EM), Office of Technology Innovation and Development. The primary product of this effort is a process solvent and preliminary flowsheet capable of meeting a target decontamination factor (DF) of 40,000 for worst-case Savannah River Site (SRS) waste with a concentration factor of 15 or higher in the 18-stage equipment configuration of the SRS Modular Caustic-Side Solvent Extraction Unit (MCU). In addition, the NG-CSSX process may be readily adapted for use in the SRS Salt Waste Processing Facility (SWPF) or in supplemental tank-waste treatment at Hanford upon appropriate solvent or flowsheet modifications. Efforts in FY 2010 focused on developing a solvent composition and process flowsheet for MCU implementation. In FY 2011 accomplishments at ORNL involved a wide array of chemical-development activities and testing up through single-stage hydraulic and mass-transfer tests in 5-cm centrifugal contactors. Under subcontract from ORNL, Argonne National Laboratory (ANL) designed a preliminary flowsheet using ORNL cesium distribution data, and Tennessee Technological University confirmed a chemical model for cesium distribution ratios (DCs) as a function of feed composition. Interlaboratory efforts were coordinated with complementary engineering tests carried out (and reported separately) by personnel at Savannah River National Laboratory (SRNL) and Savannah River Remediation (SRR) with helpful advice by Parsons Engineering and General Atomics on aspects of possible SWPF implementation.

  15. Next Generation Solvent Development for Caustic-Side Solvent Extraction of Cesium

    Energy Technology Data Exchange (ETDEWEB)

    Moyer, Bruce A. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Birdwell, Joseph F. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Bonnesen, Peter V. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Bruffey, Stephanie [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

    2014-03-01

    This report summarizes the FY 2010 and 2011 accomplishments at Oak Ridge National Laboratory (ORNL) in developing the Next Generation Caustic-Side Solvent Extraction (NG-CSSX) process, referred to commonly as the Next Generation Solvent (NGS), under funding from the U.S. Department of Energy, Office of Environmental Management (DOE-EM), Office of Technology Innovation and Development. The primary product of this effort is a process solvent and preliminary flowsheet capable of meeting a target decontamination factor (DF) of 40,000 for worst-case Savannah River Site (SRS) waste with a concentration factor of 15 or higher in the 18-stage equipment configuration of the SRS Modular Caustic-Side Solvent Extraction Unit (MCU). In addition, the NG-CSSX process may be readily adapted for use in the SRS Salt Waste Processing Facility (SWPF) or in supplemental tank-waste treatment at Hanford upon appropriate solvent or flowsheet modifications. Efforts in FY 2010 focused on developing a solvent composition and process flowsheet for MCU implementation. In FY 2011 accomplishments at ORNL involved a wide array of chemical-development activities and testing up through single-stage hydraulic and mass-transfer tests in 5-cm centrifugal contactors. Under subcontract from ORNL, Argonne National Laboratory (ANL) designed a preliminary flowsheet using ORNL cesium distribution data, and Tennessee Technological University confirmed a chemical model for cesium distribution ratios (DCs) as a function of feed composition. Inter laboratory efforts were coordinated with complementary engineering tests carried out (and reported separately) by personnel at Savannah River National Laboratory (SRNL) and Savannah River Remediation (SRR) with helpful advice by Parsons Engineering and General Atomics on aspects of possible SWPF implementation.

  16. Next Generation Solvent (NGS): Development for Caustic-Side Solvent Extraction of Cesium

    Energy Technology Data Exchange (ETDEWEB)

    Moyer, Bruce A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Birdwell, Jr, Joseph F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bonnesen, Peter V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bruffey, Stephanie H. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Delmau, Laetitia Helene [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Duncan, Nathan C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ensor, Dale [Tennessee Technological Univ., Cookeville, TN (United States); Hill, Talon G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Denise L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Rajbanshi, Arbin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Roach, Benjamin D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Szczygiel, Patricia L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sloop, Jr., Frederick V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Stoner, Erica L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Williams, Neil J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2014-03-01

    This report summarizes the FY 2010 and 2011 accomplishments at Oak Ridge National Laboratory (ORNL) in developing the Next Generation Caustic-Side Solvent Extraction (NG-CSSX) process, referred to commonly as the Next Generation Solvent (NGS), under funding from the U.S. Department of Energy, Office of Environmental Management (DOE-EM), Office of Technology Innovation and Development. The primary product of this effort is a process solvent and preliminary flowsheet capable of meeting a target decontamination factor (DF) of 40,000 for worst-case Savannah River Site (SRS) waste with a concentration factor of 15 or higher in the 18-stage equipment configuration of the SRS Modular Caustic-Side Solvent Extraction Unit (MCU). In addition, the NG-CSSX process may be readily adapted for use in the SRS Salt Waste Processing Facility (SWPF) or in supplemental tank-waste treatment at Hanford upon appropriate solvent or flowsheet modifications. Efforts in FY 2010 focused on developing a solvent composition and process flowsheet for MCU implementation. In FY 2011 accomplishments at ORNL involved a wide array of chemical-development activities and testing up through single-stage hydraulic and mass-transfer tests in 5-cm centrifugal contactors. Under subcontract from ORNL, Argonne National Laboratory (ANL) designed a preliminary flowsheet using ORNL cesium distribution data, and Tennessee Technological University confirmed a chemical model for cesium distribution ratios (DCs) as a function of feed composition. Interlaboratory efforts were coordinated with complementary engineering tests carried out (and reported separately) by personnel at Savannah River National Laboratory (SRNL) and Savannah River Remediation (SRR) with helpful advice by Parsons Engineering and General Atomics on aspects of possible SWPF implementation.

  17. Single Stage Contactor Testing Of The Next Generation Solvent Blend

    Energy Technology Data Exchange (ETDEWEB)

    Herman, D. T.; Peters, T. B.; Duignan, M. R.; Williams, M. R.; Poirier, M. R.; Brass, E. A.; Garrison, A. G.; Ketusky, E. T.

    2014-01-06

    The Modular Caustic Side Solvent Extraction (CSSX) Unit (MCU) facility at the Savannah River Site (SRS) is actively pursuing the transition from the current BOBCalixC6 based solvent to the Next Generation Solvent (NGS)-MCU solvent to increase the cesium decontamination factor. To support this integration of NGS into the MCU facility the Savannah River National Laboratory (SRNL) performed testing of a blend of the NGS (MaxCalix based solvent) with the current solvent (BOBCalixC6 based solvent) for the removal of cesium (Cs) from the liquid salt waste stream. This testing utilized a blend of BOBCalixC6 based solvent and the NGS with the new extractant, MaxCalix, as well as a new suppressor, tris(3,7dimethyloctyl) guanidine. Single stage tests were conducted using the full size V-05 and V-10 liquid-to-liquid centrifugal contactors installed at SRNL. These tests were designed to determine the mass transfer and hydraulic characteristics with the NGS solvent blended with the projected heel of the BOBCalixC6 based solvent that will exist in MCU at time of transition. The test program evaluated the amount of organic carryover and the droplet size of the organic carryover phases using several analytical methods. The results indicate that hydraulically, the NGS solvent performed hydraulically similar to the current solvent which was expected. For the organic carryover 93% of the solvent is predicted to be recovered from the stripping operation and 96% from the extraction operation. As for the mass transfer, the NGS solvent significantly improved the cesium DF by at least an order of magnitude when extrapolating the One-stage results to actual Seven-stage extraction operation with a stage efficiency of 95%.

  18. Compound forming extractants, solvating solvents and inert solvents IUPAC chemical data series

    CERN Document Server

    Marcus, Y; Kertes, A S

    2013-01-01

    Equilibrium Constants of Liquid-Liquid Distribution Reactions, Part III: Compound Forming Extractants, Solvating Solvents, and Inert Solvents focuses on the compilation of equilibrium constants of various compounds, such as acids, ions, salts, and aqueous solutions. The manuscript presents tables that show the distribution reactions of carboxylic and sulfonic acid extractants and their dimerization and other reactions in the organic phase and extraction reactions of metal ions from aqueous solutions. The book also states that the inorganic anions in these solutions are irrelevant, since they d

  19. Scenarios Evaluation Tool for Chlorinated Solvent MNA

    Energy Technology Data Exchange (ETDEWEB)

    Vangelas, Karen; Michael J. Truex; Charles J. Newell; Brian Looney

    2007-02-28

    Over the past three decades, much progress has been made in the remediation of chlorinated solvents from the subsurface. Yet these pervasive contaminants continue to present a significant challenge to the U.S. Department of Energy (DOE), other federal agencies, and other public and private organizations. The physical and chemical properties of chlorinated solvents make it difficult to rapidly reach the low concentrations typically set as regulatory limits. These technical challenges often result in high costs and long remediation time frames. In 2003, the DOE through the Office of Environmental Management funded a science-based technical project that uses the U.S. Environmental Protection Agency's technical protocol (EPA, 1998) and directives (EPA, 1999) on Monitored Natural Attenuation (MNA) as the foundation on which to introduce supporting concepts and new scientific developments that will support remediation of chlorinated solvents based on natural attenuation processes. This project supports the direction in which many site owners want to move to complete the remediation of their site(s), that being to complete the active treatment portion of the remedial effort and transition into MNA. The overarching objective of the effort was to examine environmental remedies that are based on natural processes--remedies such as Monitored Natural Attenuation (MNA) or Enhanced Attenuation (EA). The research program did identify several specific opportunities for advances based on: (1) mass balance as the central framework for attenuation based remedies, (2) scientific advancements and achievements during the past ten years, (3) regulatory and policy development and real-world experience using MNA, and (4) exploration of various ideas for integrating attenuation remedies into a systematic set of ''combined remedies'' for contaminated sites. These opportunities are summarized herein and are addressed in more detail in referenced project documents and

  20. Pediatric vascular access

    International Nuclear Information System (INIS)

    Pediatric interventional radiologists are ideally suited to provide vascular access services to children because of inherent safety advantages and higher success from using image-guided techniques. The performance of vascular access procedures has become routine at many adult interventional radiology practices, but this service is not as widely developed at pediatric institutions. Although interventional radiologists at some children's hospitals offer full-service vascular access, there is little or none at others. Developing and maintaining a pediatric vascular access service is a challenge. Interventionalists skilled in performing such procedures are limited at pediatric institutions, and institutional support from clerical staff, nursing staff, and technologists might not be sufficiently available to fulfill the needs of such a service. There must also be a strong commitment by all members of the team to support such a demanding service. There is a slippery slope of expected services that becomes steeper and steeper as the vascular access service grows. This review is intended primarily as general education for pediatric radiologists learning vascular access techniques. Additionally, the pediatric or adult interventional radiologist seeking to expand services might find helpful tips. The article also provides education for the diagnostic radiologist who routinely interprets radiographs containing vascular access devices. (orig.)

  1. Pediatric vascular access

    Energy Technology Data Exchange (ETDEWEB)

    Donaldson, James S. [Northwestern University, Feinberg School of Medicine, Department of Medical Imaging, Children' s Memorial Hospital, Chicago, IL (United States)

    2006-05-15

    Pediatric interventional radiologists are ideally suited to provide vascular access services to children because of inherent safety advantages and higher success from using image-guided techniques. The performance of vascular access procedures has become routine at many adult interventional radiology practices, but this service is not as widely developed at pediatric institutions. Although interventional radiologists at some children's hospitals offer full-service vascular access, there is little or none at others. Developing and maintaining a pediatric vascular access service is a challenge. Interventionalists skilled in performing such procedures are limited at pediatric institutions, and institutional support from clerical staff, nursing staff, and technologists might not be sufficiently available to fulfill the needs of such a service. There must also be a strong commitment by all members of the team to support such a demanding service. There is a slippery slope of expected services that becomes steeper and steeper as the vascular access service grows. This review is intended primarily as general education for pediatric radiologists learning vascular access techniques. Additionally, the pediatric or adult interventional radiologist seeking to expand services might find helpful tips. The article also provides education for the diagnostic radiologist who routinely interprets radiographs containing vascular access devices. (orig.)

  2. PULSED MIXER-SETTLER SOLVENT EXTRACTION CONTACTORS

    Science.gov (United States)

    Figg, W.S.

    1958-08-12

    A mixer-settler extractor is described for contacting immiscible liquids having different specific gravities in order to withdraw one or more components from one liquid with the aid of the other liquid. The extractor consists of a hollow column, a rotary drive shafi extending : through the column with a number of impellers spaced thereon, an equal nunnber of separator plate sets each consisting of one fluorothene and one stainless steel plate with peripheral recesses and flow slots mounted on the column, and a pulse generator. This apparatus is particularly useful in solvent extraction processes for recovering plutonium from aqueous acidic solutions of irradiated uranium.

  3. Cleaning with solvents methods and machinery

    CERN Document Server

    Durkee, John

    2014-01-01

    High-precision cleaning is required across many sectors, including aerospace, defense, medical device manufacturing, pharmaceutical processing, semiconductor/electronics, and more. In this comprehensive reference work, solvent cleaning equipment is thoroughly covered with a focus on the engineering details of its operation and selection. Key data is provided alongside practical guidance, giving scientists and engineers in multiple sectors the information they need not only to choose the correct machine in the first place, but also how to operate it effectively and efficiently. Low emission

  4. Applicability of carbon and boron nitride nanotubes as biosensors: Effect of biomolecular adsorption on the transport properties of carbon and boron nitride nanotubes

    Science.gov (United States)

    Zhong, Xiaoliang; Mukhopadhyay, Saikat; Gowtham, S.; Pandey, Ravindra; Karna, Shashi P.

    2013-04-01

    The effect of molecular adsorption on the transport properties of single walled carbon and boron nitride nanotubes (CNTs and BNNTs) is investigated using density functional theory and non-equilibrium Green's function methods. The calculated I-V characteristics predict noticeable changes in the conductivity of semiconducting BNNTs due to physisorption of nucleic acid base molecules. Specifically, guanine which binds to the side wall of BNNT significantly enhances its conductivity by introducing conduction channels near the Fermi energy of the bioconjugated system. For metallic CNTs, a large background current masks relatively small changes in current due to the biomolecular adsorption. The results therefore suggest the suitability of BNNTs for biosensing applications.

  5. Market Access and Welfare

    DEFF Research Database (Denmark)

    Raimondos-Møller, Pascalis; Woodland, Alan D.

    According to the literature, well known tariff reform rules that are guaranteed to increase welfare will not necessarily increase market access, while rules that are guaranteed to increase market access will not necessarily increase welfare. Such conflict between welfare and market access...... objectives of trade policy is problematic and calls for finding alternative tariff reform rules that can achieve both objectives at the same time. The present paper contributes to this aim by using a new set of tariff reforms that are based on local optimality. Using such reforms it is shown that market...

  6. Access 2010 for dummies

    CERN Document Server

    Ulrich Fuller, Laurie

    2010-01-01

    A friendly, step-by-step guide to the Microsoft Office database application Access may be the least understood and most challenging application in the Microsoft Office suite. This guide is designed to help anyone who lacks experience in creating and managing a database learn to use Access 2010 quickly and easily. In the classic For Dummies tradition, the book provides an education in Access, the interface, and the architecture of a database. It explains the process of building a database, linking information, sharing data, generating reports, and much more.As the Micr

  7. Extra- and intrathoracic access.

    Science.gov (United States)

    Lazarides, Miltos K; Georgakarakos, Efstratios I; Schoretsanitis, Nikolaos

    2014-01-01

    The most complex patients requiring vascular access are those with bilateral central vein occlusions. Endovascular repair of the central lesions when feasible allow upper extremity use for access. When endovascular repair is not feasible, femoral vein transposition should be the next choice. When lower limb access sites have been exhausted or are contraindicated as in obese patients and in patients with peripheral arterial obstructive disease, a range of extrathoracic "exotic" extra-anatomic access procedures as the necklace cross-chest arteriovenous (AV) grafts, the ipsilateral axillo-axillary loops, the brachial-jugular AV grafts, the axillo-femoral AV grafts or even intra-thoracic ones as the right atrial AV bypasses represent the vascular surgeon's last resort. The selection among those extra-anatomical chest-wall procedures should be based upon each patient's anatomy or patient-specific factors. PMID:24817469

  8. Access cavity preparation.

    Science.gov (United States)

    Adams, N; Tomson, P L

    2014-03-01

    Each stage of root canal treatment should be carried out to the highest possible standard. The access cavity is arguably the most important technical stage, as subsequent preparation of the root canal(s) can be severely comprised if this is not well executed. Inadequate access can lead to canals being left untreated, poorly disinfected, difficult to shape and obturate, and may ultimately lead to the failure of the treatment. This paper highlights common features in root canal anatomy and outlines basic principles for locating root canals and producing a good access cavity. It also explores each phase of the preparation in detail and offers suggestions of instruments that have been specifically designed to overcome potential difficulties in the process. Good access design and preparation will result in an operative environment which will facilitate cleaning, shaping and obturation of the root canal system in order to maximise success.

  9. Accessibility and assistive products

    Science.gov (United States)

    Rodríguez-Porrero, Cristina

    2009-01-01

    Introduction Accessibility and assistive products and technologies are needed to ensure the rights of persons with disabilities and older persons. Many developments have been implemented in laws, standards, markets and from the consumers perspective, at international, European and national levels. The real issue is that not all the potential users benefit from the use of assistive products or accessible measures. Discussion Innovative methods are needed to allow all potential users to have real advantage of assistive technologies and accessible and design for all facilities. Best practices will be presented and existing gaps and recommendations will be discussed. Cost-benefits aspects will also be presented. Conclusion In order to get advantages from opportunities of globalization, hard work and responsibilities of all stakeholders are needed, so that assistive products and accessibility reach a whole range of situations and environments and contribute to ensure quality of life in a society for all.

  10. Access/AML

    Data.gov (United States)

    Department of Transportation — The AccessAML is a web-based internet single application designed to reduce the vulnerability associated with several accounts assinged to a single users. This is a...

  11. Recovery of plutonium from solvent wash solutions

    International Nuclear Information System (INIS)

    A number of potential alternatives to the acid hydrolysis recovery of Pu were investigated. The most promising alternative for short-term use appears to be an anion exchange process that would eliminate the long boiling times and the multiple-pass concentration steps needed with the solvent extraction process because it separates the Pu from the dibutyl phosphate (DBP) while at the same time concentrating the Pu. However, restart of the Primary Recovery Column (PRC) to process this solution would require significant administrative effort. The original boiling recovery by acid hydrolysis followed by solvent extraction is probably the most expedient way to process the Pu-DBP-carbonate solution currently stored in tank 13.5 even with its long processing times and dilute product concentration. Anion exchange of a heat stabilized acidified solution is a more efficient process, but requires restart of the PRC. Extended-boiling acid hydrolysis or anion exchange of a heat stabilized acidified solution provide two well developed alternatives for recovery of the Pu from the tank 13.5 carbonate. Further work defining additional recovery processes is not planned at this time

  12. Natural deep eutectic solvents: cytotoxic profile.

    Science.gov (United States)

    Hayyan, Maan; Mbous, Yves Paul; Looi, Chung Yeng; Wong, Won Fen; Hayyan, Adeeb; Salleh, Zulhaziman; Mohd-Ali, Ozair

    2016-01-01

    The purpose of this study was to investigate the cytotoxic profiles of different ternary natural deep eutectic solvents (NADESs) containing water. For this purpose, five different NADESs were prepared using choline chloride as a salt, alongside five hydrogen bond donors (HBD) namely glucose, fructose, sucrose, glycerol, and malonic acid. Water was added as a tertiary component during the eutectics preparation, except for the malonic acid-based mixture. Coincidentally, the latter was found to be more toxic than any of the water-based NADESs. A trend was observed between the cellular requirements of cancer cells, the viscosity of the NADESs, and their cytotoxicity. This study also highlights the first time application of the conductor-like screening model for real solvent (COSMO-RS) software for the analysis of the cytotoxic mechanism of NADESs. COSMO-RS simulation of the interactions between NADESs and cellular membranes' phospholipids suggested that NADESs strongly interacted with cell surfaces and that their accumulation and aggregation possibly defined their cytotoxicity. This reinforced the idea that careful selection of NADESs components is necessary, as it becomes evident that organic acids as HBD highly contribute to the increasing toxicity of these neoteric mixtures. Nevertheless, NADESs in general seem to possess relatively less acute toxicity profiles than their DESs parents. This opens the door for future large scale utilization of these mixtures. PMID:27386357

  13. Solvent viscosity dependence for enzymatic reactions

    CERN Document Server

    Sitnitsky, A E

    2008-01-01

    A mechanism for relationship of solvent viscosity with reaction rate constant at enzyme action is suggested. It is based on fluctuations of electric field in enzyme active site produced by thermally equilibrium rocking (cranckshaft motion) of the rigid plane (in which the dipole moment $\\approx 3.6 D$ lies) of a favourably located and oriented peptide group (or may be a few of them). Thus the rocking of the plane leads to fluctuations of the electric field of the dipole moment. These fluctuations can interact with the reaction coordinate because the latter in its turn has transition dipole moment due to separation of charges at movement of the reacting system along it. The rocking of the plane of the peptide group is sensitive to the microviscosity of its environment in protein interior and the latter is a function of the solvent viscosity. Thus we obtain an additional factor of interrelationship for these characteristics with the reaction rate constant. We argue that due to the properties of the cranckshaft ...

  14. Solvent induced track sensitization. Extraction of oligomers

    Science.gov (United States)

    Apel, P.; Angert, N.; Brüchle, W.; Hermann, H.; Kampschulte, U.; Klein, P.; Kravets, L. I.; Oganessian, Yu. Ts.; Remmert, G.; Spohr, R.; Steckenreiter, T.; Trautmann, C.; Vetter, J.

    1994-04-01

    Oligomer extraction from polyethylene terephthalate (PET) irradiated by xenon ions of 11.4 MeV/u is investigated using UV spectrophotometry and gel permeation chromatography (GPC). The cyclic trimer is identified as the predominant diffusing species removed during extraction by dimethyl formamide (DMF). Extraction dynamics is modeled by a rapid (time constant ≈ 2 min) and a slow (time constant ≈ 100 min) diffusion process attributed to the latent ion tracks and to the virgin material, respectively. Thereby latent tracks act simultaneously as irrigation and drainage pipes for the transfer of the solvent into and the extraction of oligomers from the polymer matrix. Thus tracks help to release osmotic pressure differences and to avoid blistering of the unirradiated polymer during solvent exchange. The total extracted mass per track shows a characteristic decrease with increasing ion fluence interpreted as oxygen effect, due to the decreasing supply of oxygen in the sample during irradiation. The extractable mass corresponds to an equivalent track diameter of initially around 10 nm contracting with increasing ion fluence to an asymptotic value around 3 nm.

  15. Non-Ideal Behavior in Solvent Extraction

    Energy Technology Data Exchange (ETDEWEB)

    Peter Zalupski

    2011-09-01

    This report presents a summary of the work performed to meet FCR&D level 3 milestone M31SW050801, 'Complete the year-end report summarizing FY11 experimental and modeling activities.' This work was carried out under the auspices of the Non-Ideality in Solvent Extraction Systems FCR&D work package. The report summarizes our initial considerations of potential influences that non-ideal chemistry may impose on computational prediction of outcomes in solvent extraction systems. The report is packaged into three separate test cases where a robustness of the prediction by SXFIT program is under scrutiny. The computational exercises presented here emphasize the importance of accurate representation of both an aqueous and organic mixtures when modeling liquid-liquid distribution systems. Case No.1 demonstrates that non-ideal behavior of HDEHP in aliphatic diluents, such as n-dodecane, interferes with the computation. Cases No.2 and No.3 focus on the chemical complexity of aqueous electrolyte mixtures. Both exercises stress the need for an improved thermodynamic model of an aqueous environment present in the europium distribution experiments. Our efforts for year 2 of this project will focus on the improvements of aqueous and non-aqueous solution models using fundamental physical properties of mixtures acquired experimentally in our laboratories.

  16. Solvents, Ethanol, Car Crashes and Tolerance: How Risky is Inhalation of Organic Solvents?

    Science.gov (United States)

    A research program in the National Health and Environmental Effects Research Laboratory of the U.S. EPA has led to some surprising considerations regarding the potential hazard of exposure to low concentrations of solvent vapors. This program involved conducting experiments to ch...

  17. Solvent sorting in (mixed solvent + electrolyte) systems: Time-resolved fluorescence measurements and theory

    Indian Academy of Sciences (India)

    Harun Al Rasidgazi; Hemant K Kashyap; Ranjit Biswas

    2015-01-01

    In this manuscriptwe explore electrolyte-induced modification of preferential solvation of a dipolar solute dissolved in a binary mixture of polar solvents. Composition dependence of solvation characteristics at a fixed electrolyte concentration has been followed. Binary mixtures of two different polarities have been employed to understand the competition between solute-ion and solute-solvent interactions. Time-resolved fluorescence Stokes shift and anisotropy have been measured for coumarin 153 (C153) in moderately polar (ethyl acetate + 1-propanol) and strongly polar (acetonitrile + propylene carbonate) binary mixtures at various mixture compositions, and in the corresponding 1.0M solutions of LiClO4. Both the mixtures show red shifts in C153 absorption and fluorescence emission upon increase of mole fraction of the less polar solvent component in presence of the electrolyte. In addition, measured average solvation times become slower and rotation times faster for the above change in the mixture composition. A semi-molecular theory based on solution density fluctuations has been developed and found to successfully capture the essential features of the measured Stokes shift dynamics of these complex multi-component mixtures. Dynamic anisotropy results have been analyzed by using both Stokes-Einstein-Debye (SED) and Dote-Kivelson-Schwartz (DKS) theories. The importance of local solvent structure around the dissolved solute has been stressed.

  18. The universal access handbook

    CERN Document Server

    Stephanidis, Constantine

    2009-01-01

    In recent years, the field of Universal Access has made significant progress in consolidating theoretical approaches, scientific methods and technologies, as well as in exploring new application domains. Increasingly, professionals in this rapidly maturing area require a comprehensive and multidisciplinary resource that addresses current principles, methods, and tools. Written by leading international authorities from academic, research, and industrial organizations and nonmarket institutions, The Universal Access Handbook covers the unfolding scientific, methodological, technological, and pol

  19. CERN access cards

    CERN Multimedia

    HR Department

    2007-01-01

    Holders of CERN access cards are reminded that the card is an official document. It is important to carry it with you at all times when you are on the site. This applies also to those on standby duty who are called out for emergency interventions. As announced in Weekly Bulletin 13/2006, any loss or theft of access cards must be declared to the competent external authorities.

  20. IMPROVING ACCESS TO DRUGS

    OpenAIRE

    Max Joseph Herman

    2012-01-01

    Although essentially not all therapies need drug intervention, drugs is still an important components in health sector, either in preventive, curative, rehabilitative or promotion efforts. Hence the access to drugs is a main problem, either in international or national scale even to the smallest unit. The problem on access to drugs is very complicated and cannot be separated especially from pharmacy management problems; moreover in general from the overall lack of policy development and effec...

  1. Effects of solvent and structure on the reactivity of 6-substituted nicotinic acids with diazodiphenylmethane in aprotic solvents

    Directory of Open Access Journals (Sweden)

    BRATISLAV Ž. JOVANOVIĆ

    2009-12-01

    Full Text Available The rate constants for the reactions of diazodiphenylmethane (DDM with 6-substituted nicotinic acids in aprotic solvents at 30 °C were determined. The obtained second order rate constants in aprotic solvents, together with literature data for benzoic and nicotinic acids in protic solvents, were used for the calculation of solvent effects, employing the Kamlet-Taft solvatochromic equation (linear solvation energy relationship – LSER in the form: log k = log k0 + s* + a + b. The correlations of the kinetic data were performed by means of multiple linear regression analysis taking appropriate solvent parameters. The sign of the equation coefficients (s, a and b were in agreement with the postulated reaction mechanism, and the mode of the solvent influences on the reaction rate is discussed based on the correlation results. A similar contribution of the non-specific solvent effect and electrophilic solvation was observed for all acids, while the highest contribution of nucleophilic solvation was influenced by their high acidity. Correlation analysis of the rate data with substituent p parameters in an appropriate solvent using the Hammett equation was also performed. The substituent effect on the acid reactivity was higher in aprotic solvents of higher dipolarity/polarizability. The mode of the transmission of the substituent effect is discussed in light of the contribution of solute–solvent interaction on the acid reactivity.

  2. Controls of functional group chemistry on calcium carbonate nucleation: Insights into systematics of biomolecular innovations for skeletal mineralization?

    Science.gov (United States)

    Dove, P. M.; Hamm, L. M.; Giuffre, A. J.

    2012-12-01

    Living organisms produce skeletal structures within a complex matrix of organic macromolecules that guide the nucleation and growth of crystalline structures into the organic-inorganic composites we know as biominerals. This type of biomolecule-directed mineralization is an ancient process as evidenced by structures in the fossil record that date to the Ediacaran (ca. 549 Ma). Our understanding of template-directed biomineralization, however, is largely based upon assumptions from studies that: 1) qualitatively demonstrate some chemical functionalities influence the nucleating mineral phase and morphology; 2) propose proteins are the primary driver to template-directed mineralization and 3) propose the ubiquitous polysaccharides are inert components. Thus, a mechanistic basis for how the underlying chemistry of macromolecules controls nucleation kinetics and thermodynamics in template-directed nucleation is not well established. Moreover, there is not yet a good appreciation for how patterns of skeletal mineralization evolved with biochemical innovations in response to environmental changes over geologic timescales. In small steps toward understanding biochemical controls on biomineralization, we test the hypothesis that the kinetics and thermodynamics of calcium carbonate (CaCO3) formation is regulated by a systematic relationship to the functional group chemistry of macromolecules. A long-term goal is to establish the energetic basis for biochemical motifs that are seen (and not seen) at sites of calcification across the phylogenetic tree. Two types of studies were conducted. The first measured nucleation rates on model biomolecular substrates with termini that are found in proteins associated with sites of calcification (-COOH, -PO4, and -SH) and two alkanethiol chain lengths (16-C and 11-C) at a variety of chemical driving forces. The measurements show functional group chemistry and molecule conformation regulate rates by a predictable relation to interfacial

  3. Method for Selection of Solvents for Promotion of Organic Reactions

    DEFF Research Database (Denmark)

    Gani, Rafiqul; Jiménez-González, Concepción; Constable, David J.C.

    2005-01-01

    A method to select appropriate green solvents for the promotion of a class of organic reactions has been developed. The method combines knowledge from industrial practice and physical insights with computer-aided property estimation tools for selection/design of solvents. In particular, it employs...... estimates of thermodynamic properties to generate a knowledge base of reaction, solvent and environment related properties that directly or indirectly influence the rate and/or conversion of a given reaction. Solvents are selected using a rules-based procedure where the estimated reaction-solvent properties...... and the solvent-environmental properties guide the decision making process. The current method is applicable only to organic reactions occurring in the liquid phase. Another gas or solid phase, which may or may not be at equilibrium with the reacting liquid phase, may also be present. The objective of this method...

  4. The effect of solvent choice on plutonium extraction with TTA

    International Nuclear Information System (INIS)

    This paper reports the relative plutonium extraction rate from 1M nitric acid with thenoyltrifluoroacetone (TTA) dissolved in several different solvents. The marked differences in extraction rate are discussed in terms of the extraction mechanism. Experiments with varied phase mixing conditions, and with varied TTA or nitrate concentrations, have been performed to help clarify the mechanisms and explain the differences in extraction rate. The results show that in several solvents, plutonium is extracted as a mixed nitrate-TTA complex. The suitability of the various solvents for differing applications was also examined. Methyl benzoate is an ideal solvent when preparing counting sources from the solvent phase. Chloroform is preferable as solvent when the plutonium is to be backwashed into nitric acid. (author)

  5. A new solvent suppression method via radiation damping effect

    Institute of Scientific and Technical Information of China (English)

    Cui Xiao-Hong; Peng Ling; Zhang Zhen-Min; Cai Shu-Hui; Chen Zhong

    2011-01-01

    Radiation damping effects induced by the dominated solvent in a solution sample can be applied to suppress the solvent signal.The precession pathway and rate back to equilibrium state between solute and solvent spins are different under radiation damping.In this paper,a series of pulse sequences using radiation damping were designed for the solvent suppression in nuclear magnetic resonance (NMR) spectroscopy.Compared to the WATERGATE method,the solute signals adjacent to the solvent would not be influenced by using the radiation damping method.The one-dimensional (1D) 1H NMR,two-dimensional (2D) gCOSY,and J-resolved experimental results show the practicability of solvent suppression via radiation damping effects in 1D and 2D NMR spectroscopy.

  6. Automated spray cleaning using flammable solvents in a glovebox

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, P.; Meirans, L.

    1998-05-01

    The phase-out of the ozone-depleting solvents has forced industry to look to solvents such as alcohol, terpenes and other flammable solvents to perform the critical cleaning processes. These solvents are not as efficient as the ozone-depleting solvents in terms of soil loading, cleaning time and drying when used in standard cleaning processes such as manual sprays or ultrasonic baths. They also require special equipment designs to meet part cleaning specifications and operator safety requirements. This paper describes a cleaning system that incorporates the automated spraying of flammable solvents to effectively perform precision cleaning processes. Key to the project`s success was the development of software that controls the robotic system and automatically generates robotic cleaning paths from three dimensional CAD models of the items to be cleaned.

  7. Trace elements retained in washed nuclear fuel reprocessing solvents

    International Nuclear Information System (INIS)

    Analysis of purified TBP extractant from solvent extraction processes at Savannah River Plant showed several stable elements and several long-lived radioisotopes. Stable elements Al, Na, Br, Ce, Hg, and Sm are found in trace quantities in the solvent. The only stable metallic element consistently found in the solvent was Al, with a concentration which varies from about 30 ppM to about 10 ppM. The halogens Br and Cl appear to be found in the solvent systems as organo halides. Radionuclides found were principally 106Ru, 129I, 3H, 235U, and 239Pu. The 129I concentration was about 1 ppM in the first solvent extraction cycle of each facility. In the other cycles, 129I concentration varied from about 0.1 to 0.5 ppM. Both 129I and 3H appear to be in the organic solvent as a result of exchange with hydrogen

  8. Solvent degradation and cleanup: a survey and recent ORNL studies

    Energy Technology Data Exchange (ETDEWEB)

    Mailen, J.C.; Tallent, O.K.

    1984-01-01

    This paper surveys the mechanisms for degradation of the tributyl phosphate and diluent components of Purex solvent by acid and radiation, reviews the problems encountered in plant operations resulting from the presence of these degradation products, and discusses methods for minimizing the formation of degradation products and accomplishing their removal. Scrubbing solutions containing sodium carbonate or hydroxylamine salts and secondary cleanup of solvents using solid sorbents are evaluated. Finally, recommendations for improved solvent cleanup are presented. 50 references, 4 figures, 3 tables.

  9. Solvent degradation and cleanup: a survey and recent ORNL studies

    International Nuclear Information System (INIS)

    This paper surveys the mechanisms for degradation of the tributyl phosphate and diluent components of Purex solvent by acid and radiation, reviews the problems encountered in plant operations resulting from the presence of these degradation products, and discusses methods for minimizing the formation of degradation products and accomplishing their removal. Scrubbing solutions containing sodium carbonate or hydroxylamine salts and secondary cleanup of solvents using solid sorbents are evaluated. Finally, recommendations for improved solvent cleanup are presented. 50 references, 4 figures, 3 tables

  10. Challenges in subsurface in situ remediation of chlorinated solvents

    OpenAIRE

    Broholm, Mette Martina; Fjordbøge, Annika Sidelmann; Christiansen, Camilla Maymann; Hønning, J.; B. H. Hansen; Nedergaard, L. W.; Kern, Kristina; Uthuppu, Basil; Jakobsen, Mogens Havsteen; Kjeldsen, Peter; Bjerg, Poul Løgstrup; Ottesen, L.

    2014-01-01

    Chlorinated solvent source zones in the subsurface pose a continuous threat to groundwater quality at many sites worldwide. In situ remediation of these sites is particularly challenging in heterogeneous fractured media and where the solvents are present as DNAPL. In situ remediation by chemical as well as biological degradation of chlorinated solvents is a contact sport and requires direct contact between the contaminant and the reactants and/or degrading microorganisms. In fractured geologi...

  11. Properties and thermal behavior of natural deep eutectic solvents

    OpenAIRE

    Craveiro, R.; Aroso, Ivo Manuel Ascensão; Flammia, V.; Carvalho, T.; Viciosa, M. T.; Dionísio, M.; Barreiros, S.; Reis, R. L.; Duarte, Ana Rita C.; Paiva, A.

    2016-01-01

    Natural deep eutectic solvents (NADES) have shown to be promising sustainable media for a wide range of applications. Nonetheless, very limited data is available on the properties of these solvents. A more comprehensive body of data on NADES is required for a deeper understanding of these solvents at molecular level, which will undoubtedly foster the development of new applications. NADES based on choline chloride, organic acids, amino acids and sugars were prepared, and their density, therma...

  12. Alcohols as hydrogen-donor solvents for treatment of coal

    Science.gov (United States)

    Ross, David S.; Blessing, James E.

    1981-01-01

    A method for the hydroconversion of coal by solvent treatment at elevated temperatures and pressure wherein an alcohol having an .alpha.-hydrogen atom, particularly a secondary alcohol such as isopropanol, is utilized as a hydrogen donor solvent. In a particular embodiment, a base capable of providing a catalytically effective amount of the corresponding alcoholate anion under the solvent treatment conditions is added to catalyze the alcohol-coal reaction.

  13. Solvent mediated self-assembly of solids

    Energy Technology Data Exchange (ETDEWEB)

    De Yoreo, J.; Wilson, W.D.; Palmore, T.

    1997-12-12

    Solvent-mediated crystallization represents a robust approach to self-assembly of nanostructures and microstructures. In organic systems, the relative ease with which the structure of hydrogen- bonded molecules can be manipulated allows for generation of a wide variety of nanoscale crystal structures. In living organisms, control over the micron-to-millimeter form of inorganic crystals is achieved through introduction of bio-organic molecules. The purpose of this proposal is to understand the interplay between solution chemistry, molecular structure, surface chemistry, and the processes of nucleation and crystal growth in solvent-mediated systems, with the goal of developing the atomic and molecular basis of a solvent-mediated self-assembly technology. We will achieve this purpose by: (1) utilizing an atomic force microscopy (AFM) approach that provides in situ, real time imaging during growth from solutions, (2) by modifying kinetic Monte Carlo (KMC) models to include solution-surface kinetics, (3) by introducing quantum chemistry (QC) calculations of the potentials of the relevant chemical species and the near-surface structure of the solution, and (4) by utilizing molecular dynamics (MD) simulations to identify the minimum energy pathways to the solid state. Our work will focus on two systems chosen to address both the manometer and micron-to-millimeter length scales of assembly, the family of 2,5- diketopiperazines (X-DKPs) and the system of CaCO{sub 3} with amino acids. Using AFM, we will record the evolution of surface morphology, critical lengths, step speeds, and step-step interactions as a function of supersaturation and temperature. In the case of the X-DKPs, these measurements will be repeated as the molecular structure of the growth unit is varied. In the case of CaCO{sub 3}, they will be performed as a function of solution chemistry including pH, ionic strength, and amino acid content. In addition, we will measure nucleation rates and orientations of

  14. Explicit- and implicit-solvent simulations of micellization in surfactant solutions.

    Science.gov (United States)

    Jusufi, Arben; Panagiotopoulos, Athanassios Z

    2015-03-24

    In this article, we focus on simulation methodologies to obtain the critical micelle concentration (cmc) and equilibrium distribution of aggregate sizes in dilute surfactant solutions. Even though it is now relatively easy to obtain micellar aggregates in simulations starting from a fully dispersed state, several major challenges remain. In particular, the characteristic times of micelle reorganization and transfer of monomers from micelles to free solution for most systems of practical interest exceed currently accessible molecular dynamics time scales for atomistic surfactant models in explicit solvent. In addition, it is impractical to simulate highly dilute systems near the cmc. We have demonstrated a strong dependence of the free surfactant concentration (frequently, but incorrectly, taken to represent the cmc in simulations) on the overall concentration for ionic surfactants. We have presented a theoretical framework for making the necessary extrapolations to the cmc. We find that currently available atomistic force fields systematically underpredict experimental cmc's, pointing to the need for the development of improved models. For strongly micellizing systems that exhibit strong hysteresis, implicit-solvent grand canonical Monte Carlo simulations represent an appealing alternative to atomistic or coarse-grained, explicit-solvent simulations. We summarize an approach that can be used to obtain quantitative, transferrable effective interactions and illustrate how this grand canonical approach can be used to interpret experimental scattering results.

  15. Study of Two Bioactive Peptides in Vacuum and Solvent by Molecular Modeling

    Science.gov (United States)

    Yaşar, F.; Demir, K.

    The thermodynamic and structural properties of Tyrosine-Glycine-Leusine-Phenylalanine (YGLF, in a one letter code) and Lysine-Valine-Leusine-Proline-Valine-Proline-Glutamine (KVLPVPQ) peptide sequences were studied by three-dimensional molecular modeling in vacuum and solution. All the three-dimensional conformations of each peptide sequences were obtained by multicanonical simulations with using ECEPP/2 force field and each simulation started from completely random initial conformation. Solvation contributions are included by a term that is proportional to solvent-accessible surface areas of peptides. In the present study, we calculated the average values of total energy, specific heat, fourth-order cumulant and end-to-end distance for two peptide sequences of milk protein as a function of temperature. With using major advantage of this simulation technique, Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of β-turn, γ-turn and helical structures. Although structural predictions of these sequences indicate both the presence of high level of γ-turns and low level of β-turns in vacuum and solvent, it was observed that these probabilities in vacuum were higher than the ones in solvent model.

  16. Electrospinning of Grooved Polystyrene Fibers: Effect of Solvent Systems

    Science.gov (United States)

    Liu, Wanjun; Huang, Chen; Jin, Xiangyu

    2015-05-01

    Secondary surface texture is of great significance to morphological variety and further expands the application areas of electrospun nanofibers. This paper presents the possibility of directly electrospinning grooved polystyrene (PS) fibers using both single and binary solvent systems. Solvents were classified as low boiling point solvent (LBPS): dichloromethane (DCM), acetone (ACE), and tetrahydrofuran (THF); high boiling point solvent (HBPS): N, N-dimethylformamide (DMF) and cyclohexanone (CYCo); and non-solvent (NS): 1-butanol (BuOH). By the systematic selection and combination of these solvents at given parameters, we found that single solvent systems produced non-grooved fibers. LBPS/DMF solvent systems resulted in fibers with different grooved textures, while LBPS/CYCo led to fibers with double grooved texture. Grooved fibers can also be fabricated from LBPS/LBPS, NS/LBPS, and NS/HBPS systems under specific conditions. The results indicated that the difference of evaporation rate (DER) between the two solvents played a key role in the formation of grooved texture. The formation of this unique texture should be attributed to three separate mechanisms, namely void-based elongation, wrinkle-based elongation, and collapsed jet-based elongation. Our findings can serve as guidelines for the preparation of ultrafine fibers with grooved secondary texture.

  17. Comparative study of solvent properties for carbon dioxide absorption

    Energy Technology Data Exchange (ETDEWEB)

    Aschenbrenner, O.; Styring, P. [University of Sheffield, Sheffield (United Kingdom)

    2010-07-01

    Several inexpensive and non-toxic solvents with low vapour pressures were investigated for their suitability as alternative solvents for the absorption of carbon dioxide from flue gas. The solvents include poly(ethylene glycol)s, poly(ethylene glycol) ethers, poly(ethylenimine) and glycerol-based substances. Solvent properties such as thermal stability, solubility of carbon dioxide and selectivity over nitrogen were investigated in a systematic study using a thermogravimetric analyser. Absorption results are reported for pure carbon dioxide and nitrogen as well as a mixture of both gases. Desorption and long-term sorption behaviour are also discussed. Glycerol and poly(ethylene glycol)s show a high solubility of carbon dioxide. Due to the high viscosity of the solvent, carbon dioxide absorption in poly(ethylenimine) is very slow in spite of the presence of favourable amine groups. PEG 300 was found to be the best solvent in this study and shows a high carbon dioxide solubility as well as good selectivity over nitrogen. The advantages of high stability, low solvent loss and low desorption energy of PEG 300 may outweigh its lower absorption capacity compared to the state-of-the-art solvent monoethanolamine, making it a potentially advantageous solvent for industrial carbon dioxide absorption processes.

  18. Discrete solvent effects on the effective interaction between charged colloids

    CERN Document Server

    Allahyarov, E

    2000-01-01

    Using computer simulations of two charged colloidal spheres with their counterions in a hard sphere solvent, we show that the granular nature of the solvent significantly influences the effective colloidal interaction. For divalent counterions, the total effective force can become attractive generated by counterion hydration, while for monovalent counterions the forces are repulsive and well-described by a solvent-induced colloidal charge renormalization. Both effects are not contained in the traditional "primitive" approaches but can be accounted for in a solvent-averaged primitive model.

  19. NMR microscopy of tissue in organic and mixed solvents

    Directory of Open Access Journals (Sweden)

    Macura Slobodan

    2013-01-01

    Full Text Available We propose to use organic and mixed solvents for nuclear magnetic resonance microscopy of fixed tissue as a means for improving image information content. NMR properties of some standard solvents (methanol, acetone, DMSO and solvents in use for tissue processing in pathology (xylenes, paraffin, ‘Clearify’ have been measured, reviewed, and analyzed. It was found that DMSO and paraffin are very useful solvents that provide images of better quality than those obtained in water (neutralized formalin buffer. This is illustrated on the formalin fixed mouse brain sections imaged at 16.4 teslas (700 MHz.

  20. Computational Analysis of Solvent Effects in NMR Spectroscopy.

    Science.gov (United States)

    Dračínský, Martin; Bouř, Petr

    2010-01-12

    Solvent modeling became a standard part of first principles computations of molecular properties. However, a universal solvent approach is particularly difficult for the nuclear magnetic resonance (NMR) shielding and spin-spin coupling constants that in part result from collective delocalized properties of the solute and the environment. In this work, bulk and specific solvent effects are discussed on experimental and theoretical model systems comprising solvated alanine zwitterion and chloroform molecules. Density functional theory computations performed on larger clusters indicate that standard dielectric continuum solvent models may not be sufficiently accurate. In some cases, more reasonable NMR parameters were obtained by approximation of the solvent with partial atomic charges. Combined cluster/continuum models yielded the most reasonable values of the spectroscopic parameters, provided that they are dynamically averaged. The roles of solvent polarizability, solvent shell structure, and bulk permeability were investigated. NMR shielding values caused by the macroscopic solvent magnetizability exhibited the slowest convergence with respect to the cluster size. For practical computations, however, inclusion of the first solvation sphere provided satisfactory corrections of the vacuum values. The simulations of chloroform chemical shifts and CH J-coupling constants were found to be very sensitive to the molecular dynamics model used to generate the cluster geometries. The results show that computationally efficient solvent modeling is possible and can reveal fine details of molecular structure, solvation, and dynamics. PMID:26614339

  1. Decontamination of radioactive contaminated protective wear using dry cleaning solvent

    International Nuclear Information System (INIS)

    Liquid waste generated by conventional decontamination of radioactive contaminated cotton protective wear using detergent affects the chemical treatment of the plant. To reduce the generation of aqueous detergent waste, dry cleaning of cotton protective wear, highly soiled with oil and grease towards decontamination was tried with organic solvents. Mineral turpentine oil (MTO) among various other organic solvents was identified as a suitable organic solvent. As MTO leaves characteristic odour on the cloth, various commercial fragrances for the removal of the odour were tried. Application of the optimised dry cleaning solvent and commercial fragrance was adopted in plant scale operation. (author)

  2. Solvent Extraction in Hydrometallurgy: Present and Future

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    During the past 10 years, there have been incremental advances in the application of solvent extraction to process hydrometallurgy. The most cited areas in the literature include chemistry, chemical engineering, pilot plants, and plant operation. Within these areas, there were considerable interest in synergism,diluents, degradation, contactors, surfactants, hydrometallurgical applications, environmental and secondary applications, and health and safety. The summary to the present is followed by a prediction for the future in the above areas of interest. These include the use of speciation; improved understanding of the role of surfactants on the system; optimization through modelling, pilot plants, and contactor selection; improvements in plant operation; further new applications; and plant safety. The review has indicated that considerable knowledge is now available to optimize and improve on process design and plant applications.

  3. Is Water a Universal Solvent for Life?

    Science.gov (United States)

    Pohorill, Andrew

    2012-01-01

    There are strong reasons to believe that the laws, principles and constraints of physics and chemistry are universal. It is much less clear how this universality translates into our understanding of the origins of life. Conventionally, discussions of this topic focus on chemistry that must be sufficiently rich to seed life. Although this is clearly a prerequisite for the emergence of living systems, I propose to focus instead on self-organization of matter into functional structures capable of reproduction, evolution and responding to environmental changes. In biology, most essential functions are largely mediated by noncovalent interactions (interactions that do not involve making or breaking chemical bonds). Forming chemical bonds is only a small part of what living systems do. There are specific implications of this point of view for universality. I will concentrate on one of these implications. Strength of non-covalent interactions must be properly tuned. If they were too weak, the system would exhibit undesired, uncontrolled response to natural fluctuations of physical and chemical parameters. If they were too strong kinetics of biological processes would be slow and energetics costly. This balance, however, is not a natural property of complex chemical systems. Instead, it has to be achieved with the aid of an appropriate solvent for life. In particular, potential solvents for life must be characterized by a high dielectric constant to ensure solubility of polar species and sufficient flexibility of biological structures stabilized by electrostatic interactions. Among these solvents, water exhibits a remarkable trait that it also promotes solvophobic (hydrophobic) interactions between non-polar species, typically manifested by a tendency of these species to aggregate and minimize their contacts with the aqueous solvent. Hydrophobic interactions are responsible, at least in part, for many self-organization phenomena in biological systems, such as the formation

  4. Oligoquinolines under Solvent-free Microwave Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Park, Kwi-Jeon; Kwon, Tae-Woo [Kyungsung University, Busan (Korea, Republic of)

    2015-01-15

    Quinolines are thermally stable and can be used as an excellent n-type semiconducting materials. Since quinolines are also known to be electron acceptor molecules, combination of various electron donor building blocks can be utilized in photonic and electronic organic light-emitting diode (OLED) applications. For example, donor.acceptor systems with phenothiazine (or carbazole) molecules as electron donors and the phenylquinoline group as an electron acceptor provide an efficient approach for the design of new materials exhibiting highly efficient charge-transfer photophysics and electroluminescence in OLEDs. We have described the Friedlander quinoline synthesis between aminobenzophenones and symmetrical diacetyl compounds having phenothiazine, carbazole, biphenyl, and phenyl moieties under solvent-free microwave irradiation in 12.98% isolated yields.

  5. Contamination removal using various solvents and methodologies

    Science.gov (United States)

    Jeppsen, J. C.

    1989-01-01

    Critical and non-critical bonding surfaces must be kept free of contamination that may cause potential unbonds. For example, an aft-dome section of a redesigned solid rocket motor that had been contaminated with hydraulic oil did not appear to be sufficiently cleaned when inspected by the optically stimulated electron emission process (Con Scan) after it had been cleaned using a hand double wipe cleaning method. As a result, current and new cleaning methodologies as well as solvent capability in removing various contaminant materials were reviewed and testing was performed. Bonding studies were also done to verify that the cleaning methods used in removing contaminants provide an acceptable bonding surface. The removal of contaminants from a metal surface and the strength of subsequent bonds were tested using the Martin Marietta and double-wipe cleaning methods. Results are reported.

  6. Oligoquinolines under Solvent-free Microwave Irradiation

    International Nuclear Information System (INIS)

    Quinolines are thermally stable and can be used as an excellent n-type semiconducting materials. Since quinolines are also known to be electron acceptor molecules, combination of various electron donor building blocks can be utilized in photonic and electronic organic light-emitting diode (OLED) applications. For example, donor.acceptor systems with phenothiazine (or carbazole) molecules as electron donors and the phenylquinoline group as an electron acceptor provide an efficient approach for the design of new materials exhibiting highly efficient charge-transfer photophysics and electroluminescence in OLEDs. We have described the Friedlander quinoline synthesis between aminobenzophenones and symmetrical diacetyl compounds having phenothiazine, carbazole, biphenyl, and phenyl moieties under solvent-free microwave irradiation in 12.98% isolated yields

  7. Organogels thermodynamics, structure, solvent role, and properties

    CERN Document Server

    Guenet, Jean-Michel

    2016-01-01

    This book provides a physics-oriented introduction to organogels with a comparison to polymer thermoreversible gels whenever relevant. The past decade has seen the development of a wide variety of newly-synthesized molecules that can spontaneously self-assemble or crystallize from their organic or aqueous solutions to produce fibrillar networks, namely organogels, with potential applications in organic electronics, light harvesting, bio-imaging, non-linear optics, and the like. This compact volume presents a detailed outlook of these novel molecular systems with special emphasis upon their thermodynamics, morphology, molecular structure, and rheology. The definition of these complex systems is also tackled, as well as the role of the solvent. The text features numerous temperature-phase diagrams for a variety of organogels as well as illustrations of their structures at the microscopic, mesoscopic and macroscopic level. A review of some potential applications is provided including hybrid functional materials ...

  8. On relation of interphase tension in the system of organic solvent-water with parameters of solvent solvation ability

    International Nuclear Information System (INIS)

    It is shown that there is a linear dependence between the empirical parameter, solvent effect (SE), characterizing solvent solvation ability, and interphase tension in the two-phase system organic solvent-water. Analyzing data for 31 solvents, it is established that the largest coefficient of reverse correlation r=-0.98 has been reached when using such an equations as SE=a+b σ/ρ 1/3, where a and b - constants, ρ - solvent density. As far as interphase activity of hyprophobic surfactant decreases linearly with the growth of SE parameter values, then it is follows from the equation found that decrease of interphase tension on the interface water-organic solvent have to lead to decrease of interphase activity of hydrophobic surfactant present in the system

  9. Enzyme catalysis in organic solvents: influence of water content, solvent composition and temperature on Candida rugosa lipase catalyzed transesterification.

    Science.gov (United States)

    Herbst, Daniela; Peper, Stephanie; Niemeyer, Bernd

    2012-12-31

    In the present study the influence of water content, solvent composition and reaction temperature on the transesterification of 1-phenylpropan-2-ol catalyzed by Candida rugosa lipase was examined. Reactions were carried out in different mixtures of hexane and tetrahydrofurane. The studies showed that an increasing water content of the organic solvent results in an increasing enzyme activity and a decreasing enantiomeric excess. Furthermore, a significant influence of the solvent hydrophilicity both on the enzyme activity and on the enantiomeric excess was found. An increase in solvent hydrophilicity leads to a decrease of enzyme activity and an increase of the enantiomeric excess. This indicates that the enzyme becomes more selective with decreasing flexibility. Similar effects were found by variation of the reaction temperature. Taken together, the decrease in conversion and the increase in selectivity with increasing solvent hydrophilicity are induced by the different water contents on the enzyme surface and not by the solvent itself.

  10. IVOA Simple Image Access

    CERN Document Server

    Dowler, Patrick; Bonnarel, François

    2016-01-01

    The Simple Image Access protocol (SIA) provides capabilities for the discovery, description, access, and retrieval of multi-dimensional image datasets, including 2-D images as well as datacubes of three or more dimensions. SIA data discovery is based on the ObsCore Data Model (ObsCoreDM), which primarily describes data products by the physical axes (spatial, spectral, time, and polarization). Image datasets with dimension greater than 2 are often referred to as datacubes, cube or image cube datasets and may be considered examples of hypercube or n-cube data. In this document the term "image" refers to general multi-dimensional datasets and is synonymous with these other terms unless the image dimensionality is otherwise specified. SIA provides capabilities for image discovery and access. Data discovery and metadata access (using ObsCoreDM) are defined here. The capabilities for drilling down to data files (and related resources) and services for remote access are defined elsewhere, but SIA also allows for dir...

  11. Sonochemical heating profile for solvents and ionic liquid doped solvents, and their application in the N-alkylation of pyrazoles.

    Science.gov (United States)

    Frizzo, Clarissa P; Bacim, Carolini; Moreira, Dayse N; Rodrigues, Leticia V; Zimmer, Geórgia C; Bonacorso, Hélio G; Zanatta, Nilo; Martins, Marcos A P

    2016-09-01

    The heating profile for 25 solvents was determined in ultrasonic probe equipment at amplitudes of 20%, 25%, and 30%. Each solvent was heated in accordance with its boiling point. The effect of vapor pressure, surface tension, and viscosity of the solvents in dissipated ultrasonic power (Up) was evaluated. Multiple regression analysis of these solvent properties and dissipated Up reveals that solvent viscosity is the property that most strongly affected dissipated Up. Experimentation involving acetonitrile doped with [BMIM][BF4] indicated faster heating than MeCN. Aprotic polar solvents such as DMSO, DMF, and MeCN were tested in the N-alkylation of pyrazoles under ultrasonic conditions. After 5min at 90°C, the reactants had been totally converted into product in these solvents. Solvents, with low dissipated Up (e.g., toluene) were tested. Conversions were lower compared to those of aprotic polar solvents. When the reactions were done in hexane, no conversion to product was observed. To check the effect of doping in solvents with low Up, [BMIM][BF4], DMSO, and DMF were selected. The conversions for toluene doped with [BMIM][BF4], DMSO, and DMF were 100%, 59%, and 25%, respectively. These conversions were greater than when done in just toluene (46%). Thus, [BMIM][BF4] was the best polar doping solvent, followed by DMSO. DMF was not considered to be a satisfactory doping solvent. No conversion was observed for reactions in the absence of base performed in DMSO, DMF, and MeCN doped with [BMIM][BF4]. PMID:27150789

  12. Support open access publishing

    DEFF Research Database (Denmark)

    Ekstrøm, Jeannette

    2013-01-01

    Projektet Support Open Access Publishing har til mål at få opdateret Sherpa/Romeo databasen (www.sherpa.ac.uk/romeo) med fagligt relevante, danske tidsskrifter. Projektet skal endvidere undersøge mulighederne for at få udviklet en database, hvor forskere på tværs af relevante tidsskriftsinformati......Projektet Support Open Access Publishing har til mål at få opdateret Sherpa/Romeo databasen (www.sherpa.ac.uk/romeo) med fagligt relevante, danske tidsskrifter. Projektet skal endvidere undersøge mulighederne for at få udviklet en database, hvor forskere på tværs af relevante...... tidsskriftsinformationer (faglig disciplin, BFI niveau, Impact Factor, Open Access) vil kunne danne sig et hurtigt overblik, for derved at kunne træffe et kvalificeret valg om, hvor og hvordan man skal publicere sine forskningsresultater....

  13. Effects of temperature and solvent concentration on the solvent crystallization of palm-based dihydroxystearic acid with isopropyl alcohol

    Institute of Scientific and Technical Information of China (English)

    Gregory F.L.Koay; Teong-Guan Chuah; Sumaiya Zainal-Abidin; Salmiah Ahmad; Thomas S.Y.Choong

    2012-01-01

    Palm-based dihydroxystearic acid of 69.55% purity was produced in a 500-kg-per-batch operation pilot plant and purified through solvent crystallization in a custom fabricated simultaneous batch crystallizer unit.The effects of temperature and solvent concentration on yield,particle size distribution and purity were studied.The purity was higher,while the yield and particle size were lower and smaller,respectively,at higher temperature and solvent concentration.The solvent crystallization process efficiency was rated at 66-69% when carried out with 70-80% isopropyl alcohol at 20 ℃.

  14. Chemisorption interaction between solvents and the gallium subgroup metals: a relationship with the ionization potential of the solvent molecules

    International Nuclear Information System (INIS)

    Experimental data characterizing chemisorption metal-solvent interaction on Ga-, (In-Ga)-, (Tl-Ga) - and Hg - electrodes in various solvents have been considered from the viewpoint of quantum-chemical notions of chemical bond formation. It is shown that there is a correlation between parameters characterizing chemisorption metal-solvent interaction on the electrodes and the change in the value of the first adiabatic ionization potential of the solvent molecule, as well as the change in electron energy on the metal Fermi level

  15. Organic & Biomolecular Chemistry

    OpenAIRE

    Zhang, Wenyu; Bryson, David I.; Crumpton, Jason B.; Wynn, Jessica; Santos, Webster L.

    2013-01-01

    On-bead high-throughput screening of a medium-sized (1000_2000 Da) branched peptideboronic acid (BPBA) library consisting of 46 656 unique sequences against HIV-1 RRE RNA generated peptides with binding affinities in the low micromolar range. In particular, BPBA1 had a Kd of 1.4 _M with RRE IIB, preference for RNA over DNA (27 fold), and selectivity of up to >75 fold against a panel of RRE IIB variants. Structure_activity studies suggest that the boronic acid moiety and ͐branching in peptide...

  16. Abstractions for biomolecular computations

    CERN Document Server

    Okunoye, Babatunde O

    2008-01-01

    Deoxyribonucleic acid is increasingly being understood to be an informational molecule, capable of information processing.It has found application in the determination of non-deterministic algorithms and in the design of molecular computing devices. This is a theoretical analysis of the mathematical properties and relations of the molecules which constituting DNA, which explains in part why DNA is a successful computing molecule.

  17. Introduction. Biomolecular simulation.

    Science.gov (United States)

    Mulholland, Adrian J

    2008-12-01

    'Everything that living things do can be understood in terms of the jigglings and wigglings of atoms' as Richard Feynman provocatively stated nearly 50 years ago. But how can we 'see' this wiggling and jiggling and understand how it drives biology? Increasingly, computer simulations of biological macromolecules are helping to meet this challenge.

  18. Biomolecular computation for bionanotechnology

    CERN Document Server

    Liu, Jian-Qin

    2006-01-01

    Computers built with moleware? The drive toward non-silicon computing is underway, and this first-of-its-kind guide to molecular computation gives researchers a firm grasp of the technologies, biochemical details, and theoretical models at the cutting edge. It explores advances in molecular biology and nanotechnology and illuminates how the convergence of various technologies is propelling computational capacity beyond the limitations of traditional hardware technology and into the realm of moleware.

  19. A newly isolated organic solvent tolerant Staphylococcus saprophyticus M36 produced organic solvent-stable lipase.

    Science.gov (United States)

    Fang, Yaowei; Lu, Zhaoxin; Lv, Fengxia; Bie, Xiaomei; Liu, Shu; Ding, Zhongyang; Xu, Weifeng

    2006-12-01

    Thirty-eight high lipase activity strains were isolated from soil, seawater, and Brassica napus. Among them, a novel organic solvent tolerant bacterium (strain M36) was isolated from the seawater in Jiangsu, China. Isolate M36 was able to grow at high concentration of benzene or toluene up to 40% (vol/vol), and later identified as Staphylococcus saprophyticus by biochemical test and 16s ribosomal DNA sequence. No work on Staphylococcus producing lipase with organic solvent tolerance has been reported so far. The lipase of strain M36 whose activity in liquid medium was 42 U mL(-1) at 24-h incubation time was stable in the presence of 25% (vol/vol) p-xylene, benzene, toluene, and hexane.

  20. Qualitative and quantitative evaluation of solvent systems for countercurrent separation.

    Science.gov (United States)

    Friesen, J Brent; Ahmed, Sana; Pauli, Guido F

    2015-01-16

    Rational solvent system selection for countercurrent chromatography and centrifugal partition chromatography technology (collectively known as countercurrent separation) studies continues to be a scientific challenge as the fundamental questions of comparing polarity range and selectivity within a solvent system family and between putative orthogonal solvent systems remain unanswered. The current emphasis on metabolomic investigations and analysis of complex mixtures necessitates the use of successive orthogonal countercurrent separation (CS) steps as part of complex fractionation protocols. Addressing the broad range of metabolite polarities demands development of new CS solvent systems with appropriate composition, polarity (π), selectivity (σ), and suitability. In this study, a mixture of twenty commercially available natural products, called the GUESSmix, was utilized to evaluate both solvent system polarity and selectively characteristics. Comparisons of GUESSmix analyte partition coefficient (K) values give rise to a measure of solvent system polarity range called the GUESSmix polarity index (GUPI). Solvatochromic dye and electrical permittivity measurements were also evaluated in quantitatively assessing solvent system polarity. The relative selectivity of solvent systems were evaluated with the GUESSmix by calculating the pairwise resolution (αip), the number of analytes found in the sweet spot (Nsw), and the pairwise resolution of those sweet spot analytes (αsw). The combination of these parameters allowed for both intra- and inter-family comparison of solvent system selectivity. Finally, 2-dimensional reciprocal shifted symmetry plots (ReSS(2)) were created to visually compare both the polarities and selectivities of solvent system pairs. This study helps to pave the way to the development of new solvent systems that are amenable to successive orthogonal CS protocols employed in metabolomic studies. PMID:25542704