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Sample records for capturing molecular structural

  1. Protein–Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, Amity; Reardon, Patrick N.; Chacon, Stephany S.; Qafoku, Nikolla P.; Washton, Nancy M.; Kleber, Markus

    2016-06-21

    Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na+-montmorillonite (001), Ca2+-montmorillonite (001), goethite (100), and Na+-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, four-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvated structure without these mineral surfaces present. Over the Na+-birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation.

  2. Structure of the Hemoglobin-IsdH Complex Reveals the Molecular Basis of Iron Capture by Staphylococcus aureus*♦

    Science.gov (United States)

    Dickson, Claire F.; Kumar, Kaavya Krishna; Jacques, David A.; Malmirchegini, G. Reza; Spirig, Thomas; Mackay, Joel P.; Clubb, Robert T.; Guss, J. Mitchell; Gell, David A.

    2014-01-01

    Staphylococcus aureus causes life-threatening disease in humans. The S. aureus surface protein iron-regulated surface determinant H (IsdH) binds to mammalian hemoglobin (Hb) and extracts heme as a source of iron, which is an essential nutrient for the bacteria. However, the process of heme transfer from Hb is poorly understood. We have determined the structure of IsdH bound to human Hb by x-ray crystallography at 4.2 Å resolution, revealing the structural basis for heme transfer. One IsdH molecule is bound to each α and β Hb subunit, suggesting that the receptor acquires iron from both chains by a similar mechanism. Remarkably, two near iron transporter (NEAT) domains in IsdH perform very different functions. An N-terminal NEAT domain binds α/β globin through a site distant from the globin heme pocket and, via an intervening structural domain, positions the C-terminal heme-binding NEAT domain perfectly for heme transfer. These data, together with a 2.3 Å resolution crystal structure of the isolated N-terminal domain bound to Hb and small-angle x-ray scattering of free IsdH, reveal how multiple domains of IsdH cooperate to strip heme from Hb. Many bacterial pathogens obtain iron from human hemoglobin using proteins that contain multiple NEAT domains and other domains whose functions are poorly understood. Our results suggest that, rather than acting as isolated units, NEAT domains may be integrated into higher order architectures that employ multiple interaction interfaces to efficiently extract heme from host proteins. PMID:24425866

  3. Structure of the hemoglobin-IsdH complex reveals the molecular basis of iron capture by Staphylococcus aureus.

    Science.gov (United States)

    Dickson, Claire F; Kumar, Kaavya Krishna; Jacques, David A; Malmirchegini, G Reza; Spirig, Thomas; Mackay, Joel P; Clubb, Robert T; Guss, J Mitchell; Gell, David A

    2014-03-01

    Staphylococcus aureus causes life-threatening disease in humans. The S. aureus surface protein iron-regulated surface determinant H (IsdH) binds to mammalian hemoglobin (Hb) and extracts heme as a source of iron, which is an essential nutrient for the bacteria. However, the process of heme transfer from Hb is poorly understood. We have determined the structure of IsdH bound to human Hb by x-ray crystallography at 4.2 Å resolution, revealing the structural basis for heme transfer. One IsdH molecule is bound to each α and β Hb subunit, suggesting that the receptor acquires iron from both chains by a similar mechanism. Remarkably, two near iron transporter (NEAT) domains in IsdH perform very different functions. An N-terminal NEAT domain binds α/β globin through a site distant from the globin heme pocket and, via an intervening structural domain, positions the C-terminal heme-binding NEAT domain perfectly for heme transfer. These data, together with a 2.3 Å resolution crystal structure of the isolated N-terminal domain bound to Hb and small-angle x-ray scattering of free IsdH, reveal how multiple domains of IsdH cooperate to strip heme from Hb. Many bacterial pathogens obtain iron from human hemoglobin using proteins that contain multiple NEAT domains and other domains whose functions are poorly understood. Our results suggest that, rather than acting as isolated units, NEAT domains may be integrated into higher order architectures that employ multiple interaction interfaces to efficiently extract heme from host proteins.

  4. Chromatin conformation capture strategies in molecular diagnostics

    NARCIS (Netherlands)

    Vree, P.J.P. de

    2015-01-01

    In this thesis I have explored the clinical potential of the 4C-technology and worked on development of a novel chromatin conformation capture based technology, called TLA. In chapter 2 I describe how the 4C-technology can be applied as a targeted strategy to identify putative fusion-genes or chromo

  5. The mechanism of selective molecular capture in carbon nanotube networks.

    Science.gov (United States)

    Wan, Yu; Guan, Jun; Yang, Xudong; Zheng, Quanshui; Xu, Zhiping

    2014-07-28

    Recently, air pollution issues have drawn significant attention to the development of efficient air filters, and one of the most promising materials for this purpose is nanofibers. We explore here the mechanism of selective molecular capture of volatile organic compounds in carbon nanotube networks by performing atomistic simulations. The results are discussed with respect to the two key parameters that define the performance of nanofiltration, i.e. the capture efficiency and flow resistance, which demonstrate the advantages of carbon nanotube networks with high surface-to-volume ratio and atomistically smooth surfaces. We also reveal the important roles of interfacial adhesion and diffusion that govern selective gas transport through the network.

  6. Theory and Application of Dissociative Electron Capture in Molecular Identification

    CERN Document Server

    Havey, C D; Jones, T; Voorhees, K J; Laramee, J A; Cody, R B; Clougherty, D P; Eberhart, Mark; Voorhees, Kent J.; Laramee, James A.; Cody, Robert B.; Clougherty, Dennis P.

    2006-01-01

    The coupling of an electron monochromator (EM) to a mass spectrometer (MS) has created a new analytical technique, EM-MS, for the investigation of electrophilic compounds. This method provides a powerful tool for molecular identification of compounds contained in complex matrices, such as environmental samples. EM-MS expands the application and selectivity of traditional MS through the inclusion of a new dimension in the space of molecular characteristics--the electron resonance energy spectrum. However, before this tool can realize its full potential, it will be necessary to create a library of resonance energy scans from standards of the molecules for which EM-MS offers a practical means of detection. Here, an approach supplementing direct measurement with chemical inference and quantum scattering theory is presented to demonstrate the feasibility of directly calculating resonance energy spectra. This approach makes use of the symmetry of the transition-matrix element of the captured electron to discriminat...

  7. Valency and molecular structure

    CERN Document Server

    Cartmell, E

    1977-01-01

    Valency and Molecular Structure, Fourth Edition provides a comprehensive historical background and experimental foundations of theories and methods relating to valency and molecular structures. In this edition, the chapter on Bohr theory has been removed while some sections, such as structures of crystalline solids, have been expanded. Details of structures have also been revised and extended using the best available values for bond lengths and bond angles. Recent developments are mostly noted in the chapter on complex compounds, while a new chapter has been added to serve as an introduction t

  8. Longitudinal capture in the radio-frequency-quadrupole structure

    Energy Technology Data Exchange (ETDEWEB)

    Inagaki, S.

    1980-03-01

    The radio-frequency-quadrupole (RFQ) linac structure not only can attain easily transverse focusing in the low-beta region, but also can obtain very high capture efficiency because of its low beta-lambda and low-particle rigidity. An optimization study of the zero space-charge longitudinal capture in an RFQ linac that yields configurations with large capture efficiency is described.

  9. Understanding molecular structure from molecular mechanics.

    Science.gov (United States)

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  10. Continuum secondary structure captures protein flexibility

    DEFF Research Database (Denmark)

    Anderson, C.A.F.; Palmer, A.G.; Brunak, Søren;

    2002-01-01

    The DSSP program assigns protein secondary structure to one of eight states. This discrete assignment cannot describe the continuum of thermal fluctuations. Hence, a continuous assignment is proposed. Technically, the continuum results from averaging over ten discrete DSSP assignments...... protein structure analysis, comparison, and prediction....... with different hydrogen bond thresholds. The final continuous assignment for a single NMR model successfully reflected the structural variations observed between all NMR models in the ensemble. The structural variations between NMR models were verified to correlate with thermal motion; these variations were...

  11. Molecular Spectrum Capture by Tuning the Chemical Potential of Graphene

    Directory of Open Access Journals (Sweden)

    Yue Cheng

    2016-05-01

    Full Text Available Due to its adjustable electronic properties and effective excitation of surface plasmons in the infrared and terahertz frequency range, research on graphene has attracted a great deal of attention. Here, we demonstrate that plasmon modes in graphene-coated dielectric nanowire (GNW waveguides can be excited by a monolayer graphene ribbon. What is more the transverse resonant frequency spectrum of the GNW can be flexibly tuned by adjusting the chemical potential of graphene, and amplitude of the resonance peak varies linearly with the imaginary part of the analyte permittivity. As a consequence, the GNW works as a probe for capturing the molecular spectrum. Broadband sensing of toluene, ethanol and sulfurous anhydride thin layers is demonstrated by calculating the changes in spectral intensity of the propagating mode and the results show that the intensity spectra correspond exactly to the infrared spectra of these molecules. This may open an effective avenue to design sensors for detecting nanometric-size molecules in the terahertz and infrared regimes.

  12. CO2 Capture with Ionic Liquids: Experiments and Molecular Simulations

    NARCIS (Netherlands)

    Ramdin, M.

    2015-01-01

    In this thesis, we investigated the potential of physical ILs for CO2 capture at pre-combustion and natural gas sweetening conditions. The performance of ILs with respect to conventional solvents is assessed in terms of gas solubilities and selectivities. The work discussed in this thesis consists o

  13. Molecular template-directed synthesis of microporous polymer networks for highly selective CO2 capture.

    Science.gov (United States)

    Shi, Yao-Qi; Zhu, Jing; Liu, Xiao-Qin; Geng, Jian-Cheng; Sun, Lin-Bing

    2014-11-26

    Porous polymer networks have great potential in various applications including carbon capture. However, complex monomers and/or expensive catalysts are commonly used for their synthesis, which makes the process complicated, costly, and hard to scale up. Herein, we develop a molecular template strategy to fabricate new porous polymer networks by a simple nucleophilic substitution reaction of two low-cost monomers (i.e., chloromethylbenzene and ethylene diamine). The polymerization reactions can take place under mild conditions in the absence of any catalysts. The resultant materials are interconnected with secondary amines and show well-defined micropores due to the structure-directing role of solvent molecules. These properties make our materials highly efficient for selective CO2 capture, and unusually high CO2/N2 and CO2/CH4 selectivities are obtained. Furthermore, the adsorbents can be completely regenerated under mild conditions. Our materials may provide promising candidates for selective capture of CO2 from mixtures such as flue gas and natural gas.

  14. Molecular electronic-structure theory

    CERN Document Server

    Helgaker, Trygve; Jorgensen, Poul

    2013-01-01

    Ab initio quantum chemistry is increasingly paired with computational methods to solve intractable problems in chemistry and molecular physics. Now in a paperback edition, this comprehensive and technical work covers all the important aspects of modern molecular electronic-structure theory, clearly explaining quantum-mechanical methods and applications to molecular equilibrium structure, atomization energies, and reaction enthalpies. Extensive numerical examples illustrate each method described. An excellent resource for researchers in quantum chemistry and anyone interested in the theory and its applications.

  15. CO{sub 2} Capture from Flue Gas Using Solid Molecular Basket Sorbents

    Energy Technology Data Exchange (ETDEWEB)

    Fillerup, Eric; Zhang, Zhonghua; Peduzzi, Emanuela; Wang, Dongxiang; Guo, Jiahua; Ma, Xiaoliang; Wang, Xiaoxing; Song, Chunshan

    2012-08-31

    The objective of this project is to develop a new generation of solid, regenerable polymeric molecular basket sorbent (MBS) for more cost-efficient capture and separation of CO{sub 2} from flue gas of coal-fired power plants. The primary goal is to develop a cost-effective MBS sorbent with better thermal stability. To improve the cost-effectiveness of MBS, we have explored commercially available and inexpensive support to replace the more expensive mesoporous molecular sieves like MCM-41 and SBA- 15. In addition, we have developed some advanced sorbent materials with 3D pore structure such as hexagonal mesoporous silica (HMS) to improve the CO{sub 2} working capacity of MBS, which can also reduce the cost for the whole CO{sub 2} capture process. During the project duration, the concern regarding the desorption rate of MBS sorbents has been raised, because lower desorption rate increases the desorption time for complete regeneration of the sorbent which in turn leads to a lower working capacity if the regeneration time is limited. Thus, the improvement in the thermal stability of MBS became a vital task for later part of this project. The improvement in the thermal stability was performed via increasing the polymer density either using higher molecular weight PEI or PEI cross-linking with an organic compound. Moreover, we have used the computational approach to estimate the interaction of CO{sub 2} with different MBSs for the fundamental understanding of CO{sub 2} sorption, which may benefit the development, design and modification of the sorbents and the process.

  16. Molecular simulation of carbon dioxide adsorption for carbon capture and storage

    Science.gov (United States)

    Tenney, Craig M.

    Capture of CO2 from fossil fuel power plants and sequestration in unmineable coal seams are achievable methods for reducing atmospheric emissions of this greenhouse gas. To aid the development of effective CO2 capture and sequestration technologies, a series of molecular simulation studies were conducted to study the adsorption of CO2 and related species onto heterogeneous, solid adsorbents. To investigate the influence of surface heterogeneity upon adsorption behavior in activated carbons and coal, isotherms were generated via grand canonical Monte Carlo (GCMC) simulation for CO2 adsorption in slit-shaped pores with several variations of chemical and structural heterogeneity. Adsorption generally increased with increasing oxygen content and the presence of holes or furrows, which acted as preferred binding sites. To investigate the potential use of the flexible metal organic framework (MOF) Cu(BF4)2(bpy)2 (bpy=bipyridine) for CO2 capture, pure- and mixed-gas adsorption was simulated at conditions representative of power plant process streams. This MOF was chosen because it displays a novel behavior in which the crystal structure reversibly transitions from an empty, zero porosity state to a saturated, expanded state at the "gate pressure". Estimates of CO2 capacity above the gate pressure from GCMC simulations using a rigid MOF model showed good agreement with experiment. The CO2 adsorption capacity and estimated heats of adsorption are comparable to common physi-adsorbents under similar conditions. Mixed-gas simulations predicted CO2/N2 and CO2/H 2selectivities higher than typical microporous materials. To more closely investigate this gating effect, hybrid Monte-Carlo/molecular-dynamics (MCMD) was used to simulate adsorption using a flexible MOF model. Simulation cell volumes remained relatively constant at low gas pressures before increasing at higher pressure. Mixed-gas simulations predicted CO2/N 2 selectivities comparable to other microporous adsorbents. To

  17. A molecular-structure hypothesis.

    Science.gov (United States)

    Boeyens, Jan C A

    2010-11-01

    The self-similar symmetry that occurs between atomic nuclei, biological growth structures, the solar system, globular clusters and spiral galaxies suggests that a similar pattern should characterize atomic and molecular structures. This possibility is explored in terms of the current molecular structure-hypothesis and its extension into four-dimensional space-time. It is concluded that a quantum molecule only has structure in four dimensions and that classical (Newtonian) structure, which occurs in three dimensions, cannot be simulated by quantum-chemical computation.

  18. Molecular Structure of Membrane Tethers

    OpenAIRE

    Baoukina, Svetlana; Marrink, Siewert J.; Tieleman, D. Peter

    2012-01-01

    Membrane tethers are nanotubes formed by a lipid bilayer. They play important functional roles in cell biology and provide an experimental window on lipid properties. Tethers have been studied extensively in experiments and described by theoretical models, but their molecular structure remains unknown due to their small diameters and dynamic nature. We used molecular dynamics simulations to obtain molecular-level insight into tether formation. Tethers were pulled from single-component lipid b...

  19. Structure and Decay at Rapid Proton Capture Waiting Points

    Science.gov (United States)

    Hove, D.; Garrido, E.; Jensen, A. S.; Fynbo, H. O. U.; Fedorov, D. V.; Zinner, N. T.

    2017-01-01

    We investigate the region of the nuclear chart around A ˜eq 70 from a three-body perspective, where we compute reaction rates for the radiative capture of two protons. One key quantity is here the photon dissociation cross section for the inverse process where two protons are liberated from the borromean nucleus by photon bombardment. We find a number of peaks at low photon energy in this cross section where each peak is located at the energy corresponding to population of a three-body resonance. Thus, for these energies the decay or capture processes proceed through these resonances. However, the next step in the dissociation process still has the option of following several paths, that is either sequential decay by emission of one proton at a time with an intermediate two-body resonance as stepping stone, or direct decay into the continuum of both protons simultaneously. The astrophysical reaction rate is obtained by folding of the cross section as function of energy with the occupation probability for a Maxwell-Boltzmann temperature distribution. The reaction rate is then a function of temperature, and of course depending on the underlying three-body bound state and resonance structures. We show that a very simple formula at low temperature reproduces the elaborate numerically computed reaction rate.

  20. A DNAzyme-mediated logic gate for programming molecular capture and release on DNA origami.

    Science.gov (United States)

    Li, Feiran; Chen, Haorong; Pan, Jing; Cha, Tae-Gon; Medintz, Igor L; Choi, Jong Hyun

    2016-06-28

    Here we design a DNA origami-based site-specific molecular capture and release platform operated by a DNAzyme-mediated logic gate process. We show the programmability and versatility of this platform with small molecules, proteins, and nanoparticles, which may also be controlled by external light signals.

  1. Molecular electronic-structure theory

    CERN Document Server

    Helgaker, Trygve; Olsen, Jeppe

    2014-01-01

    Ab initio quantum chemistry has emerged as an important tool in chemical research and is appliced to a wide variety of problems in chemistry and molecular physics. Recent developments of computational methods have enabled previously intractable chemical problems to be solved using rigorous quantum-mechanical methods. This is the first comprehensive, up-to-date and technical work to cover all the important aspects of modern molecular electronic-structure theory. Topics covered in the book include: * Second quantization with spin adaptation * Gaussian basis sets and molecular-integral evaluati

  2. Molecular Simulation on Microstructure of Ionic Liquids in Capture of CO2

    Institute of Scientific and Technical Information of China (English)

    YUE Zhen-uo; LIU Xiao-min; ZHAO Yu-ling; ZHANG Xiao-chun; LU Xing-mei; ZHANG Suo-jiang

    2011-01-01

    Molecular dynamic simulation is used to study the microstructure of four kinds of ionic liquids (ILs),[Emim]PF6,[Emim][Tf2N],[PC6,6,6,14]PF6 and [PC6,6,6,14][Tf2N] in the capture process of CO2.Radial distribution function (RDF) and spatial distribution function (SDF) are used to analyze the microscopic properties of these systems.The calculated results show that the space distribution of CO2 around ILs determines the capability of ionic liquids for capturing CO2.Based on the analysis of SDF,CO2 and PF6- are overlapped partially around [Emim]+ in [Emim]PF6-CO2 mixture.When the anion is [Tf2N]-,cations are mainly distributed on one side of [Tf2N]- near N atom,and CO2 is concentrated on two sides near the fluoroalkylgroup (-CF3),and there is little overlapped district between cation and CO2.In [PC6,6,6,14]PF6-CO2 mixture,layered structure is found and CO2 is much nearer to PF6- than [PC6,6,6,14]+.Based on the analysis of RDF,in the phosphonium-based ILs,the highest distribution densities of anions and CO2 around cations are about 6 and 3 times as their average ones respectively,while in the imidazolium-based ILs,they are about 3 and 2 respectively,this means that the distributions of CO2 and anions around the imidazolium-based ILs are more evenly distributed than those around the phosphonium-bascd ILs.

  3. Prediction of molecular crystal structures

    CERN Document Server

    Beyer, T

    2001-01-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of parac...

  4. Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24

    Science.gov (United States)

    Owenson, Brian; Macelroy, Robert D.; Pohorille, Andrew

    1988-01-01

    The molecular dynamics of chloride capture from water by the tetraprotonated cryptand SC24 has been studied for the cases of 19 distances between the criptand and the chloride. The chloride capture is found to be characterized by a rapid cooperative change in the conformation of the cryptand when the Cl(-) begins to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, such that they point toward the chloride.

  5. Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs).

    Science.gov (United States)

    Cantsilieris, Stuart; Stessman, Holly A; Shendure, Jay; Eichler, Evan E

    2017-01-01

    Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform.

  6. Molecular Dynamics Simulations Capture the Misfolding of the Bovine Prion Protein at Acidic pH

    Directory of Open Access Journals (Sweden)

    Chin Jung Cheng

    2014-02-01

    Full Text Available Bovine spongiform encephalopathy (BSE, or mad cow disease, is a fatal neurodegenerative disease that is transmissible to humans and that is currently incurable. BSE is caused by the prion protein (PrP, which adopts two conformers; PrPC is the native innocuous form, which is α-helix rich; and PrPSc is the β-sheet rich misfolded form, which is infectious and forms neurotoxic species. Acidic pH induces the conversion of PrPC to PrPSc. We have performed molecular dynamics simulations of bovine PrP at various pH regimes. An acidic pH environment induced conformational changes that were not observed in neutral pH simulations. Putative misfolded structures, with nonnative β-strands formed in the flexible N-terminal domain, were found in acidic pH simulations. Two distinct pathways were observed for the formation of nonnative β-strands: at low pH, hydrophobic contacts with M129 nucleated the nonnative β-strand; at mid-pH, polar contacts involving Q168 and D178 facilitated the formation of a hairpin at the flexible N-terminus. These mid- and low pH simulations capture the process of nonnative β-strand formation, thereby improving our understanding of how PrPC misfolds into the β-sheet rich PrPSc and how pH factors into the process.

  7. Prediction of molecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Theresa

    2001-07-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  8. Proton transfer step in the carbon dioxide capture by monoethanol amine: a theoretical study at the molecular level.

    Science.gov (United States)

    Iida, Kenji; Sato, Hirofumi

    2012-02-23

    An aqueous solution of monoethanol amine (MEA) has been utilized in an industrial process of CO(2) absorption. The chemical reaction between CO(2) and MEA, which is employed in the process, consists of two steps. After the formation of the MEA-CO(2) complex ("capture"), a proton transfers from the complex to give a final product. In the present study, the overall mechanism of the reaction is discussed, especially focusing on the proton transfer step. Using RISM-SCF-SEDD, a hybrid method of electronic structure theory and statistical mechanics for molecular liquid, we clarified that the role of MEA as a base is crucial in the proton transfer step.

  9. Rapid discovery of peptide capture candidates with demonstrated specificity for structurally similar toxins

    Science.gov (United States)

    Sarkes, Deborah A.; Hurley, Margaret M.; Coppock, Matthew B.; Farrell, Mikella E.; Pellegrino, Paul M.; Stratis-Cullum, Dimitra N.

    2016-05-01

    Peptides have emerged as viable alternatives to antibodies for molecular-based sensing due to their similarity in recognition ability despite their relative structural simplicity. Various methods for peptide capture reagent discovery exist, including phage display, yeast display, and bacterial display. One of the primary advantages of peptide discovery by bacterial display technology is the speed to candidate peptide capture agent, due to both rapid growth of bacteria and direct utilization of the sorted cells displaying each individual peptide for the subsequent round of biopanning. We have previously isolated peptide affinity reagents towards protective antigen of Bacillus anthracis using a commercially available automated magnetic sorting platform with improved enrichment as compared to manual magnetic sorting. In this work, we focus on adapting our automated biopanning method to a more challenging sort, to demonstrate the specificity possible with peptide capture agents. This was achieved using non-toxic, recombinant variants of ricin and abrin, RiVax and abrax, respectively, which are structurally similar Type II ribosomal inactivating proteins with significant sequence homology. After only two rounds of biopanning, enrichment of peptide capture candidates binding abrax but not RiVax was achieved as demonstrated by Fluorescence Activated Cell Sorting (FACS) studies. Further sorting optimization included negative sorting against RiVax, proper selection of autoMACS programs for specific sorting rounds, and using freshly made buffer and freshly thawed protein target for each round of biopanning for continued enrichment over all four rounds. Most of the resulting candidates from biopanning for abrax binding peptides were able to bind abrax but not RiVax, demonstrating that short peptide sequences can be highly specific even at this early discovery stage.

  10. Ontological Status of Molecular Structure

    OpenAIRE

    Giuseppe Del Re

    1998-01-01

    Molecular structure (MS) has been treated as a convention or an epiphenomenon by physicists and quantum chemists interpreting the mathematical formalism of quantum mechanics as the essential reality criterion in the submicroscopic world (R2 world). This paper argues that, (a) even in the R2 world there is a class of entities which are real per se, even though they cannot be separated from their material support, and MS may belong to that class; (b) MS actualizes a particular molecule from the...

  11. Molecular motors: how to make models that can be used to convey the concept of molecular ratchets and thermal capture.

    Science.gov (United States)

    DoHarris, Lindsay; Giesler, Amanda; Humber, Brent; Sukumar, Aravin; Janssen, Luke J

    2011-06-01

    A wide variety of cellular processes use molecular motors, including processive motors that move along some form of track (e.g., myosin with actin, kinesin or dynein with tubulin) and polymerases that move along a template (e.g., DNA and RNA polymerases, ribosomes). In trying to understand how these molecular motors actually move, many apply their understanding of how man-made motors work: the latter use some form of energy to exert a force or torque on its load. However, quite a different mechanism has been proposed to possibly account for the movement of molecular motors. Rather than hydrolyzing ATP to push or pull their load, they might use their own thermal vibrational energy as well as that of their load and their environment to move the load, capturing those movements that occur along a desired vector or axis and resisting others; ATP hydrolysis is required to make backward movements impossible. This intriguing thermal capture or Brownian ratchet model is relatively more difficult to convey to students. In this report, we describe several teaching aids that are very easily constructed using widely available household materials to convey the concept of a molecular ratchet.

  12. Interactive Modelling of Molecular Structures

    Science.gov (United States)

    Rustad, J. R.; Kreylos, O.; Hamann, B.

    2004-12-01

    The "Nanotech Construction Kit" (NCK) [1] is a new project aimed at improving the understanding of molecular structures at a nanometer-scale level by visualization and interactive manipulation. Our very first prototype is a virtual-reality program allowing the construction of silica and carbon structures from scratch by assembling them one atom at a time. In silica crystals or glasses, the basic building block is an SiO4 unit, with the four oxygen atoms arranged around the central silicon atom in the shape of a regular tetrahedron. Two silicate units can connect to each other by their silicon atoms covalently bonding to one shared oxygen atom. Geometrically, this means that two tetrahedra can link at their vertices. Our program is based on geometric representations and uses simple force fields to simulate the interaction of building blocks, such as forming/breaking of bonds and repulsion. Together with stereoscopic visualization and direct manipulation of building blocks using wands or data gloves, this enables users to create realistic and complex molecular models in short amounts of time. The NCK can either be used as a standalone tool, to analyze or experiment with molecular structures, or it can be used in combination with "traditional" molecular dynamics (MD) simulations. In a first step, the NCK can create initial configurations for subsequent MD simulation. In a more evolved setup, the NCK can serve as a visual front-end for an ongoing MD simulation, visualizing changes in simulation state in real time. Additionally, the NCK can be used to change simulation state on-the-fly, to experiment with different simulation conditions, or force certain events, e.g., the forming of a bond, and observe the simulation's reaction. [1] http://graphics.cs.ucdavis.edu/~okreylos/ResDev/NanoTech

  13. CSMB | Center For Structural Molecular Biology

    Data.gov (United States)

    Federal Laboratory Consortium — The Center for Structural Molecular Biologyat ORNL is dedicated to developing instrumentation and methods for determining the 3-dimensional structures of proteins,...

  14. Fractal Structure of Molecular Clouds

    OpenAIRE

    Datta, Srabani

    2001-01-01

    Compelling evidence exists to show that the structure of molecular clouds is fractal in nature. In this paper, the author reiterates this view and, in addition, asserts that not only is cloud geometry fractal, but that they also have a common characteristic - they are similar in shape to the Horsehead nebula in Orion. This shape can be described by the Julia function f(x)= z^2 + c,where both z and c are complex quantities and c = -0.745429 + 0.113008i. The dynamical processes responsible for ...

  15. Rotational spectra and molecular structure

    CERN Document Server

    Wollrab, James E

    1967-01-01

    Physical Chemistry, A Series of Monographs: Rotational Spectra and Molecular Structure covers the energy levels and rotational transitions. This book is divided into nine chapters that evaluate the rigid asymmetric top molecules and the nuclear spin statistics for asymmetric tops. Some of the topics covered in the book are the asymmetric rotor functions; rotational transition intensities; classes of molecules; nuclear spin statistics for linear molecules and symmetric tops; and classical appearance of centrifugal and coriolis forces. Other chapters deal with the energy levels and effects of ce

  16. Molecular simulation studies of CO2 adsorption by carbon model compounds for carbon capture and sequestration applications.

    Science.gov (United States)

    Liu, Yangyang; Wilcox, Jennifer

    2013-01-02

    Effects of oxygen-containing surface functionalities on the adsorption of mixtures including CO(2)/CH(4), CO(2)/N(2), and CO(2)/H(2)O have been investigated in the current work. Together with Bader charge analysis, electronic structure calculations have provided the initial framework comprising both the geometry and corresponding charge information required to carry out statistical-based molecular simulations. The adsorption isotherms and selectivity of CO(2) from CO(2)/N(2), CO(2)/CH(4), and CO(2)/H(2)O gas mixtures were determined by grand canonical Monte Carlo simulations at temperature/pressure conditions relevant to carbon capture and sequestration applications. The interactions between the surfaces with induced polarity and nonpolar/polar molecules have been investigated. It has been observed that, due to the induced polarity of the surface functionalization, the selectivity of CO(2) over CH(4) increases from approximately 2 to higher than 5, and the selectivity of CO(2) over N(2) increases from approximately 5 to 20, especially in the low-pressure regime. However, water vapor will always preferentially adsorb over CO(2) in carbon-based systems containing oxygen functionalized surfaces at conditions relevant to carbon capture application. Molecular simulation results indicate that the surface chemistry in micropores is tunable thereby influencing the selectivity for enhanced uptake of CO(2).

  17. Flow Structures and Energy Capture from an Oscillating Hydrofoil

    Science.gov (United States)

    Franck, Jennifer; Frank, Sarah; Mandre, Shreyas

    2013-11-01

    The flow surrounding an oscillating hydrofoil in a uniform freestream is computationally investigated for hydrokinetic energy capture. Simulations are performed on an elliptical hydrofoil using 2D Direct Numerical Simulation (DNS) for low Reynolds number and 3D Large-Eddy Simulations (LES) for high Reynolds number simulations at 80,000. A non-inertial reference frame is utilized for rigid-body motion of the hydrofoil, which is prescribed a sinusoidal motion in pitch and heave. The kinematic parameters are varied and the resulting flow features are correlated with positive or negative energy capture. In an effort to optimize the stroke, variations in the sinusoidal heave and pitch signals are systematically explored and analyzed for future closed-loop control.

  18. Molecular diagnosis of putative Stargardt disease by capture next generation sequencing.

    Science.gov (United States)

    Zhang, Xiao; Ge, Xianglian; Shi, Wei; Huang, Ping; Min, Qingjie; Li, Minghan; Yu, Xinping; Wu, Yaming; Zhao, Guangyu; Tong, Yi; Jin, Zi-Bing; Qu, Jia; Gu, Feng

    2014-01-01

    Stargardt Disease (STGD) is the commonest genetic form of juvenile or early adult onset macular degeneration, which is a genetically heterogeneous disease. Molecular diagnosis of STGD remains a challenge in a significant proportion of cases. To address this, seven patients from five putative STGD families were recruited. We performed capture next generation sequencing (CNGS) of the probands and searched for potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes. Seven disease-causing mutations in ABCA4 and two in PROM1 were identified by CNGS, which provides a confident genetic diagnosis in these five families. We also provided a genetic basis to explain the differences among putative STGD due to various mutations in different genes. Meanwhile, we show for the first time that compound heterozygous mutations in PROM1 gene could cause cone-rod dystrophy. Our findings support the enormous potential of CNGS in putative STGD molecular diagnosis.

  19. Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals.

    Science.gov (United States)

    Wang, Linjun; Akimov, Alexey V; Chen, Liping; Prezhdo, Oleg V

    2013-11-07

    The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

  20. Anion-Functionalized Task-Specific Ionic Liquids: Molecular Origin of Change in Viscosity upon CO2 Capture.

    Science.gov (United States)

    Li, Ailin; Tian, Ziqi; Yan, Tianying; Jiang, De-en; Dai, Sheng

    2014-12-26

    The structure and dynamics of a task-specific ionic liquid (TSIL), trihexyl(tetradecyl)phosphonium imidazolate, before and after absorbing CO(2) were studied with a molecular dynamics (MD) simulation. This particular ionic liquid is one of several newly discovered azole-based TSILs for equimolar CO(2) capture. Unlike other TSILs whose viscosity increases drastically upon reaction with CO(2), its viscosity decreases after CO(2) absorption. This unique behavior was confirmed in our MD simulation. We find that after CO(2) absorption the translational dynamics of the whole system is accelerated, accompanied by an accelerated rotational dynamics of the cations. Radial distribution function and spatial distribution function analyses show that the anions become asymmetric after reaction with CO(2), and this causes the imbalance of the interaction between the positive and negative regions of the ions. The interaction between the phosphorus atom of the cation and oxygen atoms of the carboxyl group on the anion is enhanced, while that between the phosphorus atom and the naked nitrogen atom of the anion is weakened. The ion-pair correlation functions further support that the weakened interaction leads to faster dissociation of cation-anion pairs, thereby causing an accelerated dynamics. Hence, the asymmetry of anions influences the dynamics of the system and affects the viscosity. This insight may help design better TSILs with decreased viscosity for CO(2) capture.

  1. A viral-human interactome based on structural motif-domain interactions captures the human infectome.

    Directory of Open Access Journals (Sweden)

    Aldo Segura-Cabrera

    Full Text Available Protein interactions between a pathogen and its host are fundamental in the establishment of the pathogen and underline the infection mechanism. In the present work, we developed a single predictive model for building a host-viral interactome based on the identification of structural descriptors from motif-domain interactions of protein complexes deposited in the Protein Data Bank (PDB. The structural descriptors were used for searching, in a database of protein sequences of human and five clinically important viruses; therefore, viral and human proteins sharing a descriptor were predicted as interacting proteins. The analysis of the host-viral interactome allowed to identify a set of new interactions that further explain molecular mechanism associated with viral infections and showed that it was able to capture human proteins already associated to viral infections (human infectome and non-infectious diseases (human diseasome. The analysis of human proteins targeted by viral proteins in the context of a human interactome showed that their neighbors are enriched in proteins reported with differential expression under infection and disease conditions. It is expected that the findings of this work will contribute to the development of systems biology for infectious diseases, and help guide the rational identification and prioritization of novel drug targets.

  2. Polysaccharides: Molecular and Supramolecular Structures. Terminology.

    NARCIS (Netherlands)

    Heinze, Thomas; Petzold-Welcke, Katrin; Dam, van J.E.G.

    2012-01-01

    This chapter summarises important issues
    about the molecular and supramolecular structure
    of polysaccharides. It describes the terminology
    of polysaccharides systematically. The
    polysaccharides are divided regarding the
    molecular structures in glucans, polyoses,
    polysaccharid

  3. Capturing the age and spatial structures of migration

    NARCIS (Netherlands)

    Rogers, A; Raymer, J; Willekens, F

    2002-01-01

    In this paper we model the structures found in the level (generation) and allocation (distribution) components of age-specific and origin-destination-specific migration flows. For the examples, we examine the regional migration patterns in the USA for four periods: 1955-60, 1965-70, 1975-80, and 198

  4. Structure of Hot Molecular Cores

    OpenAIRE

    Rolffs, Rainer

    2011-01-01

    High-mass stars form deeply embedded in dense molecular gas, which they heat up and ionize due to their high energy output. During an early phase, the ionization is confined to small regions, and the stellar radiation is absorbed by dust. The high temperatures lead to the evaporation of ice mantles around dust grains, and many highly excited and complex molecules can be observed in these Hot Molecular Cores. At later stages, the whole molecular cloud is ionized and disrupted, and a...

  5. Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.

    Science.gov (United States)

    Laponogov, Ivan; Veselkov, Dennis A; Crevel, Isabelle M-T; Pan, Xiao-Su; Fisher, L Mark; Sanderson, Mark R

    2013-11-01

    Type II topoisomerases regulate DNA supercoiling and chromosome segregation. They act as ATP-operated clamps that capture a DNA duplex and pass it through a transient DNA break in a second DNA segment via the sequential opening and closure of ATPase-, G-DNA- and C-gates. Here, we present the first 'open clamp' structures of a 3-gate topoisomerase II-DNA complex, the seminal complex engaged in DNA recognition and capture. A high-resolution structure was solved for a (full-length ParE-ParC55)2 dimer of Streptococcus pneumoniae topoisomerase IV bound to two DNA molecules: a closed DNA gate in a B-A-B form double-helical conformation and a second B-form duplex associated with closed C-gate helices at a novel site neighbouring the catalytically important β-pinwheel DNA-binding domain. The protein N gate is present in an 'arms-wide-open' state with the undimerized N-terminal ParE ATPase domains connected to TOPRIM domains via a flexible joint and folded back allowing ready access both for gate and transported DNA segments and cleavage-stabilizing antibacterial drugs. The structure shows the molecular conformations of all three gates at 3.7 Å, the highest resolution achieved for the full complex to date, and illuminates the mechanism of DNA capture and transport by a type II topoisomerase.

  6. Crystalline molecular machines: Encoding supramolecular dynamics into molecular structure

    OpenAIRE

    Garcia-Garibay, Miguel A.

    2005-01-01

    Crystalline molecular machines represent an exciting new branch of crystal engineering and materials science with important implications to nanotechnology. Crystalline molecular machines are crystals built with molecules that are structurally programmed to respond collectively to mechanic, electric, magnetic, or photonic stimuli to fulfill specific functions. One of the main challenges in their construction derives from the picometric precision required for their mechanic operation within the...

  7. Molecular and Supermolecular Structure of Commercial Pyrodextrins.

    Science.gov (United States)

    Le Thanh-Blicharz, Joanna; Błaszczak, Wioletta; Szwengiel, Artur; Paukszta, Dominik; Lewandowicz, Grażyna

    2016-09-01

    Size exclusion chromatography with triple detection as well as infrared spectroscopy studies of commercially available pyrodextrins proved that these molecules are characterized not only by significantly lower molecular mass, in comparison to that of native starch, but also by increased branching. Therefore, pyrodextrins adopt a very compact structure in solution and show Newtonian behavior under shear in spite of their molecular masses of tens of thousands Daltons. The results also indicate that 50% reduction of digestibility of pyrodextrins is, to a minor extent, caused by formation of low-molecular color compounds containing carbonyl functional groups. The main reason is, as postulated in the literature, transglycosidation that leads to decreased occurrence of α-1,4-glycoside bonds in the molecular structure. In the process of dextrinization starch also undergoes changes in supermolecular structure, which, however, have no influence on digestibility. Likewise, the effect of formation of low-molecular colorful compounds containing carbonyl groups is not crucial.

  8. Differential Estimates of Southern Flying Squirrel (Glaucomys volans) Population Structure Based on Capture Method.

    Energy Technology Data Exchange (ETDEWEB)

    Laves, Kevin S.; Loeb, Susan C.

    2006-01-01

    ABSTRACT.—It is commonly assumed that population estimates derived from trapping small mammals are accurate and unbiased or that estimates derived from different capture methods are comparable. We captured southern flying squirrels (Glaucomys volans) using two methods to study their effect on red-cockaded woodpecker (Picoides borealis) reproductive success. Southern flying squirrels were captured at and removed from 30 red-cockaded woodpecker cluster sites during March to July 1994 and 1995 using Sherman traps placed in a grid encompassing a red-cockaded woodpecker nest tree and by hand from red-cockaded woodpecker cavities. Totals of 195 (1994) and 190 (1995) red-cockaded woodpecker cavities were examined at least three times each year. Trappability of southern flying squirrels in Sherman traps was significantly greater in 1995 (1.18%; 22,384 trap nights) than in 1994 (0.42%; 20,384 trap nights), and capture rate of southern flying squirrels in cavities was significantly greater in 1994 (22.7%; 502 cavity inspections) than in 1995 (10.8%; 555 cavity inspections). However, more southern flying squirrels were captured per cavity inspection than per Sherman trap night in both years. Male southern flying squirrels were more likely to be captured from cavities than in Sherman traps in 1994, but not in 1995. Both male and female juveniles were more likely to be captured in cavities than in traps in both years. In 1994 males in reproductive condition were more likely to be captured in cavities than in traps and in 1995 we captured significantly more reproductive females in cavities than in traps. Our data suggest that population estimates based solely on one trapping method may not represent true population size or structure of southern flying squirrels.

  9. Journal of Molecular Structure: THEOCHEM

    OpenAIRE

    Mundim, K.C.; Malbouisson, L.A.C.; Dorfman, S.; Fuks, D.; Van Humbeeck, J.; Liubich, V.

    2001-01-01

    Texto completo: acesso restrito. p. 191–197 The results of atomistic simulations of migration and formation energies of mono- and di-vacancies in bulk tungsten are presented in our paper. The interatomic potential for tungsten was extracted with the recursive procedure from ab initio calculations of the cohesive energy. A stochastic molecular dynamics using a generalized simulated annealing procedure was employed in the simulations. Calculated values of mono- and di-vacancies energy parame...

  10. Irreversible Change of the Pore Structure of ZIF-8 in Carbon Dioxide Capture with Water Coexistence

    DEFF Research Database (Denmark)

    Liu, Huang; Guo, Ping; Regueira Muñiz, Teresa

    2016-01-01

    showed an irreversible change of its framework, which occurs during the CO2 capture process. It was found that there is an irreversible chemical reaction among ZIF-8, water, and CO2, which creates both zinc carbonate (or zinc carbonate hydroxides) and single 2-methylimidazole crystals, and therefore......The performance of zeolitic imidazolate framework 8 (ZIF-8) for CO2 capture under three different conditions (wetted ZIF-8, ZIF-8/water slurry, and ZIF-8/water-glycol slurry) was systemically investigated. This investigation included the study of the pore structure stability of ZIF-8 by using X...... the pore structure of ZIF-8 collapses. It is suggested therefore that care must be taken when using ZIF-8 or products containing ZIF-8 for gas capture, gas separation, or other applications where both water and acid gases coexist....

  11. Mercury capture by selected Bulgarian fly ashes: Influence of coal rank and fly ash carbon pore structure on capture efficiency

    Science.gov (United States)

    Kostova, I.J.; Hower, J.C.; Mastalerz, Maria; Vassilev, S.V.

    2011-01-01

    Mercury capture by fly ash C was investigated at five lignite- and subbituminous-coal-burning Bulgarian power plants (Republika, Bobov Dol, Maritza East 2, Maritza East 3, and Sliven). Although the C content of the ashes is low, never exceeding 1.6%, the Hg capture on a unit C basis demonstrates that the low-rank-coal-derived fly ash carbons are more efficient in capturing Hg than fly ash carbons from bituminous-fired power plants. While some low-C and low-Hg fly ashes do not reveal any trends of Hg versus C, the 2nd and, in particular, the 3rd electrostatic precipitator (ESP) rows at the Republika power plant do have sufficient fly ash C range and experience flue gas sufficiently cool to capture measurable amounts of Hg. The Republika 3rd ESP row exhibits an increase in Hg with increasing C, as observed in other power plants, for example, in Kentucky power plants burning Appalachian-sourced bituminous coals. Mercury/C decreases with an increase in fly ash C, suggesting that some of the C is isolated from the flue gas stream and does not contribute to Hg capture. Mercury capture increases with an increase in Brunauer-Emmett-Teller (BET) surface area and micropore surface area. The differences in Hg capture between the Bulgarian plants burning low-rank coal and high volatile bituminous-fed Kentucky power plants suggests that the variations in C forms resulting from the combustion of the different ranks also influence the efficiency of Hg capture. ?? 2010 Elsevier Ltd.

  12. Capturing the transient species at the electrode-electrolyte interface by in situ dynamic molecular imaging

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Jiachao; Zhou, Yufan; Hua, Xin; Liu, Songqin; Zhu, Zihua; Yu, Xiao-Ying

    2016-09-01

    The electrochemical interface between the solid electrode and liquid electrolyte has long been studied because of its importance in electrical energy storage, material synthesis, catalysis, and energy conversions.1 However, such interfaces are complex and extremely difficult to observe directly and are poorly under-stood due to lack of true in situ tools.2 Although electrochemical techniques have been widely used to investigate such interfaces, they are based on macroscopic models or current changes that could not provide direct ionic and molecular information of the interfacial structure. Many in situ and ex situ spectroscopy and microscopy techniques have been used to study the solid–liquid (s–l) interface.3,4 In situ TEM in sealed liquid cells has notably become a popular choice to provide structural information of s–l at the atomic level.5,6 However, real-time spatial mapping of the ionic and molecular intermediate species at the dynamic inter-face still remains a key challenge.

  13. Solvents for CO2 capture. Structure-activity relationships combined with vapour-liquid-equilibrium measurements

    NARCIS (Netherlands)

    Mergler, Y.L.; Rumley-Van Gurp, R.; Brasser, P.; Koning, M.C. de; Goetheer, E.L.V.

    2011-01-01

    In this study a systematic approach was chosen to test and characterize amine systems for CO2 capture. Vapour-liquid-equilibrium measurements were performed on a homologue series of amines, with ethylene amine as base structure. Various functional groups were used that ranged in chemical and physica

  14. Quantum mechanics of molecular structures

    CERN Document Server

    Yamanouchi, Kaoru

    2012-01-01

    At a level accessible to advanced undergraduates, this textbook explains the fundamental role of quantum mechanics in determining the structure, dynamics, and other properties of molecules. Readers will come to understand the quantum-mechanical basis for harmonic oscillators, angular momenta and scattering processes. Exercises are provided to help readers deepen their grasp of the essential phenomena.

  15. Dynamics of fragment capture for cluster structures of weakly bound 7Li

    Directory of Open Access Journals (Sweden)

    Shrivastava A.

    2013-12-01

    Full Text Available Role of cluster structures of 7Li on reaction dynamics have been studied by performing exclusive measurements of prompt-γ rays from residues with scattered particles at energy, E/Vb = 1.6, with 198Pt target. Yields of the residues resulting after capture of t and 4,5,6He, corresponding to different excitation energies of the composite system were estimated. The results were compared with three body classical-dynamical model for breakup fusion, constrained by the measured fusion, α and t capture cross-sections. The cross-section of residues from capture of α and t agreed well with the prediction of the model showing dominance of the two step process - breakup fusion, while those from tightly bound 6He showed massive transfer to be the dominant mechanism.

  16. Hamiltonian Mapping Revisited: Calibrating Minimalist Models to Capture Molecular Recognition by Intrinsically Disordered Proteins.

    Science.gov (United States)

    Law, Sean M; Ahlstrom, Logan S; Panahi, Afra; Brooks, Charles L

    2014-10-02

    Molecular recognition by intrinsically disordered proteins (IDPs) plays a central role in many critical cellular processes. Toward achieving detailed mechanistic understanding of IDP-target interactions, here we employ the "Hamiltonian mapping" methodology, which is rooted in the weighted histogram analysis method (WHAM), for the fast and efficient calibration of structure-based models in studies of IDPs. By performing reference simulations on a given Hamiltonian, we illustrate for two model IDPs how this method can extrapolate thermodynamic behavior under a range of modified Hamiltonians, in this case representing changes in the binding affinity (Kd) of the system. Given sufficient conformational sampling in a single trajectory, Hamiltonian mapping accurately reproduces Kd values from direct simulation. This method may be generally applied to systems beyond IDPs in force field optimization and in describing changes in thermodynamic behavior as a function of external conditions for connection with experiment.

  17. [Oligoglycine surface structures: molecular dynamics simulation].

    Science.gov (United States)

    Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V

    2010-01-01

    The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.

  18. Likelihood analysis of spatial capture-recapture models for stratified or class structured populations

    Science.gov (United States)

    Royle, J. Andrew; Sutherland, Christopher S.; Fuller, Angela K.; Sun, Catherine C.

    2015-01-01

    We develop a likelihood analysis framework for fitting spatial capture-recapture (SCR) models to data collected on class structured or stratified populations. Our interest is motivated by the necessity of accommodating the problem of missing observations of individual class membership. This is particularly problematic in SCR data arising from DNA analysis of scat, hair or other material, which frequently yields individual identity but fails to identify the sex. Moreover, this can represent a large fraction of the data and, given the typically small sample sizes of many capture-recapture studies based on DNA information, utilization of the data with missing sex information is necessary. We develop the class structured likelihood for the case of missing covariate values, and then we address the scaling of the likelihood so that models with and without class structured parameters can be formally compared regardless of missing values. We apply our class structured model to black bear data collected in New York in which sex could be determined for only 62 of 169 uniquely identified individuals. The models containing sex-specificity of both the intercept of the SCR encounter probability model and the distance coefficient, and including a behavioral response are strongly favored by log-likelihood. Estimated population sex ratio is strongly influenced by sex structure in model parameters illustrating the importance of rigorous modeling of sex differences in capture-recapture models.

  19. Exploring RNA structure by integrative molecular modelling

    DEFF Research Database (Denmark)

    Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

    2010-01-01

    RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...... in three dimensions (3D) and used as building blocks assembled manually during a bioinformatic interactive process. Comparing the models to the corresponding crystal structures has validated the method as being powerful to predict the RNA topology and architecture while being less accurate regarding...

  20. Study on Molecular Structure of TATFIW

    Institute of Scientific and Technical Information of China (English)

    LI Li-jie; LI Yan-yue; LU Lin; CHEN Shu-sen; CHEN Hua-xiong; JIN Shao-hua; ZHAO Xin-qi

    2008-01-01

    The molecular structure of triacetyltriformylhexaazaisowurtzitane (TATFIW) is optimized by using Gaussian98 software package at the level of B3LYP/6-31G. Theoretically analyzed the TATFIW molecular structure, namely bond length, bond angle, dihedral angle and the charge distribution, it was found that hydrogen bond exists in TATFIW, and acetyl is easily taken off than formyl in the nitrolysis with nitric-sulfuric mixed acid. These results mentioned above agree with experiments. The comparison of calculated vibration frequency and intensity with the experiment values are also given.

  1. Rotational structure in molecular infrared spectra

    CERN Document Server

    di Lauro, Carlo

    2013-01-01

    Recent advances in infrared molecular spectroscopy have resulted in sophisticated theoretical and laboratory methods that are difficult to grasp without a solid understanding of the basic principles and underlying theory of vibration-rotation absorption spectroscopy. Rotational Structure in Molecular Infrared Spectra fills the gap between these recent, complex topics and the most elementary methods in the field of rotational structure in the infrared spectra of gaseous molecules. There is an increasing need for people with the skills and knowledge to interpret vibration-rotation spectra in ma

  2. Structural basis for hemoglobin capture by Staphylococcus aureus cell-surface protein, IsdH.

    Science.gov (United States)

    Krishna Kumar, Kaavya; Jacques, David A; Pishchany, Gleb; Caradoc-Davies, Tom; Spirig, Thomas; Malmirchegini, G Reza; Langley, David B; Dickson, Claire F; Mackay, Joel P; Clubb, Robert T; Skaar, Eric P; Guss, J Mitchell; Gell, David A

    2011-11-01

    Pathogens must steal iron from their hosts to establish infection. In mammals, hemoglobin (Hb) represents the largest reservoir of iron, and pathogens express Hb-binding proteins to access this source. Here, we show how one of the commonest and most significant human pathogens, Staphylococcus aureus, captures Hb as the first step of an iron-scavenging pathway. The x-ray crystal structure of Hb bound to a domain from the Isd (iron-regulated surface determinant) protein, IsdH, is the first structure of a Hb capture complex to be determined. Surface mutations in Hb that reduce binding to the Hb-receptor limit the capacity of S. aureus to utilize Hb as an iron source, suggesting that Hb sequence is a factor in host susceptibility to infection. The demonstration that pathogens make highly specific recognition complexes with Hb raises the possibility of developing inhibitors of Hb binding as antibacterial agents.

  3. Anatomy of molecular structures in $^{20}$Ne

    CERN Document Server

    Zhou, E F; Li, Z P; Meng, J; Ring, P

    2015-01-01

    We present a beyond mean-field study of clusters and molecular structures in low-spin states of $^{20}$Ne with a multireference relativistic energy density functional, where the dynamical correlation effects of symmetry restoration and quadrupole-octupole shapes fluctuation are taken into account with projections on parity, particle number and angular momentum in the framework of the generator coordinate method. Both the energy spectrum and the electric multipole transition strengths for low-lying parity-doublet bands are better reproduced after taking into account the dynamical octupole vibration effect. Consistent with the finding in previous antisymmetrized molecular dynamics studies, a rotation-induced dissolution of the $\\alpha+^{16}$O molecular structure in $^{20}$Ne is predicted and this peculiar phenomenon is partially attributed to the special deformation-dependent moment of inertia.

  4. Molecular Structure of Human-Liver Glycogen.

    Directory of Open Access Journals (Sweden)

    Bin Deng

    Full Text Available Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets.

  5. Molecular Structure of Human-Liver Glycogen

    Science.gov (United States)

    Deng, Bin; Sullivan, Mitchell A.; Chen, Cheng; Li, Jialun; Powell, Prudence O.; Hu, Zhenxia; Gilbert, Robert G.

    2016-01-01

    Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets. PMID:26934359

  6. Low-cost structured-light based 3D capture system design

    Science.gov (United States)

    Dong, Jing; Bengtson, Kurt R.; Robinson, Barrett F.; Allebach, Jan P.

    2014-03-01

    Most of the 3D capture products currently in the market are high-end and pricey. They are not targeted for consumers, but rather for research, medical, or industrial usage. Very few aim to provide a solution for home and small business applications. Our goal is to fill in this gap by only using low-cost components to build a 3D capture system that can satisfy the needs of this market segment. In this paper, we present a low-cost 3D capture system based on the structured-light method. The system is built around the HP TopShot LaserJet Pro M275. For our capture device, we use the 8.0 Mpixel camera that is part of the M275. We augment this hardware with two 3M MPro 150 VGA (640 × 480) pocket projectors. We also describe an analytical approach to predicting the achievable resolution of the reconstructed 3D object based on differentials and small signal theory, and an experimental procedure for validating that the system under test meets the specifications for reconstructed object resolution that are predicted by our analytical model. By comparing our experimental measurements from the camera-projector system with the simulation results based on the model for this system, we conclude that our prototype system has been correctly configured and calibrated. We also conclude that with the analytical models, we have an effective means for specifying system parameters to achieve a given target resolution for the reconstructed object.

  7. Molecular sieve supported ionic liquids as efficient adsorbent for CO2 capture

    Directory of Open Access Journals (Sweden)

    Yang Na

    2015-01-01

    Full Text Available [NH3e-mim][BF4], [OHe-mim][BF4] and [HOEAm] were selected and supported onto molecular sieves NaY, USY, SAPO-34 and MCM-41, to prepare supported ionic liquids. It was found that [NH3e-mim][BF4]/NaY has excellent CO2 adsorption performance, with adsorption capacity of 0.108 mmolCO2/g. This paper investigates the optimal adsorption conditions and recyclability of [NH3e-mim][BF4]/NaY. The results show that [NH3e-mim][BF4]/NaY has good CO2 adsorption under the condition of 20°C and 20% ILs loading amount. By vacuum heating, CO2 adsorption capacity reaches 0.451mmolCO2/g at fifth runs and reduces to 0.29mmolCO2/g at tenth runs. The structure and characterization of the [NH3e-mim][BF4]/NaY was examined by FT-IR, XRD, SEM and TG-DSC. TG-DSC also shows that it has good thermostability below 50°C.

  8. Structural Analysis of Molecular Clouds: Dendrograms

    CERN Document Server

    Rosolowsky, E W; Kauffmann, J; Goodman, A A

    2008-01-01

    We demonstrate the utility of dendrograms at representing the essential features of the hierarchical structure of the isosurfaces for molecular line data cubes. The dendrogram of a data cube is an abstraction of the changing topology of the isosurfaces as a function of contour level. The ability to track hierarchical structure over a range of scales makes this analysis philosophically different from local segmentation algorithms like CLUMPFIND. Points in the dendrogram structure correspond to specific volumes in data cubes defined by their bounding isosurfaces. We further refine the technique by measuring the properties associated with each isosurface in the analysis allowing for a multiscale calculation of molecular gas properties. Using COMPLETE 13CO(1-0) data from the L1448 region in Perseus and mock observations of a simulated data cube, we identify regions that have a significant contribution by self-gravity to their energetics on a range of scales. We find evidence for self-gravitation on all spatial sc...

  9. Imaging molecular structure with photoelectron diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Boll, Rebecca

    2014-07-02

    The possibility to study the structure of polyatomic gas-phase molecules by photoelectron diffraction is investigated with the goal of developing a method capable of imaging ultrafast photochemical reactions with femtosecond temporal and sub-Angstroem spatial resolution. The fluorine 1s-level of adiabatically laser-aligned 1-ethynyl-4-fluorobenzene (C{sub 8}H{sub 5}F) molecules was ionized by X-ray pulses from the Linac Coherent Light Source Free-Electron Laser, and the angular distributions of photoelectrons with kinetic energies between 30 and 60 eV were recorded by velocity map imaging. Comparison with density functional theory calculations allows relating the measured distributions to the molecular structure. The results of an IR-pump, X-ray-probe experiment on aligned 1,4-dibromobenzene (C{sub 6}H{sub 4}Br{sub 2})molecules are presented to explore the potential of photoelectron diffraction for time-resolved imaging. The influence of the alignment laser pulse on the pumping and probing step is discussed. Laser-alignment is contrasted with determination of the molecular orientation by photoelectron-photoion coincidences for an exemplary data set on 1-ethynyl-4-fluorobenzene molecules recorded at the PETRA III synchrotron. Both methods are evaluated with respect to their applicability to record time-dependent snapshots of molecular structure. The results obtained in this work indicate possible future avenues for investigating ultrafast molecular dynamics using X-ray Free-Electron Lasers.

  10. Molecular and structural analysis of viscoelastic properties

    Science.gov (United States)

    Yapp, Rebecca D.; Kalyanam, Sureshkumar; Insana, Michael F.

    2007-03-01

    Elasticity imaging is emerging as an important tool for breast cancer detection and monitoring of treatment. Viscoelastic image contrast in breast lesions is generated by disease specific processes that modify the molecular structure of connective tissues. We showed previously that gelatin hydrogels exhibit mechanical behavior similar to native collagen found in breast tissue and therefore are suitable as phantoms for elasticity imaging. This paper summarizes our study of the viscoelastic properties of hydrogels designed to discover molecular-scale sources of elasticity image contrast.

  11. Intermediate structure in the /sup 238/U neutron capture cross section

    Energy Technology Data Exchange (ETDEWEB)

    Perez, R.B.; de Saussure, G.

    1975-10-01

    Recent measurements of the /sup 238/U neutron capture cross section show large fluctuations in the unresolved resonance region. To test whether or not the observed long-range fluctuation of the neutron capture represent departures from the compound nuclear model, the Wald-Wolfowitz runs and correlation tests were applied to the /sup 238/U neutron capture data obtained at ORELA. The Wald-Wolfowitz runs test deals with the statistic, R, which is the number of unbroken sequences of data points above or below a given reference line. This statistic is to be compared with the expected value of runs E(R) +- sigma(R) arising from randomly distributed data. In the correlation test we have computed the first serial correlation coefficient of the data as well as its expected value and variance for a set of random data. In both tests one computes the probability, P, for the given statistical entity to depart from its expected value by more than epsilon standard deviations. Both tests confirm the presence of intermediate structure between 5 and 100 keV. The range of the structure far exceeds the width of the experimental resolution and level widths. 3 tables, 2 figures. (auth)

  12. Role of the cluster structure of {sup 7}Li in the dynamics of fragment capture

    Energy Technology Data Exchange (ETDEWEB)

    Shrivastava, A., E-mail: aradhana@barc.gov.in [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Navin, A. [GANIL, CEA/DSM - CNRS/IN2P3, Bd Henri Becquerel, BP 55027, F-14076 Caen Cedex 5 (France); Diaz-Torres, A. [ECT, Villa Tambosi, I-38123 Villazzano, Trento (Italy); Nanal, V. [DNAP, Tata Institute of Fundamental Research, Mumbai 400005 (India); Ramachandran, K. [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Rejmund, M. [GANIL, CEA/DSM - CNRS/IN2P3, Bd Henri Becquerel, BP 55027, F-14076 Caen Cedex 5 (France); Bhattacharyya, S. [Variable Energy Cyclotron Centre, 1/AF Bidhan Nagar, Kolkata 700064 (India); Chatterjee, A.; Kailas, S. [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Lemasson, A. [GANIL, CEA/DSM - CNRS/IN2P3, Bd Henri Becquerel, BP 55027, F-14076 Caen Cedex 5 (France); Palit, R. [DNAP, Tata Institute of Fundamental Research, Mumbai 400005 (India); Parkar, V.V. [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Pillay, R.G. [DNAP, Tata Institute of Fundamental Research, Mumbai 400005 (India); Rout, P.C. [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Sawant, Y. [DNAP, Tata Institute of Fundamental Research, Mumbai 400005 (India)

    2013-01-08

    Exclusive measurements of prompt {gamma}-rays from the heavy-residues with various light charged particles in the {sup 7}Li + {sup 198}Pt system, at an energy near the Coulomb barrier (E/V{sub b}{approx}1.6) are reported. Recent dynamic classical trajectory calculations, constrained by the measured fusion, {alpha}- and t-capture cross-sections have been used to explain the excitation energy dependence of the residue cross-sections. These calculations distinctly illustrate a two-step process, breakup followed by fusion, in case of the capture of t and {alpha} clusters; whereas for {sup 6}He+p and {sup 5}He+d configurations, massive transfer is inferred to be the dominant mechanism. The present work clearly demonstrates the role played by the cluster structures of {sup 7}Li in understanding the reaction dynamics at energies around the Coulomb barrier.

  13. Role of the cluster structure of $^7$Li in the dynamics of fragment capture

    CERN Document Server

    Shrivastava, A; Diaz-Torres, A; Nanal, V; Ramachandran, K; Rejmund, M; Bhattacharyya, S; Chatterjee, A; Kailas, S; Lemasson, A; Palit, R; Parkar, V V; Pillay, R G; Rout, P C; Sawant, Y

    2012-01-01

    Exclusive measurements of prompt $\\gamma$-rays from the heavy-residues with various light charged particles in the $^7$Li + $^{198}$Pt system, at an energy near the Coulomb barrier (E/$V_b$ $\\sim$ 1.6) are reported. Recent dynamic classical trajectory calculations, constrained by the measured fusion, $\\alpha$ and $t$ capture cross-sections have been used to explain the excitation energy dependence of the residue cross-sections. These calculations distinctly illustrate a two step process, breakup followed by fusion in case of the capture of $t$ and $\\alpha$ clusters; whereas for $^{6}$He + $p$ and $^{5}$He + $d$ configurations, massive transfer is inferred to be the dominant mechanism. The present work clearly demonstrates the role played by the cluster structures of $^7$Li in understanding the reaction dynamics at energies around the Coulomb barrier.

  14. Molecular simulations of nitrogen-doped hierarchical carbon adsorbents for post-combustion CO2 capture.

    Science.gov (United States)

    Psarras, Peter; He, Jiajun; Wilcox, Jennifer

    2016-10-19

    A present challenge in the mitigation of anthropogenic CO2 emissions involves the design of less energy- and water-intensive capture technologies. Sorbent-based capture represents a promising solution, as these materials have negligible water requirements and do not incur the heavy energy penalties associated with solvent regeneration. However, to be considered competitive with traditional technologies (i.e., MEA capture), these sorbents must exhibit a high CO2 loading capacity and high CO2/N2 selectivity. It has been reported that ultramicroporous character and surface nitrogen functionality are of great importance to the enhancement of CO2 capacity and CO2/N2 selectivity. However, the role of pore size in combination with surface functionality in the enhancement of these properties remains unclear. To investigate these effects, grand canonical Monte Carlo (GCMC) simulations were carried out on pure and N-functionalized 3-layer graphitic slit-pore models and compared to experimental results for two high performing materials reported elsewhere. We show that the quaternary, pyridinic, and especially the oxidized pyridinic group lend to enhanced performance, with the latter providing exceptional CO2 loading (4.31 mmol g(-1)) and CO2/N2 selectivity (138.3 : 1). Increasing surface nitrogen content resulted in enhanced loading and excellent CO2/N2 selectivity (45.8 : 1-55.9 : 1), provided that the sorbent has significant ultramicroporous character. Additionally, we elucidate a threshold pore width, under which N-functionalization becomes increasingly influential on performance parameters, and show how this threshold changes with application (PC vs. NGCC capture). Finally, we propose that an alternative functionality - the nitroso group - may be responsible for the enhanced performance of some recent materials reported in the literature.

  15. Turbulent Velocity Structure in Molecular Clouds

    CERN Document Server

    Ossenkopf, V; Ossenkopf, Volker; Low, Mordecai-Mark Mac

    2002-01-01

    We compare velocity structure observed in the Polaris Flare molecular cloud at scales ranging from 0.015 pc to 20 pc to the velocity structure of a suite of simulations of supersonic hydrodynamic and MHD turbulence computed with the ZEUS MHD code. We examine different methods of characterising the structure, including a scanning-beam size-linewidth relation, structure functions, velocity and velocity difference probability distribution functions (PDFs), and the Delta-variance wavelet transform, and use them to compare models and observations. The Delta-variance is most sensitive in detecting characteristic scales and varying scaling laws, but is limited in the observational application by its lack of intensity weighting. We compare the true velocity PDF in our models to simulated observations of velocity centroids and average line profiles in optically thin lines, and find that the line profiles reflect the true PDF better. The observed velocity structure is consistent with supersonic turbulence showing a com...

  16. Interatomic Coulombic electron capture in atomic, molecular, and quantum dot systems

    Directory of Open Access Journals (Sweden)

    Bande Annika

    2015-01-01

    Full Text Available The interatomic Coulombic electron capture (ICEC process has recently been predicted theoretically for clusters of atoms and molecules. For an atom A capturing an electron e(ε it competes with the well known photorecombination, because in an environment of neutral or anionic neighboring atoms B, A can transfer its excess energy in the ultrafast ICEC process to B which is then ionized. The cross section for e(ε + A + B → A− + B+ + e(ε′ has been obtained in an asymptotic approximation based on scattering theory for several clusters [1,2]. It was found that ICEC starts dominating the PR for distances among participating species of nanometers and lower. Therefore, we believe that the ICEC process might be of importance in the atmosphere, in biological systems, plasmas, or in nanostructured materials. As an example for the latter, ICEC has been investigated by means of electron dynamics in a model potential for semiconductor double quantum dots (QDs [3]. In the simplest case one QD captures an electron while the outgoing electron is emitted from the other. The reaction probability for this process was found to be relatively large.

  17. Effects of problem characteristics, capturing problem structure and using analogies on high school students’ success on problem-solving

    OpenAIRE

    Pedro GARCÍA GALLEGO; Sanjosé López, Vicente; SOLAZ-PORTOLÉS, Joan Josep

    2015-01-01

    This study analyses the influence of academic level, academic itinerary, word problem’s context and structure, capturing problem structure, and using analogies on problem-solving. A factorial design was used with one within-subjects variable and several between-subjects variables, which have been selected depending on the hypothesis in question. Two types of booklets containing two word problems and questions about capturing problem structure and using analogies in problem solving, were admin...

  18. 2004 Reversible Associations in Structure & Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  19. Laser slowing of CaF molecules to near the capture velocity of a molecular MOT

    Science.gov (United States)

    Hemmerling, Boerge; Chae, Eunmi; Ravi, Aakash; Anderegg, Loic; Drayna, Garrett K.; Hutzler, Nicholas R.; Collopy, Alejandra L.; Ye, Jun; Ketterle, Wolfgang; Doyle, John M.

    2016-09-01

    Laser slowing of CaF molecules down to the capture velocity of a magneto-optical trap for molecules is achieved. Starting from a two-stage buffer gas beam source, we apply frequency-broadened ‘white-light’ slowing and observe approximately 6× {10}4 CaF molecules in a single pulse with velocities 10 ± 4 m s-1. CaF is a candidate for collisional studies in the mK regime. This work represents a significant step towards magneto-optical trapping of CaF.

  20. Laser slowing of CaF molecules to near the capture velocity of a molecular MOT

    CERN Document Server

    Hemmerling, Boerge; Ravi, Aakash; Anderegg, Loic; Drayna, Garrett K; Hutzler, Nicholas R; Collopy, Alejandra L; Ye, Jun; Ketterle, Wolfgang; Doyle, John M

    2016-01-01

    Laser slowing of CaF molecules down to the capture velocity of a magneto-optical trap (MOT) for molecules is achieved. Starting from a two-stage buffer gas beam source, we apply frequency-broadened "white-light" slowing and observe approximately 6x10^4 CaF molecules with velocities near 10\\,m/s. CaF is a candidate for collisional studies in the mK regime. This work represents a significant step towards magneto-optical trapping of CaF.

  1. Molecular markers of extracellular matrix remodeling in glioblastoma vessels: microarray study of laser-captured glioblastoma vessels.

    Science.gov (United States)

    Pen, Ally; Moreno, Maria J; Martin, Joel; Stanimirovic, Danica B

    2007-04-15

    Glioblastoma multiforme (GBM) are the most malignant and vascularized brain tumors. The aberrant vascular phenotype of GBM could be exploited for diagnosis or therapeutic targeting. This study identified new molecular markers of GBM vessels, using a combination of laser capture microdissection (LCM) microscopy, RNA amplification, and microarray analyses to compare vessels from nonmalignant human brain and GBM tumors. Forty-two genes were differentially expressed in GBM vessels compared to nonmalignant brain vessels. Validation of differentially expressed genes was performed by literature mining, Q-PCR, and immunohistochemistry. Among the differentially expressed genes, only 64% were previously associated with vessels, angiogenesis, gliomas, and/or cancer. The upregulation of genes encoding secreted extracellular proteins IGFBP7 and SPARC was confirmed by Q-PCR in LCM-captured vessels. Whereas SPARC and IGFBP7 protein were absent in nonmalignant brain vessels, a distinct immunoreactivity patterns were observed in GBM sections whereby SPARC was strongly expressed in perivascular cells adjacent to GBM vessels while GBM endothelial cells were immunostained for IGFBP7. IGFBP7 immunoreactivity was also detected on the abluminal side of GBM vessels deposited between strands of vascular basal lamina. The study discerns unique molecular characteristics of GBM vessels compared with nonmalignant brain vessels that could potentially be used for diagnostic or therapeutic purposes.

  2. Capturing relativistic wakefield structures in plasmas using ultrashort high-energy electrons as a probe

    Science.gov (United States)

    Zhang, C. J.; Hua, J. F.; Xu, X. L.; Li, F.; Pai, C.-H.; Wan, Y.; Wu, Y. P.; Gu, Y. Q.; Mori, W. B.; Joshi, C.; Lu, W.

    2016-07-01

    A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of the wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime, and it can also qualitatively map the major features of nonlinear wakes. The capturing of the injection in a nonlinear wake is demonstrated through 3D PIC simulations as an example of the application of this new method.

  3. Capturing relativistic wakefield structures in plasmas using ultrashort high-energy electrons as a probe.

    Science.gov (United States)

    Zhang, C J; Hua, J F; Xu, X L; Li, F; Pai, C-H; Wan, Y; Wu, Y P; Gu, Y Q; Mori, W B; Joshi, C; Lu, W

    2016-07-11

    A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of the wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime, and it can also qualitatively map the major features of nonlinear wakes. The capturing of the injection in a nonlinear wake is demonstrated through 3D PIC simulations as an example of the application of this new method.

  4. Studying the capture cross sections of structural elements by measuring neutron balance in multiplying media

    Energy Technology Data Exchange (ETDEWEB)

    Golubev, V.N.; Dulin, V.A.; Kazanskij, Yu.A.

    1986-10-01

    To refine neutron capture cross sections for structural elements used in fast power reactors the neutron balance in multiplying media with neutron multiplication factor K/sub infinity/=1 has been studied at KBR and ERMINE critical assemblies. Reactivity of multiplying cells consisting of uranium and structural elements is measured as well as reactivity coefficients of individual structural materials. Corresponding calculations are performed using the versions of group constants applied in designing the fast reactors in the USSR and France. The CARNAVAL 4 constant version predicts well a fraction of neutron absorptions in steel and nickel for the spectra typical for a power reactor (ERMINE assembly). For softer spectra (KBR assembly) the agreement with experiment is better when the BNAB-78 constant version is used.

  5. Boron Subphthalocyanine Based Molecular Triad Systems for the Capture of Solar Energy.

    Science.gov (United States)

    Storm, Freja E; Olsen, Stine T; Hansen, Thorsten; De Vico, Luca; Jackson, Nicholas E; Ratner, Mark A; Mikkelsen, Kurt V

    2016-10-06

    In this study a number of chromophores based on boron subphthalocyanines are investigated for use in the future design of organic photovoltaic devices based on molecular triad systems. The computational study is performed at the TD-DFT CAM-B3LYP/6-311G(d) level of theory. The absorption spectra of these chromophores are simulated using TD-DFT and compared to experimental results. All investigated chromophores absorb light in the visible range and thus are suitable for absorption of sunlight in solar cell applications. On the basis of energy-level alignments, suitable combinations of moieties for a molecular triad system are proposed. The molecular triads will be used in future work as the functional part of organic photovoltaic devices, where the chromophore will be used both to absorb the incoming solar radiation and to increase the distance between the separated charges on donor and acceptor units to increase the lifetime of the charge-separated state.

  6. Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure

    Science.gov (United States)

    2014-08-30

    properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to

  7. Molecular basis and consequences of a deletion in the amelogenin gene, analyzed by capture PCR

    Energy Technology Data Exchange (ETDEWEB)

    Lagerstroem-Fermer, M.; Pettersson, U.; Landegren, U. (Univ. of Uppsala (Sweden))

    1993-07-01

    A mutation that disrupts the gene for one of the major proteins in tooth enamel has been investigated. The mutation is located in the amelogenin gene and causes X-linked amelogenesis imperfecta, characterized by defective mineralization of tooth enamel. The authors have isolated the breakpoints of a 5-kb deletion in the amelogenin gene on the basis of nucleotide sequence information located upstream of the lesion, using a technique termed capture PCR. The deletion removes five of the seven exons, spanning from the second intron to the last exon. Only the first two codons for the mature protein remain, consistent with the relatively severe phenotype of affected individuals in the present family. The mutation appears to have arisen as an illegitimate recombination event since of 11 nucleotide positions immediately surrounding the two breakpoints, 9 are identical. 17 refs., 3 figs., 1 tab.

  8. A Structure-Based Mechanism for Vesicle Capture by the Multisubunit Tethering Complex Dsl1

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Y.; Yip, C; Tripathi, A; Huie, D; Jeffrey, P; Walz, T; Hughson, F

    2009-01-01

    Vesicle trafficking requires membrane fusion, mediated by SNARE proteins, and upstream events that probably include tethering, an initial long-range attachment between a vesicle and its target organelle. Among the factors proposed to mediate tethering are a set of multisubunit tethering complexes (MTCs). The Dsl1 complex, with only three subunits, is the simplest known MTC and is essential for the retrograde traffic of COPI-coated vesicles from the Golgi to the ER. To elucidate structural principles underlying MTC function, we have determined the structure of the Dsl1 complex, revealing a tower containing at its base the binding sites for two ER SNAREs and at its tip a flexible lasso for capturing vesicles. The Dsl1 complex binds to individual SNAREs via their N-terminal regulatory domains and also to assembled SNARE complexes; moreover, it is capable of accelerating SNARE complex assembly. Our results suggest that even the simplest MTC may be capable of orchestrating vesicle capture, uncoating, and fusion.

  9. Measurements of structural material capture to uranium-235 fission rate ratios in an intermediate spectrum assembly

    Energy Technology Data Exchange (ETDEWEB)

    Azzoni, P.; Benzi, V.; Chiodi, P.L.; Giuliani, C.; Guardini, S.; Marrasi, R.; Salomoni, A.; Tassan, S.

    1980-10-01

    Experimental determinations of capture rates of structural materials used in fast breeder reactors, such as iron, chromium, nickel, and stainless steel, normalized to the /sup 235/U fission rate, were performed. The aim of these experiments was to check structural material multigroup cross-section libraries in the 1- to 100-keV range, where substantial discrepancies among various cross-section evaluations are not yet resolved. The experiments were carried out in an ARGONAUTtype RB-2 reactor, using the Null Reactivity Oscillation method, on test media composed of quasi-homogeneous loose particle mixtures. Comparisons were carried out with corresponding calculated values, showing a trend of these values to overestimate the measured quantities. These results are not in disagreement with the indications of recent /sup 235/U cross-section measurements as far as the sigma /SUB c/ /sigma /SUB f/ of /sup 235/U is concerned.

  10. Ultrasonic array imaging of multilayer structures using full matrix capture and extended phase shift migration

    Science.gov (United States)

    Wu, Haiteng; Chen, Jian; Yang, Keji; Hu, Xuxiao

    2016-04-01

    Multilayer structures have been widely used in industrial fields, and non-destructive evaluation of these structures is of great importance to assure their quality and performance. Recently, ultrasonic array imaging using full matrix capture, e.g. the total focusing method (TFM), has been shown to increase sensitivity to small defects and improve imaging resolution in homogeneous media. However, it cannot be applied to multilayer structures directly, due to the sound velocity variation in different layers and because refraction occurs at layer interfaces, which gives rise to difficulties in determining the propagation path and time. To overcome these problems, an extended phase shift migration (EPSM) is proposed for the full matrix imaging of multilayer structures in this paper. Based on the theory of phase shift migration for monostatic pulse-echo imaging, full matrix imaging using EPSM is derived by extrapolating the wavefields in both transmission and reception, and extended to the multilayer case. The performance of the proposed algorithm is evaluated by full matrix imaging of a two-layer structure with side-drilled holes conducted both in the simulation and the experiment. The results verify that the proposed algorithm is capable of full matrix imaging of a layered structure with a high resolution and signal-to-noise ratio. For comparison, full matrix imaging using the TFM with root-mean-squared velocity is also performed, and the results demonstrate that the proposed algorithm is superior to the TFM in improving both the image quality and resolution.

  11. Phenol soluble modulin (PSM) variants of community-associated methicillin-resistant Staphylococcus aureus (MRSA) captured using mass spectrometry-based molecular networking.

    Science.gov (United States)

    Gonzalez, David J; Vuong, Lisa; Gonzalez, Isaiah S; Keller, Nadia; McGrosso, Dominic; Hwang, John H; Hung, Jun; Zinkernagel, Annelies; Dixon, Jack E; Dorrestein, Pieter C; Nizet, Victor

    2014-05-01

    Molecular genetic analysis indicates that the problematic human bacterial pathogen methicillin-resistant Staphylococcus aureus possesses more than 2000 open reading frames in its genome. This number of potential gene products, coupled with intrinsic mechanisms of posttranslational modification, endows methicillin-resistant Staphylococcus aureus with a highly complex biochemical repertoire. Recent proteomic and metabolomic advances have provided methodologies to better understand and characterize the biosynthetic factors released by microbial organisms. Here, the emerging tool of mass spectrometry-based molecular networking was used to visualize and map the repertoire of biosynthetic factors produced by a community-associated methicillin-resistant Staphylococcus aureus strain representative of the epidemic USA300 clone. In particular, the study focused on elucidating the complexity of the recently discovered phenol soluble modulin family of peptides when placed under various antibiotic treatment stresses. Novel PSM truncated variant peptides were captured, and the type of variants that were clustered by the molecular networks platform changed in response to the different antibiotic treatment conditions. After discovery, a group of the peptides were selected for functional analysis in vitro. The peptides displayed bioactive properties including the ability to induce proinflammatory responses in human THP-1 monocytes. Additionally, the tested peptides did not display antimicrobial activity as previously reported for other phenol soluble modulin truncated variants. Our findings reveal that the PSM family of peptides are quite structurally diverse, and suggest a single phenol soluble modulin parent peptide can functionally spawn differential bioactivities in response to various external stimuli.

  12. Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture.

    Science.gov (United States)

    Conte, N; Varela, I; Grove, C; Manes, N; Yusa, K; Moreno, T; Segonds-Pichon, A; Bench, A; Gudgin, E; Herman, B; Bolli, N; Ellis, P; Haddad, D; Costeas, P; Rad, R; Scott, M; Huntly, B; Bradley, A; Vassiliou, G S

    2013-09-01

    Advances in sequencing technologies are giving unprecedented insights into the spectrum of somatic mutations underlying acute myeloid leukaemia with a normal karyotype (AML-NK). It is clear that the prognosis of individual patients is strongly influenced by the combination of mutations in their leukaemia and that many leukaemias are composed of multiple subclones, with differential susceptibilities to treatment. Here, we describe a method, employing targeted capture coupled with next-generation sequencing and tailored bioinformatic analysis, for the simultaneous study of 24 genes recurrently mutated in AML-NK. Mutational analysis was performed using open source software and an in-house script (Mutation Identification and Analysis Software), which identified dominant clone mutations with 100% specificity. In each of seven cases of AML-NK studied, we identified and verified mutations in 2-4 genes in the main leukaemic clone. Additionally, high sequencing depth enabled us to identify putative subclonal mutations and detect leukaemia-specific mutations in DNA from remission marrow. Finally, we used normalised read depths to detect copy number changes and identified and subsequently verified a tandem duplication of exons 2-9 of MLL and at least one deletion involving PTEN. This methodology reliably detects sequence and copy number mutations, and can thus greatly facilitate the classification, clinical research, diagnosis and management of AML-NK.

  13. Molecular Models of Genetic and Organismic Structures

    CERN Document Server

    Baianu, I C

    2004-01-01

    In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

  14. Carbon dioxide capture in 2-aminoethanol aqueous solution from ab initio molecular dynamics simulations

    Science.gov (United States)

    Kubota, Yoshiyuki; Ohnuma, Toshiharu; Bučko, Tomáš

    2017-03-01

    The reaction of carbon dioxide (CO2) with aqueous 2-aminoethanol (MEA) has been investigated using both blue moon ensemble and metadynamics approaches combined with ab initio molecular dynamics (AIMD) simulations. The AIMD simulations predicted the spontaneous deprotonation of the intermediate compound, MEA zwitterion, and they were used to study two possible routes for subsequent proton transfer reactions: the formation of the protonated MEA and the formation of MEA carbamic acid. The free-energy curve depicted by blue moon ensemble technique supported the favorable deprotonation of MEA zwitterion. The overall free-energy profile showed the favorable formation of the ionic products of MEA carbamate ion and protonated MEA.

  15. Molecular Modeling of the Chain Structures of Polybenzoxazines

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The structures and properties of benzoxazines were investigated by virtue of molecular modeling at a molecular level. By means of Cerius software(version 4.0) supplied by Molecular Simulations Inc., the molecular mechanics and the molecular dynamics were performed under a PCFF force field. Five kinds of the polymeric chains of benzoxazines were created by using polymer builder and energy minimization. The relaxation process was conducted with both energy minimization and molecular dynamics.

  16. Elastic network models capture the motions apparent within ensembles of RNA structures.

    Science.gov (United States)

    Zimmermann, Michael T; Jernigan, Robert L

    2014-06-01

    The role of structure and dynamics in mechanisms for RNA becomes increasingly important. Computational approaches using simple dynamics models have been successful at predicting the motions of proteins and are often applied to ribonucleo-protein complexes but have not been thoroughly tested for well-packed nucleic acid structures. In order to characterize a true set of motions, we investigate the apparent motions from 16 ensembles of experimentally determined RNA structures. These indicate a relatively limited set of motions that are captured by a small set of principal components (PCs). These limited motions closely resemble the motions computed from low frequency normal modes from elastic network models (ENMs), either at atomic or coarse-grained resolution. Various ENM model types, parameters, and structure representations are tested here against the experimental RNA structural ensembles, exposing differences between models for proteins and for folded RNAs. Differences in performance are seen, depending on the structure alignment algorithm used to generate PCs, modulating the apparent utility of ENMs but not significantly impacting their ability to generate functional motions. The loss of dynamical information upon coarse-graining is somewhat larger for RNAs than for globular proteins, indicating, perhaps, the lower cooperativity of the less densely packed RNA. However, the RNA structures show less sensitivity to the elastic network model parameters than do proteins. These findings further demonstrate the utility of ENMs and the appropriateness of their application to well-packed RNA-only structures, justifying their use for studying the dynamics of ribonucleo-proteins, such as the ribosome and regulatory RNAs.

  17. Metal organoclays with compacted structure for truly physical capture of hydrogen

    Science.gov (United States)

    Tahir, M. Nazir; Sennour, Radia; Arus, Vasilica Alisa; Sallam, Lamyaa M.; Roy, René; Azzouz, Abdelkrim

    2017-03-01

    Truly reversible capture of hydrogen was achieved at ambient conditions on Pd-loaded organo-montmorillonites obtained by photo-addition of different thiols on propargylated-TRIS cations already grafted on the clay surface. TEM insights showed that more than 90% of Pd0 incorporated occur as 0.3-0.5 nm subnanoparticles (PdSNPs). XPS and NMR analyses revealed simultaneous strong S:Pd0 and O:Pd0 interactions that "cement" the organic moiety around PdSNPs. The significant decrease in porosity suggests a compacted structure that impedes not only metal aggregation, but also hydrogen diffusion in the metal bulk. Thus, hydrogen appears to adsorb mainly via physical condensation around PdSNPs. These thiol-clay matrices showed hydrogen surface affinity factors of up to 0.51 mmol m-2 at ambient temperature and pressure. This is higher than those reported for much more sophisticated materials. DSC measurements showed very low desorption heat between 20 and 80 °C. Hydrogen release was achieved merely under vacuum or slight heating starting from 40 °C and was almost completed up to 85 °C. This provides a proof of concept of truly reversible capture of hydrogen for concentration and/or storage purposes. Such a performance has never been achieved at ambient temperature and pressure. These findings open new prospects to develop low-cost materials for reversible hydrogen storage without energy and safety constraints.

  18. A structured approach for selecting carbon capture process models : A case study on monoethanolamine

    NARCIS (Netherlands)

    van der Spek, Mijndert; Ramirez, Andrea

    2014-01-01

    Carbon capture and storage is considered a promising option to mitigate CO2 emissions. This has resulted in many R&D efforts focusing at developing viable carbon capture technologies. During carbon capture technology development, process modeling plays an important role. Selecting an appropriate pro

  19. Water Vapor Adsorption Capacity of Thermally Fluorinated Carbon Molecular Sieves for CO2 Capture

    Directory of Open Access Journals (Sweden)

    Jin-Young Jung

    2013-01-01

    Full Text Available The surfaces of carbon molecular sieves (CMSs were thermally fluorinated to adsorb water vapor. The fluorination of the CMSs was performed at various temperatures (100, 200, 300, and 400°C to investigate the effects of the fluorine gas (F2 content on the surface properties. Fluorine-related functional groups formed were effectively generated on the surface of the CMSs via thermal fluorination process, and the total pore volume and specific surface area of the pores in the CMSs increased during the thermal fluorination process, especially those with diameters ≤ 8 Å. The water vapor adsorption capacity of the thermally fluorinated CMSs increased compared with the as-received CMSs, which is attributable to the increased specific surface area and to the semicovalent bonds of the C–F groups.

  20. Demonstration of anisotropic fluid closure capturing the kinetic structure of magnetic reconnection.

    Science.gov (United States)

    Ohia, O; Egedal, J; Lukin, V S; Daughton, W; Le, A

    2012-09-14

    Collisionless magnetic reconnection in high-temperature plasmas has been widely studied through fluid-based models. Here, we present results of fluid simulation implementing new equations of state for guide-field reconnection. The new fluid closure accurately accounts for the anisotropic electron pressure that builds in the reconnection region due to electric and magnetic trapping of electrons. In contrast to previous fluid models, our fluid simulation reproduces the detailed reconnection region as observed in fully kinetic simulations. We hereby demonstrate that the new fluid closure self-consistently captures all the physics relevant to the structure of the reconnection region, providing a gateway to a renewed and deeper theoretical understanding of reconnection in weakly collisional regimes.

  1. Manipulation of molecular structures with magnetic fields

    NARCIS (Netherlands)

    Boamfa, M.I.

    2003-01-01

    The present thesis deals with the use of magnetic fields as a handle to manipulate matter at a molecular level and as a tool to probe molecular properties or inter molecular interactions. The work consists of in situ optical studies of (polymer) liquid crystals and molecular aggregates in high magne

  2. Molecular structure of the collagen triple helix.

    Science.gov (United States)

    Brodsky, Barbara; Persikov, Anton V

    2005-01-01

    The molecular conformation of the collagen triple helix confers strict amino acid sequence constraints, requiring a (Gly-X-Y)(n) repeating pattern and a high content of imino acids. The increasing family of collagens and proteins with collagenous domains shows the collagen triple helix to be a basic motif adaptable to a range of proteins and functions. Its rodlike domain has the potential for various modes of self-association and the capacity to bind receptors, other proteins, GAGs, and nucleic acids. High-resolution crystal structures obtained for collagen model peptides confirm the supercoiled triple helix conformation, and provide new information on hydrogen bonding patterns, hydration, sidechain interactions, and ligand binding. For several peptides, the helix twist was found to be sequence dependent, and such variation in helix twist may serve as recognition features or to orient the triple helix for binding. Mutations in the collagen triple-helix domain lead to a variety of human disorders. The most common mutations are single-base substitutions that lead to the replacement of one Gly residue, breaking the Gly-X-Y repeating pattern. A single Gly substitution destabilizes the triple helix through a local disruption in hydrogen bonding and produces a discontinuity in the register of the helix. Molecular information about the collagen triple helix and the effect of mutations will lead to a better understanding of function and pathology.

  3. Capturing relativistic wake eld structures in plasmas using ultrashort high-energy electrons as a probe

    CERN Document Server

    Zhang, C J; Xu, X L; Li, F; Pai, C -H; Wan, Y; Wu, Y P; Gu, Y Q; Mori, W B; Joshi, C; Lu, W

    2016-01-01

    A new method capable of capturing coherent electric field structures propagating at nearly the speed of light in plasma with a time resolution as small as a few femtoseconds is proposed. This method uses a few femtoseconds long relativistic electron bunch to probe the wake produced in a plasma by an intense laser pulse or an ultra-short relativistic charged particle beam. As the probe bunch traverses the wake, its momentum is modulated by the electric field of the wake, leading to a density variation of the probe after free-space propagation. This variation of probe density produces a snapshot of the wake that can directly give many useful information of the wake structure and its evolution. Furthermore, this snapshot allows detailed mapping of the longitudinal and transverse components of the wakefield. We develop a theoretical model for field reconstruction and verify it using 3-dimensional particle-in-cell (PIC) simulations. This model can accurately reconstruct the wakefield structure in the linear regime...

  4. Vision-based system identification technique for building structures using a motion capture system

    Science.gov (United States)

    Oh, Byung Kwan; Hwang, Jin Woo; Kim, Yousok; Cho, Tongjun; Park, Hyo Seon

    2015-11-01

    This paper presents a new vision-based system identification (SI) technique for building structures by using a motion capture system (MCS). The MCS with outstanding capabilities for dynamic response measurements can provide gage-free measurements of vibrations through the convenient installation of multiple markers. In this technique, from the dynamic displacement responses measured by MCS, the dynamic characteristics (natural frequency, mode shape, and damping ratio) of building structures are extracted after the processes of converting the displacement from MCS to acceleration and conducting SI by frequency domain decomposition. A free vibration experiment on a three-story shear frame was conducted to validate the proposed technique. The SI results from the conventional accelerometer-based method were compared with those from the proposed technique and showed good agreement, which confirms the validity and applicability of the proposed vision-based SI technique for building structures. Furthermore, SI directly employing MCS measured displacements to FDD was performed and showed identical results to those of conventional SI method.

  5. Molecular dynamics study of ice structural evolution

    Institute of Scientific and Technical Information of China (English)

    Wang Yan; Dong Shun-Le

    2008-01-01

    Molecular dynamics simulation is employed to study the structural evolution of low density amorphous ice during its compression from one atmosphere to 2.5 GPa. Calculated results show that high density amorphous ice is formed at an intermediate pressure of~1.0GPa; the O-O-O bond angle ranges from 83° to 113°, and the O-H...O bond is bent from 112° to 160°. Very high density amorphous ice is obtained by quenching to 80K and decompressing the ice to ambient pressure from 160 K/1.3 GPa or 160 K/1.7 GPa; and the next-nearest O-O length is found to be 0.310 nm, just 0.035 nm beyond the nearest O-O distance of 0.275 nm.

  6. Freezing capture of polymorphic aggregates of bolaamphiphilic (L)-valine-based molecular hydrogelators.

    Science.gov (United States)

    Nebot, Vicent J; Díaz-Oltra, Santiago; Smets, Johan; Fernández Prieto, Susana; Miravet, Juan F; Escuder, Beatriu

    2014-05-01

    Nanostructured xerogels have been prepared by the freeze-drying of hydrogels and aggregates formed by bolaamphiphilic L-valine derivatives after aging under different environmental conditions. A wide variety of shapes and sizes has been achieved by a simple methodology. These nanostructures have been studied by SEM and WAXD and a dramatic influence of structural flexibility on the kinetics of aggregation has been observed. Such flexibility and a modulation of the hydrophobic effect have shown a profound influence in the packing of these compounds and revealed a high degree of polymorphism.

  7. Molecular Component Structures Mediated Formation of Self-assemblies

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Molecular recognition directed self-assemblies from complementary molecular components, melamine and barbituric acid derivatives were studied by means of NMR, fluorescence, and TEM. It was found that both the process of the self-assembly and the morphologies of the result ed self-assemblies could be mediated by modifying the structures of the molecular components used. The effect of the structures of the molecular components on the formation of the self-as semblies was discussed in terms of intermolecular interactions.

  8. Nanotexture optimization by oxygen plasma of mesoporous silica thin film for enrichment of low molecular weight peptides captured from human serum

    Institute of Scientific and Technical Information of China (English)

    Louis; BROUSSEAU; Ali; BOUAMRANI; Mauro; FERRARI

    2010-01-01

    The optimization of mesoporous silica thin films by nanotexturing using oxygen plasma versus thermal oxidation was investigated.Calcination in oxygen plasma provides superior control over pore formation with regard to the pore surface and higher fidelity to the structure of the polymer template.The resulting porous film offers an ideal substrate for the selective partitioning of peptides from complex mixtures.The improved chemico-physical characteristics of porous thin films(pore size distribution,nanostructure,surface properties and pore connectivity) were systematically characterized with XRD,Ellipsometry,FTIR,TEM and N2 adsorption/desorption isotherm.The enrichment of low molecular weight proteins captured from human serum on mesoporous silica thin films fabricated by both methodologies was investigated by comparison of their MALDI-TOF MS profiles.This novel on-chip fractionation technology offers advantages in recovering the low molecular weight peptides from human serum,which has been recognized as an informative resource for early diagnosis of cancer and other diseases.

  9. Investigation of CO2 capture mechanisms of liquid-like nanoparticle organic hybrid materials via structural characterization

    KAUST Repository

    Park, Youngjune

    2011-01-01

    Nanoparticle organic hybrid materials (NOHMs) have been recently developed that comprise an oligomeric or polymeric canopy tethered to surface-modified nanoparticles via ionic or covalent bonds. It has already been shown that the tunable nature of the grafted polymeric canopy allows for enhanced CO 2 capture capacity and selectivity via the enthalpic intermolecular interactions between CO2 and the task-specific functional groups, such as amines. Interestingly, for the same amount of CO2 loading NOHMs have also exhibited significantly different swelling behavior compared to that of the corresponding polymers, indicating a potential structural effect during CO2 capture. If the frustrated canopy species favor spontaneous ordering due to steric and/or entropic effects, the inorganic cores of NOHMs could be organized into unusual structural arrangements. Likewise, the introduction of small gaseous molecules such as CO2 could reduce the free energy of the frustrated canopy. This entropic effect, the result of unique structural nature, could allow NOHMs to capture CO2 more effectively. In order to isolate the entropic effect, NOHMs were synthesized without the task-specific functional groups. The relationship between their structural conformation and the underlying mechanisms for the CO2 absorption behavior were investigated by employing NMR and ATR FT-IR spectroscopies. The results provide fundamental information needed for evaluating and developing novel liquid-like CO2 capture materials and give useful insights for designing and synthesizing NOHMs for more effective CO2 capture. © the Owner Societies 2011.

  10. Molecular structure input on the web

    Directory of Open Access Journals (Sweden)

    Ertl Peter

    2010-02-01

    Full Text Available Abstract A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential. The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

  11. Capturing ultrafast photoinduced local structural distortion of BiFeO3

    Energy Technology Data Exchange (ETDEWEB)

    Wen, Haidan [Argonne National Lab. (ANL), Argonne, IL (United States); Sassi, Michel [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Luo, Zhenlin [Univ. of Science and Technology of China, Hefei (China); Adamo, Carolina [Cornell Univ., Ithaca, NY (United States); Schlom, Darrell G. [Cornell Univ., Ithaca, NY (United States); Cornell Univ., Ithaca, NY (United States). Kavli Inst. for Nanoscale Science; Rosso, Kevin M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Zhang, Xiaoyi [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-10-14

    The interaction of light with materials is an intensively studied research forefront, in which the coupling of radiation energy to selective degrees of freedom offers contact-free tuning of functionalities on ultrafast time scales. Capturing the fundamental processes and understanding the mechanism of photoinduced structural rearrangement are essential to applications such as photo-active actuators and efficient photovoltaic devices. Using ultrafast x-ray absorption spectroscopy aided by density functional theory calculations, we reveal the local structural arrangement around the transition metal atom in a unit cell of the photoferroelectric archetype BiFeO3 film. The out-of-plane elongation of the unit cell is accompanied by the in-plane shrinkage with minimal change of interaxial lattice angles upon photoexcitation. This anisotropic elastic deformation of the unit cell is driven by localized electric field as a result of photoinduced charge separation, in contrast to a global lattice constant increase and lattice angle variations as a result of heating. The finding of a photoinduced elastic unit cell deformation elucidates a microscopic picture of photocarrier-mediated non-equilibrium processes in polar materials.

  12. Lifetime and structures of TLEs captured by high-speed camera on board aircraft

    Science.gov (United States)

    Takahashi, Y.; Sanmiya, Y.; Sato, M.; Kudo, T.; Inoue, T.

    2012-12-01

    Temporal development of sprite streamer is the manifestation of the local electric field and conductivity. Therefore, in order to understand the mechanisms of sprite, which show a large variety in temporal and spatial structures, the detailed analysis of both fine and macro-structures with high time resolution are to be the key approach. However, due to the long distance from the optical equipments to the phenomena and to the contamination by aerosols, it's not easy to get clear images of TLEs on the ground. In the period of June 27 - July 10, 2011, a combined aircraft and ground-based campaign, in support of NHK Cosmic Shore project, was carried with two jet airplanes under collaboration between NHK, Japan Broadcasting Corporation, and universities. On 8 nights out of 16 standing-by, the jets took off from the airport near Denver, Colorado, and an airborne high speed camera captured over 60 TLE events at a frame rate of 8000-10,000 /sec. Some of them show several tens of streamers in one sprite event, which repeat splitting at the down-going end of streamers or beads. The velocities of the bottom ends and the variations of their brightness are traced carefully. It is found that the top velocity is maintained only for the brightest beads and others become slow just after the splitting. Also the whole luminosity of one sprite event has short time duration with rapid downward motion if the charge moment change of the parent lightning is large. The relationship between diffuse glows such as elves and sprite halos, and subsequent discrete structure of sprite streamers is also examined. In most cases the halo and elves seem to show inhomogenous structures before being accompanied by streamers, which develop to bright spots or streamers with acceleration of the velocity. Those characteristics of velocity and lifetime of TLEs provide key information of their generation mechanism.

  13. Natural materials for carbon capture.

    Energy Technology Data Exchange (ETDEWEB)

    Myshakin, Evgeniy M. (National Energy Technology Laboratory, Pittsburgh, PA); Romanov, Vyacheslav N. (National Energy Technology Laboratory, Pittsburgh, PA); Cygan, Randall Timothy

    2010-11-01

    Naturally occurring clay minerals provide a distinctive material for carbon capture and carbon dioxide sequestration. Swelling clay minerals, such as the smectite variety, possess an aluminosilicate structure that is controlled by low-charge layers that readily expand to accommodate water molecules and, potentially, carbon dioxide. Recent experimental studies have demonstrated the efficacy of intercalating carbon dioxide in the interlayer of layered clays but little is known about the molecular mechanisms of the process and the extent of carbon capture as a function of clay charge and structure. A series of molecular dynamics simulations and vibrational analyses have been completed to assess the molecular interactions associated with incorporation of CO2 in the interlayer of montmorillonite clay and to help validate the models with experimental observation.

  14. High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

    Directory of Open Access Journals (Sweden)

    Soichi Inagaki

    Full Text Available Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

  15. Age-structured mark-recapture analysis: A virtual-population-analysis-based model for analyzing age-structured capture-recapture data

    Science.gov (United States)

    Coggins, L.G.; Pine, William E.; Walters, C.J.; Martell, S.J.D.

    2006-01-01

    We present a new model to estimate capture probabilities, survival, abundance, and recruitment using traditional Jolly-Seber capture-recapture methods within a standard fisheries virtual population analysis framework. This approach compares the numbers of marked and unmarked fish at age captured in each year of sampling with predictions based on estimated vulnerabilities and abundance in a likelihood function. Recruitment to the earliest age at which fish can be tagged is estimated by using a virtual population analysis method to back-calculate the expected numbers of unmarked fish at risk of capture. By using information from both marked and unmarked animals in a standard fisheries age structure framework, this approach is well suited to the sparse data situations common in long-term capture-recapture programs with variable sampling effort. ?? Copyright by the American Fisheries Society 2006.

  16. Capturing structure and function in an embryonic heart with Biophotonic tools

    Directory of Open Access Journals (Sweden)

    Ganga eKarunamuni

    2014-09-01

    Full Text Available Disturbed cardiac function (flow, excitation, contraction, calcium transients at an early stage of development has been shown to correlate with and may lead to cellular/molecular, functional and structural cardiac anomalies at later stages culminating in the congenital heart defects (CHDs that present at birth. It is not surprising that cardiac function, which drives embryonic and extraembryonic circulation, is also connected to neural and placental development. While our knowledge of molecular and cellular steps in cardiac development is growing rapidly, our understanding of the role of cardiovascular function in the embryo is still rudimentary. One reason for the scanty information in this area is that the tools to study early cardiac function are limited. Recently developed and adapted Biophotonic tools may overcome the challenges of studying the tiny fragile beating heart. In this chapter, the strengths and limitations of Biophotonic tools will be described with emphasis on Optical Coherence Tomography (OCT. OCT can be used for detailed structural and functional studies of the tubular and looping avian embryo heart under physiological conditions. The same hearts can be subsequently rapidly and quantitatively phenotyped at a later stage using OCT. When combined with other tools such as Optimal Mapping (OM and Optical Pacing (OP, OCT has the potential to reveal in spatial and temporal detail the biophysical changes that can potentially impact mechanotransduction pathways. This information may provide better explanations for the etiology of the CHDs when interwoven with our understanding of the multiple molecular pathways that have been described to be involved. Examples of application of these tools to study the etiology of CHDs are presented. Directions for future directions and advances in the use of Biophotonic tools are discussed.

  17. Molecular structures and intramolecular dynamics of pentahalides

    Science.gov (United States)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  18. Microspectroscopy as applied to the study of wood molecular structure

    DEFF Research Database (Denmark)

    Fackler, Karin; Thygesen, Lisbeth Garbrecht

    2013-01-01

    Microspectroscopy gives access to spatially resolved information on the molecular structure and chemical composition of a material. For a highly heterogeneous and anisotropic material like wood, such information is essential when assessing structure/property relationships such as moisture...

  19. Highly ordered structures of peptides by using molecular scaffolds.

    Science.gov (United States)

    Moriuchi, Toshiyuki; Hirao, Toshikazu

    2004-06-20

    Protein secondary structures such as alpha-helices, beta-sheets, and beta-turns are important in inducing the three-dimensional structure and biological activity of proteins. Designing secondary structure mimics composed of short peptides has attracted much attention not only to gain fundamental insight into the factors affecting protein folding but also to develop pharmacologically useful compounds, artificial receptors, asymmetric catalysts, and new materials. In this tutorial review, we focus on molecular scaffolds employed to induce beta-sheet-like structure in attached peptide chains, thereby creating highly ordered molecular structures, and discuss the versatility of these molecular scaffolds to regulate the attached peptide strands in the appropriate dimensions.

  20. Molecular structure and motion in zero field magnetic resonance

    Energy Technology Data Exchange (ETDEWEB)

    Jarvie, T.P.

    1989-10-01

    Zero field magnetic resonance is well suited for the determination of molecular structure and the study of motion in disordered materials. Experiments performed in zero applied magnetic field avoid the anisotropic broadening in high field nuclear magnetic resonance (NMR) experiments. As a result, molecular structure and subtle effects of motion are more readily observed.

  1. Cost structure of a postcombustion CO2 capture system using CaO.

    Science.gov (United States)

    Abanades, J Carlos; Grasa, G; Alonso, M; Rodriguez, N; Anthony, E J; Romeo, L M

    2007-08-01

    This paper presents the basic economics of an emerging concept for CO2 capture from flue gases in power plants. The complete system includes three key cost components: a full combustion power plant, a second power plant working as an oxy-fired fluidized bed calciner, and a fluidized bed carbonator interconnected with the calciner and capturing CO2 from the combustion power plant. The simplicity in the economic analysis is possible because the key cost data for the two major first components are well established in the open literature. It is shown that there is clear scope for a breakthrough in capture cost to around 15 $/t of CO2 avoided with this system. This is mainly because the capture system is generating additional power (from the additional coal fed to the calciner) and because the avoided CO2 comes from the capture of the CO2 generated by the coal fed to the calciner and the CO2 captured (as CaCO3) from the flue gases of the existing power plant, that is also released in the calciner.

  2. Molecular structure and centrifugal distortion in methylthioethyne

    NARCIS (Netherlands)

    Engelsen, D. den

    1969-01-01

    The investigation of the microwave spectra of five isotopic species of methylthioethyne, HCCSCH3 enabled a fairly reliable calculation to be made of bond lengths and angles. The centrifugal distortion parameters are related to molecular vibrations.

  3. Molecular catalysts structure and functional design

    CERN Document Server

    Gade, Lutz H

    2014-01-01

    Highlighting the key aspects and latest advances in the rapidly developing field of molecular catalysis, this book covers new strategies to investigate reaction mechanisms, the enhancement of the catalysts' selectivity and efficiency, as well as the rational design of well-defined molecular catalysts. The interdisciplinary author team with an excellent reputation within the community discusses experimental and theoretical studies, along with examples of improved catalysts, and their application in organic synthesis, biocatalysis, and supported organometallic catalysis. As a result, readers wil

  4. Capturing Thoughts, Capturing Minds?

    DEFF Research Database (Denmark)

    Nielsen, Janni

    2004-01-01

    Think Aloud is cost effective, promises access to the user's mind and is the applied usability technique. But 'keep talking' is difficult, besides, the multimodal interface is visual not verbal. Eye-tracking seems to get around the verbalisation problem. It captures the visual focus of attention...

  5. Molecular dynamics modeling of structural battery components

    NARCIS (Netherlands)

    Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.

    2015-01-01

    A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion compo

  6. Capturing appearance

    Science.gov (United States)

    Rushmeier, Holly E.

    2005-01-01

    For computer graphics applications, capturing the appearance parameters of objects (reflectance, transmittance and small scale surface structures), is as important as capturing the overall shape. We briefly review recent approaches developed by the computer graphics community to solve this problem. Excellent results have been obtained by various researchers measuring spatially varying reflectance functions for some classes of objects. We will consider some challenges from two of the remaining problematic classes of objects. First we will describe our experience scanning and modeling the throne of Tutankhamen. The major difficulties in this case were that the base shape was a highly detailed non-convex geometry with complex topology, and the shape was covered by optically uncooperative gold and silver. Then we will discuss some observations from our ongoing project to scan and model historic buildings on the Yale campus. The major difficulties in this second case are quantity of data and the lack of control over acquisition conditions.

  7. Colour Chemistry, Part I, Principles, Colour, and Molecular Structure

    Science.gov (United States)

    Hallas, G.

    1975-01-01

    Discusses various topics in color chemistry, including the electromagnetic spectrum, the absorption and reflection of light, additive and subtractive color mixing, and the molecular structure of simple colored substances. (MLH)

  8. Molecular and Crystal Structures of Three Berberine Derivatives

    OpenAIRE

    Jiří Dostál; Zdirad Žák; Marek NeÄÂas; Milan PotáÄÂek; Stanislav Man

    2001-01-01

    Berberine azide, berberine thiocyanate, and 8-cyano-8H-berberine were prepared from berberine chloride, a quaternary protoberberine alkaloid. The molecular and crystal structures of all compounds are reported and discussed.

  9. Accelerated electronic structure-based molecular dynamics simulations of shock-induced chemistry

    Science.gov (United States)

    Cawkwell, Marc

    2015-06-01

    The initiation and progression of shock-induced chemistry in organic materials at moderate temperatures and pressures are slow on the time scales available to regular molecular dynamics simulations. Accessing the requisite time scales is particularly challenging if the interatomic bonding is modeled using accurate yet expensive methods based explicitly on electronic structure. We have combined fast, energy conserving extended Lagrangian Born-Oppenheimer molecular dynamics with the parallel replica accelerated molecular dynamics formalism to study the relatively sluggish shock-induced chemistry of benzene around 13-20 GPa. We model interatomic bonding in hydrocarbons using self-consistent tight binding theory with an accurate and transferable parameterization. Shock compression and its associated transient, non-equilibrium effects are captured explicitly by combining the universal liquid Hugoniot with a simple shrinking-cell boundary condition. A number of novel methods for improving the performance of reactive electronic structure-based molecular dynamics by adapting the self-consistent field procedure on-the-fly will also be discussed. The use of accelerated molecular dynamics has enabled us to follow the initial stages of the nucleation and growth of carbon clusters in benzene under thermodynamic conditions pertinent to experiments.

  10. Adaptive modelling of structured molecular representations for toxicity prediction

    Science.gov (United States)

    Bertinetto, Carlo; Duce, Celia; Micheli, Alessio; Solaro, Roberto; Tiné, Maria Rosaria

    2012-12-01

    We investigated the possibility of modelling structure-toxicity relationships by direct treatment of the molecular structure (without using descriptors) through an adaptive model able to retain the appropriate structural information. With respect to traditional descriptor-based approaches, this provides a more general and flexible way to tackle prediction problems that is particularly suitable when little or no background knowledge is available. Our method employs a tree-structured molecular representation, which is processed by a recursive neural network (RNN). To explore the realization of RNN modelling in toxicological problems, we employed a data set containing growth impairment concentrations (IGC50) for Tetrahymena pyriformis.

  11. The Chain Structure of Ultrahigh Molecular Weight Polyacrylonitrile

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The chemical composition, molecular weight and its distribution, the bonding structure and the regulation of ultranigh molecular weight polyacrylonitrile (UHMW-PAN)prepared by aqueous suspension polymerization were determined by FIIR, viscometry, GPC, 1H-NMR and 13C-NMR. The mechanical properties of the porous hollow fiber prepared by UHMW-PAN were discussed to provide a theoretical basis for the preparation of ideal precursors of the porous hollow oxidation fiber.Ke ywords : ultrahigh molecular weight, pol yacrylonitrile ,chain structure.

  12. Molecular structure of diatomic lanthanide compounds

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The molecular constants of selected diatomic lanthanide compounds(LaH, LaO, LaF, EuH, EuO, EuF, EuS, GdO, GdF, GdH, YbH, YbO, YbF, YbS, LuH, LuO and LuF) have been calcu-lated by using relativistic small-core pseudopotentials and optimized(14s13p10d8f6g)/ [6s6p5d4f3g] valence basis sets. The results are in good agreement with available experimental data, with exception of YbO and LuF. The reasons for the discrepancies in case of YbO are due to a complicated mixing of configurations in the ground state, whereas in case of LuF the binding energy estimated by experimentalists appears to be too low.

  13. Molecular structure of diatomic lanthanide compounds

    Institute of Scientific and Technical Information of China (English)

    曹晓燕; 刘文剑; MichaelDolg

    2002-01-01

    The molecular constants of selected diatomic lanthanide compounds (LaH, LaO, LaF, EuH, EuO, EuF, EuS, GdO, GdF, GdH, YbH, YbO, YbF, YbS, LuH, LuO and LuF) have been calculated by using relativistic small-core pseudopotentials and optimized (14s13p10d8f6g)/ [6s6p5d4f3g] valence basis sets. The results are in good agreement with available experimental data, with exception of YbO and LuF. The reasons for the discrepancies in case of YbO are due to a complicated mixing of configurations in the ground state, whereas in case of LuF the binding energy estimated by experimentalists appears to be too low.

  14. Capturing intracellular pH dynamics by coupling its molecular mechanisms within a fully tractable mathematical model.

    Directory of Open Access Journals (Sweden)

    Yann Bouret

    Full Text Available We describe the construction of a fully tractable mathematical model for intracellular pH. This work is based on coupling the kinetic equations depicting the molecular mechanisms for pumps, transporters and chemical reactions, which determine this parameter in eukaryotic cells. Thus, our system also calculates the membrane potential and the cytosolic ionic composition. Such a model required the development of a novel algebraic method that couples differential equations for slow relaxation processes to steady-state equations for fast chemical reactions. Compared to classical heuristic approaches based on fitted curves and ad hoc constants, this yields significant improvements. This model is mathematically self-consistent and allows for the first time to establish analytical solutions for steady-state pH and a reduced differential equation for pH regulation. Because of its modular structure, it can integrate any additional mechanism that will directly or indirectly affect pH. In addition, it provides mathematical clarifications for widely observed biological phenomena such as overshooting in regulatory loops. Finally, instead of including a limited set of experimental results to fit our model, we show examples of numerical calculations that are extremely consistent with the wide body of intracellular pH experimental measurements gathered by different groups in many different cellular systems.

  15. Molecular Structure of Aminoguanidine Sulfate Monohydrate

    Institute of Scientific and Technical Information of China (English)

    CHEN Hong-yan; ZHANG Tong-lai; QIAO Xiao-jing; YANG Li; SHAO Feng-lei

    2006-01-01

    The single crystal of aminoguanidine sulfate monohydrate [(AG)2SO4·H2O] is obtained and its structure is determined by X-ray diffraction analysis. The compound crystallizes in orthorhombic system with space group Pnma and the empirical formula C2H16N8O5S. The unit cell parameters are as follows: a=0.6759(2)nm, b=1.4131(5)nm, c=1.1650(4)nm, V=1.1128(6)n m3, Z=4, Dc=1.578g/cm3, F(000)=560, s=1.069, μ(MoKα)=0.318mm-1. The final R and Wr are 0.0312 and 0.0833, respectively. The title compound is an ionic compound and its structure unit consists of two aminoguanidium cations, one sulfate anion and one crystal water molecule, which are interconnected by electrostatic forces and hydrogen bond s into net structure, making the title compound very stable. Under a linear heat ingrate, the thermal decomposition processes of (AG)2SO4·H2O have one en dothermal dehydration stage, one melting process and one exothermic decomposition stage at 50-400℃, and can evolve abundant gas products.

  16. Molecular Eigensolution Symmetry Analysis and Fine Structure

    Directory of Open Access Journals (Sweden)

    William G. Harter

    2013-01-01

    Full Text Available Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES. Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES used in Born-Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v, then applied to families of Oh clusters in SF6 spectra and to extreme clusters.

  17. Chiral fluorinated α-sulfonyl carbanions: enantioselective synthesis and electrophilic capture, racemization dynamics, and structure.

    Science.gov (United States)

    Hellmann, Gunther; Hack, Achim; Thiemermann, Eric; Luche, Olaf; Raabe, Gerhard; Gais, Hans-Joachim

    2013-03-18

    Enantiomerically pure triflones R(1) CH(R(2) )SO2 CF3 have been synthesized starting from the corresponding chiral alcohols via thiols and trifluoromethylsulfanes. Key steps of the syntheses of the sulfanes are the photochemical trifluoromethylation of the thiols with CF3 Hal (Hal=halide) or substitution of alkoxyphosphinediamines with CF3 SSCF3 . The deprotonation of RCH(Me)SO2 CF3 (R=CH2 Ph, iHex) with nBuLi with the formation of salts [RC(Me)SO2 CF3 ]Li and their electrophilic capture both occurred with high enantioselectivities. Displacement of the SO2 CF3 group of (S)-MeOCH2 C(Me)(CH2 Ph)SO2 CF3 (95 % ee) by an ethyl group through the reaction with AlEt3 gave alkane MeOCH2 C(Me)(CH2 Ph)Et of 96 % ee. Racemization of salts [R(1) C(R(2) )SO2 CF3 ]Li follows first-order kinetics and is mainly an enthalpic process with small negative activation entropy as revealed by polarimetry and dynamic NMR (DNMR) spectroscopy. This is in accordance with a Cα S bond rotation as the rate-determining step. Lithium α-(S)-trifluoromethyl- and α-(S)-nonafluorobutylsulfonyl carbanion salts have a much higher racemization barrier than the corresponding α-(S)-tert-butylsulfonyl carbanion salts. Whereas [PhCH2 C(Me)SO2 tBu]Li/DMPU (DMPU = dimethylpropylurea) has a half-life of racemization at -105 °C of 2.4 h, that of [PhCH2 C(Me)SO2 CF3 ]Li at -78 °C is 30 d. DNMR spectroscopy of amides (PhCH2 )2 NSO2 CF3 and (PhCH2 )N(Ph)SO2 CF3 gave NS rotational barriers that seem to be distinctly higher than those of nonfluorinated sulfonamides. NMR spectroscopy of [PhCH2 C(Ph)SO2 R]M (M=Li, K, NBu4 ; R=CF3 , tBu) shows for both salts a confinement of the negative charge mainly to the Cα atom and a significant benzylic stabilization that is weaker in the trifluoromethylsulfonyl carbanion. According to crystal structure analyses, the carbanions of salts {[PhCH2 C(Ph)SO2 CF3 ]Li⋅L}2 (L=2 THF, tetramethylethylenediamine (TMEDA)) and [PhCH2 C(Ph)SO2 CF3 ]NBu4 have

  18. Continuous Molecular Fields Approach Applied to Structure-Activity Modeling

    CERN Document Server

    Baskin, Igor I

    2013-01-01

    The Method of Continuous Molecular Fields is a universal approach to predict various properties of chemical compounds, in which molecules are represented by means of continuous fields (such as electrostatic, steric, electron density functions, etc). The essence of the proposed approach consists in performing statistical analysis of functional molecular data by means of joint application of kernel machine learning methods and special kernels which compare molecules by computing overlap integrals of their molecular fields. This approach is an alternative to traditional methods of building 3D structure-activity and structure-property models based on the use of fixed sets of molecular descriptors. The methodology of the approach is described in this chapter, followed by its application to building regression 3D-QSAR models and conducting virtual screening based on one-class classification models. The main directions of the further development of this approach are outlined at the end of the chapter.

  19. Giant Molecular Cloud Structure and Evolution

    Science.gov (United States)

    Hollenbach, David (Technical Monitor); Bodenheimer, P. H.

    2003-01-01

    Bodenheimer and Burkert extended earlier calculations of cloud core models to study collapse and fragmentation. The initial condition for an SPH collapse calculation is the density distribution of a Bonnor-Ebert sphere, with near balance between turbulent plus thermal energy and gravitational energy. The main parameter is the turbulent Mach number. For each Mach number several runs are made, each with a different random realization of the initial turbulent velocity field. The turbulence decays on a dynamical time scale, leading the cloud into collapse. The collapse proceeds isothermally until the density has increased to about 10(exp 13) g cm(exp -3). Then heating is included in the dense regions. The nature of the fragmentation is investigated. About 15 different runs have been performed with Mach numbers ranging from 0.3 to 3.5 (the typical value observed in molecular cloud cores is 0.7). The results show a definite trend of increasing multiplicity with increasing Mach number (M), with the number of fragments approximately proportional to (1 + M). In general, this result agrees with that of Fisher, Klein, and McKee who published three cases with an AMR grid code. However our results show that there is a large spread about this curve. For example, for M=0.3 one case resulted in no fragmentation while a second produced three fragments. Thus it is not only the value of M but also the details of the superposition of the various velocity modes that play a critical role in the formation of binaries. Also, the simulations produce a wide range of separations (10-1000 AU) for the multiple systems, in rough agreement with observations. These results are discussed in two conference proceedings.

  20. [Crystal and molecular structure of cytisine salts].

    Science.gov (United States)

    Niedźwiecka, Julia; Przybył, Anna K; Kubicki, Maciej

    2012-01-01

    Cytisine is an alkaloid of plant origin. It is a toxic substance, obtained on an industrial scale from Laburnum anagyroides also known as common laburnum. Today is used in the preparation of anti-smoking products as an agonist of nicotinic receptors nAChR-alpha4beta2. Thanks to crystallographic methods we can examine and describe with high accuracy the actual structure of complex chemical compounds. This work aims to present a series of tests carried out on crystals of cytisine salts, after a prior isolation of cytisine from the seeds of laburnum anagyroides.

  1. Ionization probes of molecular structure and chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, P.M. [State Univ. of New York, Stony Brook (United States)

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  2. Linking numerical simulations of molecular cloud structure with observations.

    Science.gov (United States)

    Kainulainen, Jouni

    2015-08-01

    Understanding the physical processes that control the life-cycle of the cold interstellar medium (ISM) is one of the key themes in the astrophysics of galaxies today. This importance derives from the role of the cold ISM as the birthplace of new stars, and consequently, as an indivisible constituent of galaxy evolution. In the current paradigm of turbulence-regulated ISM, star formation is controlled by the internal structure of individual molecular clouds, which in turn is set by a complex interplay of turbulence, gravity, and magnetic fields in the clouds. It is in the very focus of the field to determine how these processes give rise to the observed structure of molecular clouds. In this talk, I will review our current efforts to confront this paradigm with the goal of observationally constraining how different processes regulate molecular cloud structure and star formation. At the heart of these efforts lies the use of numerical simulations of gravo-turbulent media to A) define physically meaningful characteristics that are sensitive to the different cloud-shaping processes, and B) determine if and how such characteristics can be recovered by observations. I will show in my talk how this approach has recently led to new constraints for some fundamental measures of the molecular cloud structure. Such constraints allow us to assess the roles of turbulence and gravity in controlling the ISM structure and star formation. I will also highlight specific recent results, focusing on the nature of filamentary structures within molecular clouds. These results may provide a novel set of observational constraints with which to challenge the turbulence-regulated ISM paradigm. Finally, I will discuss the current challenges and open questions in understanding the link between molecular cloud structure and star formation, and speculate on key directions to aim the near-future studies.

  3. Syntheses and molecular structures of new cali.

    Science.gov (United States)

    Attner, J; Radius, U

    2001-01-01

    An unusual disproportionation reaction of the molybdenum(IV) and tungsten(IV) chlorides [MCl4L2] (M=Mo, L=Et2S, Et2O; M=W; L= Et2S) in the presence of p-tBu-calix[4]arene (Cax(OH)4) and triethylamine leads to d0 complexes [(CaxO4)[CaxO2(OH)2]M] (1) and d3 compounds (HNEt3)2[(CaxO4)2M2] (2). Complexes la (M = Mo), 1b (M = W), and the HCl adduct of 2a (M = Mo) have been structurally characterized. Compound 1a represents one of the few examples of a well-characterized molybdenum(VI) hexa-alkoxide complex of the type [Mo(OR)6]. Isolation and structural characterization of the side product [(CaxO4W)[kappa2(O)-kappa1(O)-CaxO3(OH)](CaxO4WCl)] (3) suggests the intermediacy of chloro-containing calix[4]arene complexes in these reaction mixtures. The reaction of 1a with HCI provides [CaxO4MoCl2] (4a), the first well-defined example of a mixed molybdenum(VI) alkoxide halide compound of the general formula [MoClx(OR)6-x].

  4. Electron capture decay of {sup 116}In and nuclear structure of double {beta} decays

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, M.; Garcia, A.; Ortiz, C.E.; Kaloskamis, N.I. [University of Notre Dame, Notre Dame, Indiana 46556 (United States); Hindi, M.M. [Physics Department, Tennessee Technological University, Cookeville, Tennessee 38505 (United States); Norman, E.B. [Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Davids, C.N. [Physics Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Civitarese, O. [Department of Physics, University of La Plata, C. C. 67, 1900-La Plata (Argentina); Suhonen, J. [Department of Physics, University of Jyvaeskylae, P.O. Box 35, SF-40351, Jyvaeskylae (Finland)

    1998-08-01

    Quasiparticle-random-phase-approximation (QRPA) calculations of double {beta} decays have not been able to reproduce data in the A=100 system. We propose the A=116 system{emdash}because of its smaller deformation{emdash}as a simpler system to test QRPA calculations. We present results of two experiments we performed, which determine the electron-capture-decay branch of {sup 116}In to be (2.27{plus_minus}0.63){times}10{sup {minus}2}{percent}, from which we deduce logft=4.39{sub {minus}0.15}{sup +0.10}. We present QRPA calculations and compare their predictions to experimental data. Finally we use these calculations to predict the 2{nu} double-{beta}-decay rate of {sup 116}Cd to the ground and excited states of {sup 116}Sn. {copyright} {ital 1998} {ital The American Physical Society}

  5. Microwave spectrum and molecular structure of PNO

    Science.gov (United States)

    Okabayashi, Toshiaki; Yamazaki, Emi; Tanimoto, Mitsutoshi

    1999-08-01

    The microwave spectra of P14N16O and its isotopomers P15N16O and P14N18O were observed in a dc glow discharge plasma of a mixture of nitric oxide and hydrogen gases over solid red phosphorus placed on the stainless steel electrode. Rotational transitions of the parent P14N16O species were measured in the ground state as well as in the vibrationally excited ν1 (PN str.), ν2 (bend), and 2ν2 states. The l=0 substate of the 2ν2 state interacts with the ν1 state through a Fermi resonance. The rotational constants determined for the ground states of the three isotopomers yield the substitution structure, rs(PN)=151.6516(87) pm and rs(NO)=119.5025(80) pm.

  6. Watching coherent molecular structural dynamics during photoreaction: beyond kinetic description

    CERN Document Server

    Lemke, Henrik T; Hartsock, Robert; van Driel, Tim Brandt; Chollet, Matthieu; Glownia, J M; Song, Sanghoon; Zhu, Diling; Pace, Elisabetta; Nielsen, Martin M; Benfatto, Maurizio; Gaffney, Kelly J; Collet, Eric; Cammarata, Marco

    2015-01-01

    A deep understanding of molecular photo-transformations occurring is challenging because of the complex interaction between electronic and nuclear structure. The initially excited electronic energy dissipates into electronic and structural reconfigurations often in less than a billionth of a second. Molecular dynamics induced by photoexcitation have been very successfully studied with femtosecond optical spectroscopies, but electronic and nuclear dynamics are often very difficult to disentangle. X-ray based spectroscopies can reduce the ambiguity between theoretical models and experimental data, but it is only with the recent development of bright ultrafast X-ray sources, that key information during transient molecular processes can be obtained on their intrinsic timescale. We use Free Electron Laser (FEL) based time-resolved X-ray Absorption Near Edge Structure (XANES) measurements around the Iron K-edge of a spin crossover prototypical compound. We reveal its transformation from the ligand-located electroni...

  7. Molecular structure of vapor-deposited amorphous selenium

    Science.gov (United States)

    Goldan, A. H.; Li, C.; Pennycook, S. J.; Schneider, J.; Blom, A.; Zhao, W.

    2016-10-01

    The structure of amorphous selenium is clouded with much uncertainty and contradictory results regarding the dominance of polymeric chains versus monomer rings. The analysis of the diffraction radial distribution functions are inconclusive because of the similarities between the crystalline allotropes of selenium in terms of the coordination number, bond length, bond angle, and dihedral angle. Here, we took a much different approach and probed the molecular symmetry of the thermodynamically unstable amorphous state via analysis of structural phase transformations. We verified the structure of the converted metastable and stable crystalline structures using scanning transmission electron microscopy. In addition, given that no experimental technique can tell us the exact three-dimensional atomic arrangements in glassy semiconductors, we performed molecular-dynamic simulations using a well-established empirical three-body interatomic potential. We developed a true vapor-deposited process for the deposition of selenium molecules onto a substrate using empirical molecular vapor compositions and densities. We prepared both vapor-deposited and melt-quenched samples and showed that the simulated radial distribution functions match very well to experiment. The combination of our experimental and molecular-dynamic analyses shows that the structures of vapor- and melt-quenched glassy/amorphous selenium are quite different, based primarily on rings and chains, respectively, reflecting the predominant structure of the parent phase in its thermodynamic equilibrium.

  8. Capturing molecular structural dynamics by 100 ps time-resolved X-ray absorption spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Sato, Tokushi [Department of Materials Science, Tokyo Institute of Technology, 2-12-1-H61 Ohokayama, Meguro-ku, Tokyo 152-8551 (Japan); Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Nozawa, Shunsuke; Ichiyanagi, Kohei [Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Tomita, Ayana [Department of Materials Science, Tokyo Institute of Technology, 2-12-1-H61 Ohokayama, Meguro-ku, Tokyo 152-8551 (Japan); Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Chollet, Matthieu [Department of Materials Science, Tokyo Institute of Technology, 2-12-1-H61 Ohokayama, Meguro-ku, Tokyo 152-8551 (Japan); Ichikawa, Hirohiko [Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Fujii, Hiroshi [Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, Myodaiji, Okazaki 444-8787 (Japan); Adachi, Shin-ichi [Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Koshihara, Shin-ya, E-mail: skoshi@cms.titech.ac.jp [Department of Materials Science, Tokyo Institute of Technology, 2-12-1-H61 Ohokayama, Meguro-ku, Tokyo 152-8551 (Japan); Non-Equilibrium Dynamics Project, ERATO, Japan Science and Technology Agency, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Frontier Research Center, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551 (Japan)

    2009-01-01

    An experimental set-up for time-resolved X-ray absorption spectroscopy with 100 ps time resolution at beamline NW14A at the Photon Factory Advanced Ring is presented. An experimental set-up for time-resolved X-ray absorption spectroscopy with 100 ps time resolution at beamline NW14A at the Photon Factory Advanced Ring is presented. The X-ray positional active feedback to crystals in a monochromator combined with a figure-of-merit scan of the laser beam position has been utilized as an essential tool to stabilize the spatial overlap of the X-ray and laser beams at the sample position. As a typical example, a time-resolved XAFS measurement of a photo-induced spin crossover reaction of the tris(1,10-phenanthrorine)iron(II) complex in water is presented.

  9. Crystal and molecular structure of aflatrem

    Directory of Open Access Journals (Sweden)

    Bruno N. Lenta

    2015-11-01

    Full Text Available The crystal structure of the title compound, C32H39NO4, confirms the absolute configuration of the seven chiral centres in the molecule. The molecule has a 1,1-dimethylprop-2-enyl substituent on the indole nucleus and this nucleus shares one edge with the five-membered ring which is, in turn, connected to a sequence of three edge-shared fused rings. The skeleton is completed by the 7,7-trimethyl-6,8-dioxabicyclo[3.2.1]oct-3-en-2-one group connected to the terminal cyclohexene ring. The two cyclohexane rings adopt chair and half-chair conformations, while in the dioxabicyclo[3.2.1]oct-3-en-2-one unit, the six-membered ring has a half-chair conformation. The indole system of the molecule exhibits a tilt of 2.02 (1° between its two rings. In the crystal, O—H...O hydrogen bonds connect molecules into chains along [010]. Weak N—H...π interactions connect these chains, forming sheets parallel to (10-1.

  10. Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

    DEFF Research Database (Denmark)

    Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

    1999-01-01

    2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v...... anthralin, the description of the vibrational structure of the compound is thus complicated by the circumstance that moment directions for transitions polarized perpendicular to the C2 axis (z) are not uniquely determined by symmetry, but can take any direction in the xy plane. The molecular vibrations...

  11. Nonlinear excitations in two-dimensional molecular structures with impurities

    DEFF Research Database (Denmark)

    Gaididei, Yuri Borisovich; Rasmussen, Kim; Christiansen, Peter Leth

    1995-01-01

    We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence of the imp......We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence...... excitations. Analytical results are in good agreement with numerical simulations of the nonlinear Schrodinger equation....

  12. Importance of Molecular Structure on the Thermophoresis of Binary Mixtures.

    Science.gov (United States)

    Kumar, Pardeep; Goswami, Debabrata

    2014-12-26

    Using thermal lens spectroscopy, we study the role of molecular structural isomers of butanol on the thermophoresis (or Soret effect) of binary mixtures of methanol in butanol. In this study, we show that the thermal lens signal due to the Soret effect changes its sign for all the different concentrations of binary mixtures of butanol with methanol except for the one containing tertiary-butanol. The magnitude and sign of the Soret coefficients strongly depend on the molecular structure of the isomers of butanol in the binary mixture with methanol. This isomerization dependence is in stark contrast to the expected mass dependence of the Soret effect.

  13. Simultaneous electrochemical immunoassay using graphene-Au grafted recombinant apoferritin-encoded metallic labels as signal tags and dual-template magnetic molecular imprinted polymer as capture probes.

    Science.gov (United States)

    Wang, De; Gan, Ning; Zhang, Huairong; Li, Tianhua; Qiao, Li; Cao, Yuting; Su, Xiurong; Jiang, Shan

    2015-03-15

    A novel electrochemical multiplexed immunoassay was designed for simultaneous determination of alpha-fetoprotein (AFP) and carcinoembryonic antigen (CEA) using recombinant apoferritin-encoded metallic nanoparticles (rApo-M) as labels and dual-template magnetic molecularly imprinted polymers (MMIPs) as capture probes. The labels were prepared by loading recombinant apoferritin (r-Apo) and separately immobilize primary antibodies (anti-AFP and anti-CEA) via Au nanoparticles of in site growth on graphene (G). The capture probes were synthesized by self-polymerization of dopamine (DA) on the Fe3O4 nanoparticles (Fe3O4 NPs) and using AFP and CEA as the template proteins, which were used to enrich the targets simultaneously. After a sandwich-type immunoreaction, the labels were captured to the surface of MMIPs. The subsequent electrochemical stripping analysis of the metal components from the immunocomplex provide a means for quantification of targets based on the peak currents of Cd and Pb. Experimental results showed the immunoassay enabled the simultaneous determination of AFP and CEA in a single run with wide dynamic ranges of 0.001-5ngmL(-1). And the detection limits of AFP and CEA were 0.3 and 0.35pgmL(-1) (S/N=3), respectively. These results suggested that the proposed multiplexed immunoassay would be applied for clinical screening of other biomarkers.

  14. A structural evaluation of the tungsten isotopes via thermal neutron capture

    CERN Document Server

    Hurst, A M; Sleaford, B W; Summers, N C; Revay, Zs; Szentmiklosi, L; Basunia, M S; Belgya, T; Escher, J E; Krticka, M

    2014-01-01

    Total radiative thermal neutron-capture $\\gamma$-ray cross sections for the $^{182,183,184,186}$W isotopes were measured using guided neutron beams from the Budapest Research Reactor to induce prompt and delayed $\\gamma$ rays from elemental and isotopically-enriched tungsten targets. These cross sections were determined from the sum of measured $\\gamma$-ray cross sections feeding the ground state from low-lying levels below a cutoff energy, E$_{\\rm crit}$, where the level scheme is completely known, and continuum $\\gamma$ rays from levels above E$_{\\rm crit}$, calculated using the Monte Carlo statistical-decay code DICEBOX. The new cross sections determined in this work for the tungsten nuclides are: $\\sigma_{0}(^{182}{\\rm W}) = 20.5(14)$ b and $\\sigma_{11/2^{+}}(^{183}{\\rm W}^{m}, 5.2 {\\rm s}) = 0.177(18)$ b; $\\sigma_{0}(^{183}{\\rm W}) = 9.37(38)$ b and $\\sigma_{5^{-}}(^{184}{\\rm W}^{m}, 8.33 \\mu{\\rm s}) = 0.0247(55)$ b; $\\sigma_{0}(^{184}{\\rm W}) = 1.43(10)$ b and $\\sigma_{11/2^{+}}(^{185}{\\rm W}^{m}, 1.67 ...

  15. Molecular Medicine: Synthesis and In Vivo Detection of Agents for use in Boron Neutron Capture Therapy. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Kabalka, G. W.

    2005-06-28

    The primary objective of the project was the development of in vivo methods for the detection and evaluation of tumors in humans. The project was focused on utilizing positron emission tomography (PET) to monitor the distribution and pharamacokinetics of a current boron neutron capture therapy (BNCT) agent, p-boronophenylalanine (BPA) by labeling it with a fluorine-18, a positron emitting isotope. The PET data was then used to develop enhanced treatment planning protocols. The study also involved the synthesis of new tumor selective BNCTagents that could be labeled with radioactive nuclides for the in vivo detection of boron.

  16. Native electrospray ionization and electron-capture dissociation for comparison of protein structure in solution and the gas phase.

    Science.gov (United States)

    Zhang, Hao; Cui, Weidong; Gross, Michael L

    2013-11-15

    The importance of protein and protein-complex structure motivates improvements in speed and sensitivity of structure determination in the gas phase and comparison with that in solution or solid state. An opportunity for the gas phase measurement is mass spectrometry (MS) combined with native electrospray ionization (ESI), which delivers large proteins and protein complexes in their near-native states to the gas phase. In this communication, we describe the combination of native ESI, electron-capture dissociation (ECD), and top-down MS for exploring the structures of ubiquitin and cytochrome c in the gas phase and their relation to those in the solid-state and solution. We probe structure by comparing the protein's flexible regions, as predicted by the B-factor in X-ray crystallography, with the ECD fragments. The underlying hypothesis is that maintenance of structure gives fragments that can be predicted from B-factors. This strategy may be applicable in general when X-ray structures are available and extendable to the study of intrinsically disordered proteins.

  17. Plant structure predicts leaf litter capture in the tropical montane bromeliad Tillandsia turneri

    Directory of Open Access Journals (Sweden)

    F. Ospina-Bautista

    Full Text Available Abstract Leaves intercepted by bromeliads become an important energy and matter resource for invertebrate communities, bacteria, fungi, and the plant itself. The relationship between bromeliad structure, defined as its size and complexity, and accumulated leaf litter was studied in 55 bromeliads of Tillandsia turneri through multiple regression and the Akaike information criterion. Leaf litter accumulation in bromeliads was best explained by size and complexity variables such as plant cover, sheath length, and leaf number. In conclusion, plant structure determines the amount of litter that enters bromeliads, and changes in its structure could affect important processes within ecosystem functioning or species richness.

  18. Structural and morphological characterization of active intermontane basins: a case of the Gubbio captured basin (Umbria Pre-Apennines, Italy)

    Science.gov (United States)

    Cavitolo, Paolo; Menichetti, Marco; Nesci, Olivia; Savelli, Daniele; Troiani, Francesco

    2014-05-01

    Intermontane basins characterize many orogenic chains, where they are originated either by crustal stretching or gravitational collapse of the axial zones of the chain. Extensional and/or transtensional mechanisms generate structures with geometries controlled by fault-bounded depressed areas, which in some cases are seismogenetic. The western sector of the Northern Apennines in Central Italy is characterized by several intermontane basins filled by continental Plio-Pleistocene sediments. At present, a few of these basins are depressed endorheic areas, whereas most of them have been captured by river upstream erosion. The morphotectonic characterization at both regional and local scale of these structures is crucial considering the associated geological hazards due to clustered seismicity and seismic-related slope-instability along the basin-margins. This work presents a multi-disciplinary approach based on new and existing data to define the structural geometries, landforms and processes related to the genesis and the morphoevolution of the intermountain valleys/captured-basins in Central Italy. Quantitative geomorphological analyses from Digital Terrain Models (DTMs) are compared with geological and structural data and with geophysical investigations of active and sismogenetic faults bordering the Gubbio valley in the Umbria Pre-Apennines in central Italy. This 4 km-wide valley extends for ca. 20 km in NW-SE direction and is bounded along the NE margin by a SW-dipping listric normal fault with an offset of 1500 m. The area locates along one of the main seismogenic portion of the Apennine chain and recorded historical (i.e., April 29, 1984: Ms 5.3) and many instrumental earthquakes. In this study, new data on the slope-instability along the basin-margins and the influence of active tectonics and gravitational phenomena on the streams incision and aggradation are also provided.

  19. Origin and structure of polar domains in doped molecular crystals

    Science.gov (United States)

    Meirzadeh, E.; Azuri, I.; Qi, Y.; Ehre, D.; Rappe, A. M.; Lahav, M.; Kronik, L.; Lubomirsky, I.

    2016-11-01

    Doping is a primary tool for the modification of the properties of materials. Occlusion of guest molecules in crystals generally reduces their symmetry by the creation of polar domains, which engender polarization and pyroelectricity in the doped crystals. Here we describe a molecular-level determination of the structure of such polar domains, as created by low dopant concentrations (<0.5%). The approach comprises crystal engineering and pyroelectric measurements, together with dispersion-corrected density functional theory and classical molecular dynamics calculations of the doped crystals, using neutron diffraction data of the host at different temperatures. This approach is illustrated using centrosymmetric α-glycine crystals doped with minute amounts of different L-amino acids. The experimentally determined pyroelectric coefficients are explained by the structure and polarization calculations, thus providing strong support for the local and global understanding of how different dopants influence the properties of molecular crystals.

  20. Molecular structure and elastic properties of thermotropic liquid crystals: Integrated molecular dynamics—Statistical mechanical theory vs molecular field approach

    Science.gov (United States)

    Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.

    2013-03-01

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  1. Density functional theory study on the molecular structure of loganin

    OpenAIRE

    Pandey, Anoop Kumar; Siddiqui, Shamoon Ahmad; Dwivedi, Apoorva; Raj, Kanwal; Misra, Neeraj

    2011-01-01

    The computational Quantum Chemistry (QC) has been used for different types of problems, for example: structural biology, surface phenomena and liquid phase. In this paper we have employed the density functional method for the study of molecular structure of loganin. The equilibrium geometry, harmonic vibrational frequencies and infrared intensities were calculated by B3LYP/6-311G (d, p) method and basis set combinations. It was found that the optimized parameters obtained by the DFT/B3LYP met...

  2. Optimization techniques in molecular structure and function elucidation

    OpenAIRE

    2009-01-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly ...

  3. Crystal and molecular structure of lancerodiol-p-hydroxybenzoate

    Directory of Open Access Journals (Sweden)

    Mohamed H Abd El-Razek

    2010-01-01

    Full Text Available Lancerodiol-p-hydroxybenzoate was isolated from the leaves of Ferula sinaica L. (Apiaceae as light needle crystals. This work reports for the first time the molecular structure and relative configuration of compound 1, established by X-ray analysis.

  4. Crystalline molecular complexes and compounds structures and principles

    CERN Document Server

    Herbstein, Frank H

    2005-01-01

    This book provides an account of the structure and properties of crystalline binary adducts. Such crystals are perhaps better known as molecular compounds and complexes and are estimated to make up one quarter of the world's crystals. More than 600 figures, 200 tables and 3500 references are included in the book.

  5. Structural changes in polytetrafluoroethylene molecular chains upon sliding against steel

    NARCIS (Netherlands)

    Shen, J.T.; Pei, Y.T.; Hosson, J.Th.M. De

    2014-01-01

    In this work, the influence of dry sliding between a steel counterpart ball and polytetrafluoroethylene (PTFE) plate sample on the transformation of PTFE molecular structure is investigated. With X-ray diffraction, differential scanning calorimetry, Fourier transform infrared (FT-IR) spectroscopy an

  6. Gas-phase structure of amyloid-β (12-28) peptide investigated by infrared spectroscopy, electron capture dissociation and ion mobility mass spectrometry.

    Science.gov (United States)

    Le, Thi Nga; Poully, Jean Christophe; Lecomte, Frédéric; Nieuwjaer, Nicolas; Manil, Bruno; Desfrançois, Charles; Chirot, Fabien; Lemoine, Jerome; Dugourd, Philippe; van der Rest, Guillaume; Grégoire, Gilles

    2013-12-01

    The gas-phase structures of doubly and triply protonated Amyloid-β12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N - Cα bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 310- and α-helix motifs.

  7. Structural basis for arabinoxylo‐oligosaccharide capture by the probiotic Bifidobacterium animalis subsp. lactis Bl‐04

    DEFF Research Database (Denmark)

    Hansen, Morten Ejby; Fredslund, Folmer; Vujicic‐Zagar, Andreja

    2013-01-01

    specificity for arabinosyl‐decorated and undecorated xylo‐oligosaccharides, with preference for tri‐ and tetra‐saccharides. Crystal structures of BlAXBP in complex with four different ligands revealed the basis for this versatility. Uniquely, the protein was able to recognize oligosaccharides in two opposite...

  8. Synthetic Architecture of MgO/C Nanocomposite from Hierarchical-Structured Coordination Polymer toward Enhanced CO2 Capture.

    Science.gov (United States)

    Li, Ping; Liu, Wen; Dennis, John S; Zeng, Hua Chun

    2017-03-22

    Highly efficient, durable, and earth-abundant solid sorbents are of paramount importance for practical carbon capture, storage, and utilization. Here, we report a novel and facile two-step strategy to synthesize a group of hierarchically structured porous MgO/C nanocomposites using flowerlike Mg-containing coordination polymer as a precursor. The new nanocomposites exhibit superb CO2 capture performance with sorption capacity up to 30.9 wt % (at 27 °C, 1 bar CO2), fast sorption kinetics, and long cycling life. Importantly, the achieved capacity is >14 times higher than that of commercial MgO, and favorably exceeds the highest value recorded to date for MgO-based sorbents under similar operating conditions. On the basis of the morphological and textural property analysis, together with CO2 sorption mechanism study using CO2-TPD and DRIFT techniques, the outstanding performance in CO2 uptake originates from unique features of this type of sorbent materials, which include hierarchical architecture, porous building blocks of nanosheets, high specific surface area (ca. 300 m(2)/g), evenly dispersed MgO nanocrystallites (ca. 3 nm) providing abundant active sites, and the in situ generated carbon matrix that acts as a stabilizer to prevent the growth and agglomeration of MgO crystallites. The nanocomposite system developed in this work shows good potential for future low-cost CO2 abatement and utilization.

  9. Molecular orientation and electronic structure at organic heterojunction interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Zhong, Shu [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Zhong, Jian Qiang; Wee, Andrew T.S. [Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); Chen, Wei, E-mail: phycw@nus.edu.sg [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); National University of Singapore (Suzhou) Research Institute, Suzhou (China)

    2015-10-01

    Highlights: • Molecular orientation at the organic heterojunction interfaces. • Energy level alignments at the organic heterojunction interfaces. • Gap-states mediated interfacial energy level alignment. - Abstract: Due to the highly anisotropic nature of π-conjugated molecules, the molecular orientation in organic thin films can significantly affect light absorption, charge transport, energy level alignment (ELA) and hence device performance. Synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy represents a powerful technique for probing molecular orientation. The aim of this review paper is to provide a balanced assessment on the investigation of molecular orientation at the organic–organic heterojunction (OOH) interface by NEXAFS, as well as the gap-states mediated orientation dependent energy level alignment at OOH interfaces. We highlight recent progress in elucidating molecular orientation at OOH interfaces dominated by various interfacial interactions, gap-states controlled orientation dependent energy level alignments at OOH interfaces, and the manipulations of molecular orientation and ELA in OOH.

  10. Molecular and structural advances in tissue factor-dependent coagulation.

    Science.gov (United States)

    Kirchhofer, D; Banner, D W

    1997-11-01

    The tissue factor:factor VIIa (TF-F.VIIa) complex is considered the physiological initiator of blood coagulation. Besides its role in normal hemostasis, this enzyme complex has been found to play an important role in various thrombotic disorders and thus has become an attractive target for the development of new anticoagulants. Recently, significant progress has been made in regard to structural and molecular aspects of TF-VIIa-initiated coagulation. A rather complete picture on how tissue factor binds to factor VIIa has emerged and is discussed in detail in this review. Also, the combined data of the TF-F.VIIa crystal structure, of naturally occurring F.VII variants, and of mutagenesis studies provide a framework to discuss molecular aspects of the tissue factor-mediated enhancement of F.VIIa catalytic efficiency and the recognition of macromolecular substrates. F.VIIa as a member of the serine protease family has an active site homologous to other coagulation factors. The release of the coordinates of the crystal structures of F.X and F.IX, together with the earlier determined thrombin structure, now allows a detailed comparison of these active centers with respect to the development of specific and potent active site inhibitors. This structural and molecular information about the TF-F.VIIa complex and other coagulation enzymes adds to our understanding of blood coagulation and should further the development of new classes of anticoagulants. (Trends Cardiovasc Med 1997;7:316-324). © 1997, Elsevier Science Inc.

  11. Insights into molecular structure and digestion rate of oat starch.

    Science.gov (United States)

    Xu, Jinchuan; Kuang, Qirong; Wang, Kai; Zhou, Sumei; Wang, Shuo; Liu, Xingxun; Wang, Shujun

    2017-04-01

    The in vitro digestibility of oat starch and its relationship with starch molecular structure was investigated. The in vitro digestion results showed that the first-order kinetic constant (k) of oat starches (OS-1 and OS-2) was lower than that of rice starch. The size of amylose chains, amylose content and degree of branching (DB) of amylopectin in oat starch were significantly higher than the corresponding parameters in rice starch. The larger molecular size of oat starch may account for its lower digestion rate. The fine structure of amylopectin showed that oat starch had less chains of DP 6-12 and DP>36, which may explain the small difference in digestion rate between oat and rice starch. The biosynthesis model from oat amylopectin fine structure data suggested a lower starch branching enzyme (SBE) activity and/or a higher starch synthase (SS) activity, which may decrease the DB of oat starch and increase its digestion rate.

  12. Topological Indices Study of Molecular Structure in Anticancer Drugs

    Directory of Open Access Journals (Sweden)

    Wei Gao

    2016-01-01

    Full Text Available Numerous studies indicate that there is strong inherent relationship between the chemical characteristics of chemical compounds and drugs (e.g., boiling point and melting point and their molecular structures. Topological indices defined on these chemical molecular structures can help researchers better understand the physical features, chemical reactivity, and biological activity. Thus, the study of the topological indices on chemical structure of chemical materials and drugs can make up for lack of chemical experiments and can provide a theoretical basis for the manufacturing of drugs and chemical materials. In this paper, we focus on the family of smart polymer which is widely used in anticancer drugs manufacturing. Several topological indices are determined in view of edge dividing methods, and these results remedy the lack of chemical and medicine experiments thus providing the theoretical basis for pharmaceutical engineering.

  13. MOLVIE: an interactive visualization environment for molecular structures.

    Science.gov (United States)

    Sun, Huandong; Li, Ming; Xu, Ying

    2003-05-01

    A Molecular visualization interactive environment (MOLVIE), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of MOLVIE, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html.

  14. Capturing Structural Dynamics in Crystalline Silicon Using Chirped Electrons from a Laser Wakefield Accelerator

    CERN Document Server

    He, Z -H; Nees, J A; Gallé, G; Scott, S A; Pérez, J R Sanchez; Lagally, M G; Krushelnick, K; Thomas, A G R; Faure, J

    2016-01-01

    Recent progress in laser wakefield acceleration has led to the emergence of a new generation of electron and X-ray sources that may have enormous benefits for ultrafast science. These novel sources promise to become indispensable tools for the investigation of structural dynamics on the femtosecond time scale, with spatial resolution on the atomic scale. Here, we demonstrate the use of laser-wakefield-accelerated electron bunches for time-resolved electron diffraction measurements of the structural dynamics of single-crystal silicon nano-membranes pumped by an ultrafast laser pulse. In our proof-of-concept study, we resolve the silicon lattice dynamics on a picosecond time scale by deflecting the momentum-time correlated electrons in the diffraction peaks with a static magnetic field to obtain the time-dependent diffraction efficiency. Further improvements may lead to femtosecond temporal resolution, with negligible pump-probe jitter being possible with future laser-wakefield-accelerator ultrafast-electron-di...

  15. Capturing Structural Dynamics in Crystalline Silicon Using Chirped Electrons from a Laser Wakefield Accelerator

    Science.gov (United States)

    He, Z.-H.; Beaurepaire, B.; Nees, J. A.; Gallé, G.; Scott, S. A.; Pérez, J. R. Sánchez; Lagally, M. G.; Krushelnick, K.; Thomas, A. G. R.; Faure, J.

    2016-11-01

    Recent progress in laser wakefield acceleration has led to the emergence of a new generation of electron and X-ray sources that may have enormous benefits for ultrafast science. These novel sources promise to become indispensable tools for the investigation of structural dynamics on the femtosecond time scale, with spatial resolution on the atomic scale. Here, we demonstrate the use of laser-wakefield-accelerated electron bunches for time-resolved electron diffraction measurements of the structural dynamics of single-crystal silicon nano-membranes pumped by an ultrafast laser pulse. In our proof-of-concept study, we resolve the silicon lattice dynamics on a picosecond time scale by deflecting the momentum-time correlated electrons in the diffraction peaks with a static magnetic field to obtain the time-dependent diffraction efficiency. Further improvements may lead to femtosecond temporal resolution, with negligible pump-probe jitter being possible with future laser-wakefield-accelerator ultrafast-electron-diffraction schemes.

  16. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

    Science.gov (United States)

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

  17. Rapid excited state structural reorganization captured by pulsed x-rays.

    Energy Technology Data Exchange (ETDEWEB)

    Chen, L. X.; Jennings, G.; Liu, T.; Gosztola, D. J.; Hessler, J. P.; Scaltrito, D. V.; Meyer, G. J.; Johns Hopkins Univ.

    2002-09-11

    Visible light excitation of [CuI(dmp)2](BArF), where dmp is 2,9-dimethyl-1,10-phenanthroline and BArF is tetrakis(3,5-bis(trifluoromethylphenyl))borate, in toluene produces a photoluminescent, metal-to-ligand charge-transfer (MLCT) excited state with a lifetime of 98 {+-} 5 ns. Probing this state within 14 ns after photoexcitation with pulsed X-rays establishes that a CuII center, borne in a CuI geometry, binds an additional ligand to form a five-coordinate complex with increased bond lengths and a coordination geometry of distorted trigonal bipyramid. The average Cu-N bond length increases in the excited state by 0.07 Angstroms. The transiently formed five-coordinate MLCT state is photoluminescent under the condition studied, indicating that the absorptive and emissive states have distinct geometries. The data represent the first X-ray characterization of a molecular excited state in fluid solution on a nanosecond time scale.

  18. Probing the Gaseous Structure of a β-Hairpin Peptide with H/D Exchange and Electron Capture Dissociation

    Science.gov (United States)

    Straus, Rita N.; Jockusch, Rebecca A.

    2017-02-01

    An improved understanding of the extent to which native protein structure is retained upon transfer to the gas phase promises to enhance biological mass spectrometry, potentially streamlining workflows and providing fundamental insights into hydration effects. Here, we investigate the gaseous conformation of a model β-hairpin peptide using gas-phase hydrogen-deuterium (H/D) exchange with subsequent electron capture dissociation (ECD). Global gas-phase H/D exchange levels, and residue-specific exchange levels derived from ECD data, are compared among the wild type 16-residue peptide GB1p and several variants. High protection from H/D exchange observed for GB1p, but not for a truncated version, is consistent with the retention of secondary structure of GB1p in the gas phase or its refolding into some other compact structure. Four alanine mutants that destabilize the hairpin in solution show levels of protection similar to that of GB1p, suggesting collapse or (re)folding of these peptides upon transfer to the gas phase. These results offer a starting point from which to understand how a key secondary structural element, the β-hairpin, is affected by transfer to the gas phase. This work also demonstrates the utility of a much-needed addition to the tool set that is currently available for the investigation of the gaseous conformation of biomolecules, which can be employed in the future to better characterize gaseous proteins and protein complexes.

  19. Probing the Gaseous Structure of a β-Hairpin Peptide with H/D Exchange and Electron Capture Dissociation

    Science.gov (United States)

    Straus, Rita N.; Jockusch, Rebecca A.

    2016-12-01

    An improved understanding of the extent to which native protein structure is retained upon transfer to the gas phase promises to enhance biological mass spectrometry, potentially streamlining workflows and providing fundamental insights into hydration effects. Here, we investigate the gaseous conformation of a model β-hairpin peptide using gas-phase hydrogen-deuterium (H/D) exchange with subsequent electron capture dissociation (ECD). Global gas-phase H/D exchange levels, and residue-specific exchange levels derived from ECD data, are compared among the wild type 16-residue peptide GB1p and several variants. High protection from H/D exchange observed for GB1p, but not for a truncated version, is consistent with the retention of secondary structure of GB1p in the gas phase or its refolding into some other compact structure. Four alanine mutants that destabilize the hairpin in solution show levels of protection similar to that of GB1p, suggesting collapse or (re)folding of these peptides upon transfer to the gas phase. These results offer a starting point from which to understand how a key secondary structural element, the β-hairpin, is affected by transfer to the gas phase. This work also demonstrates the utility of a much-needed addition to the tool set that is currently available for the investigation of the gaseous conformation of biomolecules, which can be employed in the future to better characterize gaseous proteins and protein complexes.

  20. Structural determinants for ligand capture by a class II preQ1 riboswitch.

    Science.gov (United States)

    Kang, Mijeong; Eichhorn, Catherine D; Feigon, Juli

    2014-02-11

    Prequeuosine (preQ1) riboswitches are RNA regulatory elements located in the 5' UTR of genes involved in the biosynthesis and transport of preQ1, a precursor of the modified base queuosine universally found in four tRNAs. The preQ1 class II (preQ1-II) riboswitch regulates preQ1 biosynthesis at the translational level. We present the solution NMR structure and conformational dynamics of the 59 nucleotide Streptococcus pneumoniae preQ1-II riboswitch bound to preQ1. Unlike in the preQ1 class I (preQ1-I) riboswitch, divalent cations are required for high-affinity binding. The solution structure is an unusual H-type pseudoknot featuring a P4 hairpin embedded in loop 3, which forms a three-way junction with the other two stems. (13)C relaxation and residual dipolar coupling experiments revealed interhelical flexibility of P4. We found that the P4 helix and flanking adenine residues play crucial and unexpected roles in controlling pseudoknot formation and, in turn, sequestering the Shine-Dalgarno sequence. Aided by divalent cations, P4 is poised to act as a "screw cap" on preQ1 recognition to block ligand exit and stabilize the binding pocket. Comparison of preQ1-I and preQ1-II riboswitch structures reveals that whereas both form H-type pseudoknots and recognize preQ1 using one A, C, or U nucleotide from each of three loops, these nucleotides interact with preQ1 differently, with preQ1 inserting into different grooves. Our studies show that the preQ1-II riboswitch uses an unusual mechanism to harness exquisite control over queuosine metabolism.

  1. Capturing the Energy Absorbing Mechanisms of Composite Structures under Crash Loading

    Science.gov (United States)

    Wade, Bonnie

    As fiber reinforced composite material systems become increasingly utilized in primary aircraft and automotive structures, the need to understand their contribution to the crashworthiness of the structure is of great interest to meet safety certification requirements. The energy absorbing behavior of a composite structure, however, is not easily predicted due to the great complexity of the failure mechanisms that occur within the material. Challenges arise both in the experimental characterization and in the numerical modeling of the material/structure combination. At present, there is no standardized test method to characterize the energy absorbing capability of composite materials to aide crashworthy structural design. In addition, although many commercial finite element analysis codes exist and offer a means to simulate composite failure initiation and propagation, these models are still under development and refinement. As more metallic structures are replaced by composite structures, the need for both experimental guidelines to characterize the energy absorbing capability of a composite structure, as well as guidelines for using numerical tools to simulate composite materials in crash conditions has become a critical matter. This body of research addresses both the experimental characterization of the energy absorption mechanisms occurring in composite materials during crushing, as well as the numerical simulation of composite materials undergoing crushing. In the experimental investigation, the specific energy absorption (SEA) of a composite material system is measured using a variety of test element geometries, such as corrugated plates and tubes. Results from several crush experiments reveal that SEA is not a constant material property for laminated composites, and varies significantly with the geometry of the test specimen used. The variation of SEA measured for a single material system requires that crush test data must be generated for a range of

  2. Neighborhood structure influences the convergence in light capture efficiency and carbon gain: an architectural approach for cloud forest shrubs.

    Science.gov (United States)

    Guzmán Q, J Antonio; Cordero S, Roberto A

    2016-06-01

    Although plant competition is recognized as a fundamental factor that limits survival and species coexistence, its relative importance on light capture efficiency and carbon gain is not well understood. Here, we propose a new framework to explain the effects of neighborhood structures and light availability on plant attributes and their effect on plant performance in two understory shade-tolerant species (Palicourea padifolia (Roem. & Schult.) C.M. Taylor & Lorence and Psychotria elata (Swartz)) within two successional stages of a cloud forest in Costa Rica. Features of plant neighborhood physical structure and light availability, estimated by hemispherical photographs, were used to characterize the plant competition. Plant architecture, leaf attributes and gas exchange parameters extracted from the light-response curve were used as functional plant attributes, while an index of light capture efficiency (silhouette to total area ratio, averaged over all viewing angles, STAR) and carbon gain were used as indicators of plant performance. This framework is based in a partial least square Path model, which suggests that changes in plant performance in both species were affected in two ways: (i) increasing size and decreasing distance of neighbors cause changes in plant architecture (higher crown density and greater leaf dispersion), which contribute to lower STAR and subsequently lower carbon gain; and (ii) reductions in light availability caused by the neighbors also decrease plant carbon gain. The effect of neighbors on STAR and carbon gain were similar for the two forests sites, which were at different stages of succession, suggesting that the architectural changes of the two understory species reflect functional convergence in response to plant competition. Because STAR and carbon gain are variables that depend on multiple plant attributes and environmental characteristics, we suggest that changes in these features can be used as a whole-plant response approach to

  3. Effect of Water Concentration on the Molecular Structure of Polyacrylate Gels

    Science.gov (United States)

    Mani, Sriramvignesh; Khabaz, Fardin; Khare, Rajesh

    2015-03-01

    Recent studies have suggested pervaporation to be a promising alternative method for separation of aqueous solution of alcohol compared to distillation based separation processes. The ability to tune the hydrophobic/hydrophilic character makes polyacrylate gels attractive candidate materials for separating water-alcohol mixture by pervaporation. Experimentally, it is observed that the amount of water absorbed in the gel i.e. the degree of swelling of the gel shows a large variation with polymer chemistry. Relatively few studies exist highlighting the effects of water concentration on the membrane separation efficiency which in turn is directly related to the internal molecular structure of the water rich membranes. In this regard, an all-atom molecular dynamics (MD) simulation is employed to study water structure in polyacrylate gels. As a first step, polyacrylate copolymer systems with varying degree of hydrophobicity are prepared using the simulated annealing polymerization technique. Atomistic structures of gels containing different amounts of water are also prepared. Effect of water content on the acrylate-water system microstructure is determined by characterizing the packing of water molecules as well as the hydrogen bonding in these systems. In addition, the change in dynamics of water molecules due to the interactions with polymer is captured by monitoring the auto-correlation function of their dipole vector.

  4. Ab initio molecular crystal structures, spectra, and phase diagrams.

    Science.gov (United States)

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  5. Molecular docking and structure-based drug design strategies.

    Science.gov (United States)

    Ferreira, Leonardo G; Dos Santos, Ricardo N; Oliva, Glaucius; Andricopulo, Adriano D

    2015-07-22

    Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

  6. Molecular structures in the charmonium spectrum: the XYZ puzzle

    Science.gov (United States)

    Ortega, P. G.; Entem, D. R.; Fernández, F.

    2013-06-01

    We study in the framework of a constituent quark model the possible contributions of molecular structures to the XYZ charmonium-like states. We analyze simultaneously the c\\bar{c} structures and the possible molecular components in the coupled channel formalism. In the 1++ sector two states appear which could be identified with X(3872) and X(3940). The recently confirmed X(3915) state appears as a mixture of c\\bar{c} and D\\bar{D} components as a JPC = 0++ state in agreement with the new measurements. A second broad resonance which may correspond with the so-called Y(3940) state is found with these quantum numbers. In the JPC = 1-- sector we also found significant contributions of the molecular structures which may affect the phenomenology. In particular the study allows us to understand the G(3900) state recently observed in Belle and BaBar. All these resonances together with the prediction of the model of a c\\bar{c} structure for Z(3930) provide a reasonable scenario for the so-called XYZ states with masses near 3.9 GeV.

  7. Benchmarking Close-range Structure from Motion 3D Reconstruction Software under Varying Capturing Conditions

    DEFF Research Database (Denmark)

    Nikolov, Ivan Adriyanov; Madsen, Claus B.

    2016-01-01

    Structure from Motion 3D reconstruction has become widely used in recent years in a number of fields such as industrial surface in- inspection, archeology, cultural heritage preservation and geomapping. A number of software solutions have been released using variations of this technique....... In this paper we analyse the state of the art of these software applications, by comparing the resultant 3D meshes qualitatively and quantitatively. We propose a number of testing scenarios using different lighting conditions, camera positions and image acquisition methods for the best in-depth analysis...... and discuss the results, the overall performance and the problems present in each software. We employ distance and roughness metrics for evaluating the final reconstruction results....

  8. Molecular detection and phylogenetic analysis of tick-borne encephalitis virus in rodents captured in the transdanubian region of Hungary.

    Science.gov (United States)

    Pintér, Réka; Madai, Mónika; Horváth, Győző; Németh, Viktória; Oldal, Miklós; Kemenesi, Gábor; Dallos, Bianka; Bányai, Krisztián; Jakab, Ferenc

    2014-08-01

    Abstract Tick-borne encephalitis virus (TBEV) infection is a common zoonotic disease affecting humans in Europe and Asia. To determine whether TBEV is present in small mammalian hosts in Hungary, liver samples of wild rodents were tested for TBEV RNA. Over a period of 7 years, a total of 405 rodents were collected at five different geographic locations of the Transdanubian region. TBEV nucleic acid was identified in four rodent species: Apodemus agrarius, A. flavicollis, Microtus arvalis, and Myodes glareolus. Out of the 405 collected rodents, 17 small mammals (4.2%) were positive for TBEV. The present study provides molecular evidence and sequence data of TBEV from rodents in Hungary.

  9. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    Science.gov (United States)

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-12-19

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit.

  10. Confinement of Ionic Liquids in Nanocages: Tailoring the Molecular Sieving Properties of ZIF-8 for Membrane-Based CO2 Capture.

    Science.gov (United States)

    Ban, Yujie; Li, Zhengjie; Li, Yanshuo; Peng, Yuan; Jin, Hua; Jiao, Wenmei; Guo, Ang; Wang, Po; Yang, Qingyuan; Zhong, Chongli; Yang, Weishen

    2015-12-14

    Fine-tuning of effective pore size of microporous materials is necessary to achieve precise molecular sieving properties. Herein, we demonstrate that room temperature ionic liquids can be used as cavity occupants for modification of the microenvironment of MOF nanocages. Targeting CO2 capture applications, we tailored the effective cage size of ZIF-8 to be between CO2 and N2 by confining an imidazolium-based ionic liquid [bmim][Tf2 N] into ZIF-8's SOD cages by in-situ ionothermal synthesis. Mixed matrix membranes derived from ionic liquid-modified ZIF-8 exhibited remarkable combinations of permeability and selectivity that transcend the upper bound of polymer membranes for CO2 /N2 and CO2 /CH4 separation. We observed an unusual response of the membranes to varying pressure, that is, an increase in the CO2 /CH4 separation factor with pressure, which is highly desirable for practical applications in natural gas upgrading.

  11. Structure and radial equilibrium of filamentary molecular clouds

    CERN Document Server

    Contreras, Yanett; Garay, Guido

    2013-01-01

    Recent dust continuum surveys have shown that filamentary structures are ubiquitous along the Galactic plane. While the study of their global properties has gained momentum recently, we are still far from fully understanding their origin and stability. Theories invoking magnetic field have been formulated to help explain the stability of filaments; however, observations are needed to test their predictions. In this paper, we investigate the structure and radial equilibrium of five filamentary molecular clouds with the aim of determining the role that magnetic field may play. To do this, we use continuum and molecular line observations to obtain their physical properties (e.g. mass, temperature and pressure). We find that the filaments have lower lineal masses compared to their lineal virial masses. Their virial parameters and shape of their dust continuum emission suggests that these filaments may be confined by a toroidal dominated magnetic field.

  12. A Modiifed Molecular Structure Mechanics Method for Analysis of Graphene

    Institute of Scientific and Technical Information of China (English)

    HUA Jun; LI Dongbo; ZHAO Dong; LIANG Shengwei; LIU Qinlong; JIA Ruiyan

    2015-01-01

    Based on molecular mechanics and the deformation characteristics of the atomic lattice structure of graphene, a modiifed molecular structure mechanics method was developed to improve the original one, that is, the semi-rigid connections were used to model the bond angle variations between the C-C bonds in graphene. The simulated results show that the equivalent space frame model with semi-rigid connections for graphene proposed in this article is a simple, efifcient, and accurate model to evaluate the equivalent elastic properties of graphene. Though the present computational model of the semi-rigid connected space frame is only applied to characterize the mechanical behaviors of the space lattices of graphene, it has more potential applications in the static and dynamic analyses of graphene and other nanomaterials.

  13. Capture reactions

    NARCIS (Netherlands)

    Endt, P.M.

    1956-01-01

    Capture reactions will be considered here from the viewpoint of the nuclear spectroscopist. Especially important to him are the capture of neutrons, protons, and alpha particles, which may proceed through narrow resonances, offering a well defined initial state for the subsequent deexcitation proces

  14. Space structure capturing and assembling by experimental free-floating robot satellite (EFFORTS) simulators

    Science.gov (United States)

    Yoshida, K.

    1993-09-01

    In order to study and validate practical availability of control schemes for in-orbit operational free-floating robots, a research group at the Tokyo Institute of Technology has developed the Experimental Free-FlOating RoboT Satellite (EFFORTS-I and II) simulators, which enable to examine 2-dimensional pseudo-micro gravity motion dynamics by air lift system. The robot model comprising a satellite base body and articulated manipulator arms with grippers and wrist force sensors, makes horizontal motion without mechanical disturbances or external forces. This paper presents the control methods and experimental results for spacecraft/manipulator control paying attention to the reaction dynamics, and assembly and deployment operation of space structures. The paper focuses the discussion of (1) hardware design of EFFORTS simulators, (2) dynamic modeling and a basic control concept for space free-floating manipulators, (3) satellite attitude control coordinating with manipulator dynamics, (4) practical force control for dexterous manipulation, and (5) experimental results on above topics.

  15. Beyond the continuum: how molecular solvent structure affects electrostatics and hydrodynamics at solid-electrolyte interfaces.

    Science.gov (United States)

    Bonthuis, Douwe Jan; Netz, Roland R

    2013-10-03

    Standard continuum theory fails to predict several key experimental results of electrostatic and electrokinetic measurements at aqueous electrolyte interfaces. In order to extend the continuum theory to include the effects of molecular solvent structure, we generalize the equations for electrokinetic transport to incorporate a space dependent dielectric profile, viscosity profile, and non-electrostatic interaction potential. All necessary profiles are extracted from atomistic molecular dynamics (MD) simulations. We show that the MD results for the ion-specific distribution of counterions at charged hydrophilic and hydrophobic interfaces are accurately reproduced using the dielectric profile of pure water and a non-electrostatic repulsion in an extended Poisson-Boltzmann equation. The distributions of Na(+) at both surface types and Cl(-) at hydrophilic surfaces can be modeled using linear dielectric response theory, whereas for Cl(-) at hydrophobic surfaces it is necessary to apply nonlinear response theory. The extended Poisson-Boltzmann equation reproduces the experimental values of the double-layer capacitance for many different carbon-based surfaces. In conjunction with a generalized hydrodynamic theory that accounts for a space dependent viscosity, the model captures the experimentally observed saturation of the electrokinetic mobility as a function of the bare surface charge density and the so-called anomalous double-layer conductivity. The two-scale approach employed here-MD simulations and continuum theory-constitutes a successful modeling scheme, providing basic insight into the molecular origins of the static and kinetic properties of charged surfaces, and allowing quantitative modeling at low computational cost.

  16. Relationship between molecular cloud structure and density PDFs

    CERN Document Server

    Stanchev, Orlin; Veltchev, Todor V; Shetty, Rahul

    2013-01-01

    Volume and column density PDFs in molecular clouds are important diagnostics for understanding their general structure. We developed a novel approach to trace the cloud structure by varying the lower PDF cut-off and exploring a suggested mass-density relationship with a power-law index $x^\\prime$. The correspondence of x' as a function of spatial scale to the slope of the high-density PDF tail is studied. To validate the proposed model, we use results from hydrodynamical simulations of a turbulent self-gravitating cloud and recent data on dust continuum emission from the Planck mission.

  17. Microspectroscopy as applied to the study of wood molecular structure

    DEFF Research Database (Denmark)

    Fackler, Karin; Thygesen, Lisbeth Garbrecht

    2013-01-01

    -induced dimensional changes, decay resistance or mechanical properties. It is, however, important to choose the right technique for the purpose at hand and to apply it in a suitable way if any new insights are to be gained. This review presents and compares three different microspectroscopic techniques: infrared......Microspectroscopy gives access to spatially resolved information on the molecular structure and chemical composition of a material. For a highly heterogeneous and anisotropic material like wood, such information is essential when assessing structure/property relationships such as moisture...

  18. Structural assembly of molecular complexes based on residual dipolar couplings.

    Science.gov (United States)

    Berlin, Konstantin; O'Leary, Dianne P; Fushman, David

    2010-07-07

    We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDCs) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein-protein complex by utilizing the RDCs' sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein-protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein-protein complex solely on the basis of experimental RDC data and the prediction of the alignment tensor from 3D structures. Thus, despite the purely angular nature of RDCs, they can be converted into intermolecular distance/translational constraints. Additionally, we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of protein complexes.

  19. Influence of amine structural characteristics on N-nitrosamine formation potential relevant to postcombustion CO2 capture systems.

    Science.gov (United States)

    Dai, Ning; Mitch, William A

    2013-11-19

    Concerns have arisen for the possible contamination of air or drinking water supplies downwind of amine-based CO2 capture facilities by potentially carcinogenic N-nitrosamines formed from reactions between flue gas NOx and amine solvents. This study evaluated the influence of amine structure on the potential to form total N-nitrosamines within the absorber and washwater units of a laboratory-scale CO2 capture reactor, and in the solvent after a pressure-cooker treatment as a mimic of desorber conditions. Among 16 amines representing 3 amine classes (alkanolamines, straight-chain and cyclic diamines, and amino acids), the order of the amine was the primary determinant of total N-nitrosamine formation in the absorber unit, with total N-nitrosamine formation in the order: secondary amines ≈ tertiary amines ≫ primary amines. Similar results were observed upon pressure-cooker treatment, due to reactions between nitrite and amines at high temperature. For secondary and tertiary amines, total N-nitrosamine formation under these desorber-like conditions appeared to be more important than in the absorber, but for primary amines, significant formation of total N-nitrosamines was only observed in the absorber. For diamines and amino acids, total N-nitrosamine accumulation rates in washwaters were lowest for primary amines. For alkanolamines, however, total N-nitrosamine accumulation in the washwater was similar regardless of alkanolamine order, due to the combined effects of amine reactivity toward nitrosation and amine volatility. While total N-nitrosamine accumulation rates in washwaters were generally 1-2 orders of magnitude lower than in the absorber, they were comparable to absorber rates for several primary amines. Decarboxylation of the amino acid sarcosine resulted in the accumulation of significant concentrations of N-nitrosodimethylamine and N-nitrodimethylamine in the washwater.

  20. Linking canopy reflectance to crop structure and photosynthesis to capture and interpret spatiotemporal dimensions of per-field photosynthetic productivity

    Science.gov (United States)

    Xue, Wei; Jeong, Seungtaek; Ko, Jonghan; Tenhunen, John

    2017-03-01

    Nitrogen and water availability alter canopy structure and physiology, and thus crop growth, yielding large impacts on ecosystem-regulating/production provisions. However, to date, explicitly quantifying such impacts remains challenging partially due to lack of adequate methodology to capture spatial dimensions of ecosystem changes associated with nitrogen and water effects. A data fitting, where close-range remote-sensing measurements of vegetation indices derived from a handheld instrument and an unmanned aerial vehicle (UAV) system are linked to in situ leaf and canopy photosynthetic traits, was applied to capture and interpret inter- and intra-field variations in gross primary productivity (GPP) in lowland rice grown under flooded conditions (paddy rice, PD) subject to three nitrogen application rates and under rainfed conditions (RF) in an East Asian monsoon region of South Korea. Spatial variations (SVs) in both GPP and light use efficiency (LUEcabs) early in the growing season were enlarged by nitrogen addition. The nutritional effects narrowed over time. A shift in planting culture from flooded to rainfed conditions strengthened SVs in GPP and LUEcabs. Intervention of prolonged drought late in the growing season dramatically intensified SVs that were supposed to seasonally decrease. Nevertheless, nitrogen addition effects on SV of LUEcabs at the early growth stage made PD fields exert greater SVs than RF fields. SVs of GPP across PD and RF rice fields were likely related to leaf area index (LAI) development less than to LUEcabs, while numerical analysis suggested that considering strength in LUEcabs and its spatial variation for the same crop type tends to be vital for better evaluation in landscape/regional patterns of ecosystem photosynthetic productivity at critical phenology stages.

  1. Structural Modeling and Molecular Dynamics Simulation of the Actin Filament

    Energy Technology Data Exchange (ETDEWEB)

    Splettstoesser, Thomas [University of Heidelberg; Holmes, Kenneth [Max Planck Institute, Heidelberg, Germany; Noe, Frank [DFG Research Center Matheon, FU Berlin, Germany; Smith, Jeremy C [ORNL

    2011-01-01

    Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.

  2. CO2 capture. Two new structures in the 2-amino-2-methyl-1-propanol (AMP) – water – CO2 system

    DEFF Research Database (Denmark)

    Ståhl, Kenny; Neerup, Randi; Fosbøl, Philip Loldrup

    2016-01-01

    for such CO2 capture. The problem is to make the absorption/desorption processes energetically and thereby economically viable. One process under investigation involves alkanoamines as absorbents in aqueous solutions. In these systems CO2 is captured either by carbonate and/orcarbamate formation. We have......Energy production and transportation is responsible for more than 60 % of our CO2 emission. In particular coal-fired power plants are big contributors. However, these large scale facilities offer the possibility to effective CO2 capture through post-combustion processes. There are several options...... studied the 2-amino-2-methyl-1-propanol (AMP) and the AMP-water phase diagramand its ability for CO2 capture. The first crystal structure in the AMP – water system has been solved from powder diffraction data: AMP trihydrate (triclinic, P-1, a = 6.5897(3), b = 6.399 (2), c = 6.3399(2) Å and α = 92.40 (3...

  3. Preparation and structure characterization of nanospherical MCM- 41 molecular sieves

    Directory of Open Access Journals (Sweden)

    CHEN Ting

    2013-04-01

    Full Text Available Nanospherical MCM-41 molecular sieves have been synthesized by using hexadecyl trimethyl ammonium bromide (CTAB as templates and tetraethyl orthosilicate (TEOS as silicon sources. XRD,SEM,FT-IR,TEM,and N2 adsorption-desorption isotherms were used to investigate the effects of the reaction temperature and aging time on the morphology and structure of the samples. The results show that the nanospherical MCM-41 particles can be obtained at reaction temperatures between 20 to 80℃. With the reaction temperature increasing,the diameter of the nanospheres increases. When the reaction temperature reaches 110℃,MCM-41 molecular sieves exhibit irregular particle morphology. With the aging time of 0-15 h,the dispersion of nanospherical MCM-41 molecular sieves is very good. However,as the aging time increases,the particle size is also increased,while agglomeration is also more serious. Besides,the optimal synthesis conditions of the nanospherical MCM-41 molecular sieves were obtained by analyzing their formation mechanism.

  4. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations

    Science.gov (United States)

    Manara, Richard M. A.; Tomasio, Susana; Khalid, Syma

    2015-01-01

    Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is “exonuclease sequencing”, in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.

  5. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations.

    Science.gov (United States)

    Manara, Richard M A; Tomasio, Susana; Khalid, Syma

    2015-01-27

    Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is "exonuclease sequencing", in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.

  6. Molecular characterization of gel and liquid-crystalline structures of fully hydrated POPC and POPE bilayers.

    Science.gov (United States)

    Leekumjorn, Sukit; Sum, Amadeu K

    2007-05-31

    Molecular dynamics simulations were used for a comprehensive study of the structural properties of monounsaturated POPC and POPE bilayers in the gel and liquid-crystalline state at a number of temperatures, ranging from 250 to 330 K. Though the chemical structures of POPC and POPE are largely similar (choline versus ethanolamine headgroup), their transformation processes from a gel to a liquid-crystalline state are contrasting. In the similarities, the lipid tails for both systems are tilted below the phase transition and become more random above the phase transition temperature. The average area per lipid and bilayer thickness were found less sensitive to phase transition changes as the unsaturated tails are able to buffer reordering of the bilayer structure, as observed from hysteresis loops in annealing simulations. For POPC, changes in the structural properties such as the lipid tail order parameter, hydrocarbon trans-gauche isomerization, lipid tail tilt-angle, and level of interdigitation identified a phase transition at about 270 K. For POPE, three temperature ranges were identified, in which the lower one (270-280 K) was associated with a pre-transition state and the higher (290-300 K) with the post-transition state. In the pre-transition state, there was a significant increase in the number of gauche arrangements formed along the lipid tails. Near the main transition (280-290 K), there was a lowering of the lipid order parameters and a disappearance of the tilted lipid arrangement. In the post-transition state, the carbon atoms along the lipid tails became less hindered as their density profiles showed uniform distributions. This study also demonstrates that atomistic simulations of current lipid force fields are capable of capturing the phase transition behavior of lipid bilayers, providing a rich set of molecular and structural information at and near the main transition state.

  7. Discovering structural alerts for mutagenicity using stable emerging molecular patterns.

    Science.gov (United States)

    Métivier, Jean-Philippe; Lepailleur, Alban; Buzmakov, Aleksey; Poezevara, Guillaume; Crémilleux, Bruno; Kuznetsov, Sergei O; Le Goff, Jérémie; Napoli, Amedeo; Bureau, Ronan; Cuissart, Bertrand

    2015-05-26

    This study is dedicated to the introduction of a novel method that automatically extracts potential structural alerts from a data set of molecules. These triggering structures can be further used for knowledge discovery and classification purposes. Computation of the structural alerts results from an implementation of a sophisticated workflow that integrates a graph mining tool guided by growth rate and stability. The growth rate is a well-established measurement of contrast between classes. Moreover, the extracted patterns correspond to formal concepts; the most robust patterns, named the stable emerging patterns (SEPs), can then be identified thanks to their stability, a new notion originating from the domain of formal concept analysis. All of these elements are explained in the paper from the point of view of computation. The method was applied to a molecular data set on mutagenicity. The experimental results demonstrate its efficiency: it automatically outputs a manageable number of structural patterns that are strongly related to mutagenicity. Moreover, a part of the resulting structures corresponds to already known structural alerts. Finally, an in-depth chemical analysis relying on these structures demonstrates how the method can initiate promising processes of chemical knowledge discovery.

  8. CO{sub 2} capture using fly ash-derived activated carbons impregnated with low molecular mass amines

    Energy Technology Data Exchange (ETDEWEB)

    Smith, K.M.; Arenillas, A.; Drage, T.C.; Snape, C.E. [University of Nottingham, Nottingham (United Kingdom). Nottingham Fuel and Energy Centre

    2005-07-01

    Two different approaches to develop high capacity CO{sub 2} sorbents are presented. Firstly, the modification of the surface chemistry of low cost carbons by impregnation with a basic nitrogen-containing polymer (i.e.polyethylenimine) is described. Relatively low molecular mass (MM) amines, namely diethanolamine (DEA, MM 105) and tetraethylenepentaamineacrylonitrile (TEPAN, MM 311) are used to produce high capacity CO{sub 2} sorbents from activated carbons derived from unburned carbon in fly ash, which have low mesoporosities. The CO{sub 2} adsorption capacity and thermal stability of the prepared sorbents was measured as a function of temperature in a thermogravimetric analyser. The results indicate that TEPAN is more effective than DEA; at a temperature of 75{sup o}C, fly ash-derived activated carbons loaded with TEPAN achieved CO{sub 2} adsorption capacities in excess of 5 wt%, which compares fabvourably with the CO{sub 2} absorption capacity of 6.5 wt% achieved with a mesoporous silica loaded with TEPAN, and outperforms fly ash-derived activated carbons loaded with PEI. TEPAN has also been shown to have a higher thermal stability than DEA. The second approach involves the development of high nitrogen content carbon matrix adsorbents by carbonisation and subsequent thermal or chemical activation of a range of materials (polyacrylonitrile, glucose-amine mixtures, melamine and urea/melamine-formaldehyde resins). The results show that although the amount of nitrogen incorporated to the final adsorbent is important, the N-functionality seems to be more relevant for increasing CO{sub 2} uptake. However, the adsorbent obtained from carbazole-sugar co-pyrolysis, despite the lower amount of N incorporated, shows high CO{sub 2} uptake, up to 9 wt%, probably because the presence of more basic functionalities as determined by XPS analysis. 9 refs., 2 figs.

  9. Molecular Diagnostics of the Internal Structure of Starspots and Sunspots

    Science.gov (United States)

    Afram, N.; Berdyugina, S. V.; Fluri, D. M.; Solanki, S. K.; Lagg, A.; Petit, P.; Arnaud, J.

    2006-12-01

    We have analyzed the usefulness of molecules as a diagnostic tool for studying solar and stellar magnetism with the molecular Zeeman and Paschen-Back effects. In the first part we concentrate on molecules that are observed in sunspots such as MgH and TiO. We present calculated molecular line profiles obtained by assuming magnetic fields of 2-3 kG and compare these synthetic Stokes profiles with spectro-polarimetric observations in sunspots. The good agreement between the theory and observations allows us to turn our attention in the second part to starspots to gain insight into their internal structure. We investigate the temperature range in which the selected molecules can serve as indicators for magnetic fields on highly active cool stars and compare synthetic Stokes profiles with our recent observations.

  10. Quantum information analysis of electronic states at different molecular structures

    CERN Document Server

    Barcza, G; Marti, K H; Reiher, M

    2010-01-01

    We have studied transition metal clusters from a quantum information theory perspective using the density-matrix renormalization group (DMRG) method. We demonstrate the competition between entanglement and interaction localization. We also discuss the application of the configuration interaction based dynamically extended active space procedure which significantly reduces the effective system size and accelerates the speed of convergence for complicated molecular electronic structures to a great extent. Our results indicate the importance of taking entanglement among molecular orbitals into account in order to devise an optimal orbital ordering and carry out efficient calculations on transition metal clusters. We propose a recipe to perform DMRG calculations in a black-box fashion and we point out the connections of our work to other tensor network state approaches.

  11. The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.

    Science.gov (United States)

    Myasnikov, Alexander G; Afonina, Zhanna A; Ménétret, Jean-François; Shirokov, Vladimir A; Spirin, Alexander S; Klaholz, Bruno P

    2014-11-07

    During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.

  12. Three decades of structure- and property-based molecular design.

    Science.gov (United States)

    Müller, Klaus

    2014-01-01

    Roche has pioneered structure- and property-based molecular design to drug discovery. While this is an ongoing development, the past three decades feature key events that have revolutionized the way drug discovery is conducted in Big Pharma industry. It has been a great privilege to have been involved in this transformation process, to have been able to collaborate with, direct, guide, or simply encourage outstanding experts in various disciplines to build and further develop what has become a major pillar of modern small-molecule drug discovery. This article is an account of major events that took place since the early decision of Roche to implement computer-assisted molecular modeling 32 years ago and is devoted to the key players involved. It highlights the internal build-up of structural biology, with protein X-ray structure determination at its core, and the early setup of bioinformatics. It describes the strategic shift to large compound libraries and high-throughput screening with the development of novel compound storage and ultra-high-throughput screening facilities, as well as the strategic return to focused screening of small motif-based compound libraries. These developments were accompanied by the rise of miniaturized parallel compound property analytics which resulted in a major paradigm shift in medicinal chemistry from linear to multi-dimensional lead optimization. The rapid growth of huge collections of property data stimulated the development of various novel data mining concepts with 'matched molecular pair' analysis and novel variants thereof playing crucial roles. As compound properties got more prominent in molecular design, exploration of specific structural motifs for property modulation became a research activity complementary to target-oriented medicinal chemistry. The exploration of oxetane is given as an example. For the sake of brevity, this account cannot detail all further developments that have taken place in each individual area of

  13. Structure of a molecular liquid GeI4

    Science.gov (United States)

    Fuchizaki, Kazuhiro; Sakagami, Takahiro; Kohara, Shinji; Mizuno, Akitoshi; Asano, Yuta; Hamaya, Nozomu

    2016-11-01

    A molecular liquid GeI4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge-I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I-I distance definitely shorter than the intramolecular one. The prepeak observed at  ˜1 Å-1 in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak’s height is confirmed by a simulation, in which the molecular size is changed.

  14. III - V semiconductor structures for biosensor and molecular electronics applications

    Energy Technology Data Exchange (ETDEWEB)

    Luber, S.M.

    2007-01-15

    The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed

  15. Selective capture and rapid identification of Panax notoginseng metabolites in rat faeces by the integration of magnetic molecularly imprinted polymers and high-performance liquid chromatography coupled with orbitrap mass spectrometry.

    Science.gov (United States)

    Cai, Qizhi; Yang, Zaiyue; Chen, Ning; Zhou, Xuemin; Hong, Junli

    2016-07-15

    In the present work, an advanced pretreatment method magnetic molecular imprinted polymers-dispersive solid phase extraction (MMIPs-DSPE) combined with the high sensitivity LTQ-Orbitrap mass spectrometry was applied to the complicated metabolites analysis of Traditional Chinese Medicines (TCMs) in complex matrices. The ginsenoside Rb1 magnetic molecular imprinted polymers (Rb1-MMIPs) were successfully synthesized for specific recognition and selective enrichment of Panax notoginseng saponin metabolites in rat faeces. The polymers were prepared by using Fe3O4@SiO2 as the supporting material, APTES as the functional monomer and TEOS as the cross-linker. The Rb1-MMIPs showed quick separation (10.8 emu/g), large adsorption capacity (636μmol/g), high selectivity and fast binding kinetics (25min). Dispersion solid-phase extraction using Rb1-MMIPs (Rb1-MMIPs-DSPE) integrated with LTQ-Orbitrap MS was applied to fish out and identify saponin metabolites from rat faeces, and totally 58 related compounds were detected within 20min, including 26 PPD-group and 32 PPT-group notoginsenoside metabolites. Parallel tests showed that Rb1-MMIPs-DSPE obtained the lowest matrix effects of 0.98-14.84% and captured the largest number of structural analogues compared with traditional pretreatment methods organic solvent extraction (OSE) and solid phase extraction (SPE).

  16. Structure-based molecular modeling approaches to GPCR oligomerization.

    Science.gov (United States)

    Kaczor, Agnieszka A; Selent, Jana; Poso, Antti

    2013-01-01

    Classical structure-based drug design techniques using G-protein-coupled receptors (GPCRs) as targets focus nearly exclusively on binding at the orthosteric site of a single receptor. Dimerization and oligomerization of GPCRs, proposed almost 30 years ago, have, however, crucial relevance for drug design. Targeting these complexes selectively or designing small molecules that affect receptor-receptor interactions might provide new opportunities for novel drug discovery. In order to study the mechanisms and dynamics that rule GPCRs oligomerization, it is essential to understand the dynamic process of receptor-receptor association and to identify regions that are suitable for selective drug binding, which may be determined with experimental methods such as Förster resonance energy transfer (FRET) or Bioluminescence resonance energy transfer (BRET) and computational sequence- and structure-based approaches. The aim of this chapter is to provide a comprehensive description of the structure-based molecular modeling methods for studying GPCR dimerization, that is, protein-protein docking, molecular dynamics, normal mode analysis, and electrostatics studies.

  17. Discriminating the drivers of edge effects on nest predation: forest edges reduce capture rates of ship rats (Rattus rattus, a globally invasive nest predator, by altering vegetation structure.

    Directory of Open Access Journals (Sweden)

    Jay Ruffell

    Full Text Available Forest edges can strongly affect avian nest success by altering nest predation rates, but this relationship is inconsistent and context dependent. There is a need for researchers to improve the predictability of edge effects on nest predation rates by examining the mechanisms driving their occurrence and variability. In this study, we examined how the capture rates of ship rats, an invasive nest predator responsible for avian declines globally, varied with distance from the forest edge within forest fragments in a pastoral landscape in New Zealand. We hypothesised that forest edges would affect capture rates by altering vegetation structure within fragments, and that the strength of edge effects would depend on whether fragments were grazed by livestock. We measured vegetation structure and rat capture rates at 488 locations ranging from 0-212 m from the forest edge in 15 forest fragments, seven of which were grazed. Contrary to the vast majority of previous studies of edge effects on nest predation, ship rat capture rates increased with increasing distance from the forest edge. For grazed fragments, capture rates were estimated to be 78% lower at the forest edge than 118 m into the forest interior (the farthest distance for grazed fragments. This relationship was similar for ungrazed fragments, with capture rates estimated to be 51% lower at the forest edge than 118 m into the forest interior. A subsequent path analysis suggested that these 'reverse' edge effects were largely or entirely mediated by changes in vegetation structure, implying that edge effects on ship rats can be predicted from the response of vegetation structure to forest edges. We suggest the occurrence, strength, and direction of edge effects on nest predation rates may depend on edge-driven changes in local habitat when the dominant predator is primarily restricted to forest patches.

  18. Discriminating the drivers of edge effects on nest predation: forest edges reduce capture rates of ship rats (Rattus rattus), a globally invasive nest predator, by altering vegetation structure.

    Science.gov (United States)

    Ruffell, Jay; Didham, Raphael K; Barrett, Paul; Gorman, Nic; Pike, Rhonda; Hickey-Elliott, Andrée; Sievwright, Karin; Armstrong, Doug P

    2014-01-01

    Forest edges can strongly affect avian nest success by altering nest predation rates, but this relationship is inconsistent and context dependent. There is a need for researchers to improve the predictability of edge effects on nest predation rates by examining the mechanisms driving their occurrence and variability. In this study, we examined how the capture rates of ship rats, an invasive nest predator responsible for avian declines globally, varied with distance from the forest edge within forest fragments in a pastoral landscape in New Zealand. We hypothesised that forest edges would affect capture rates by altering vegetation structure within fragments, and that the strength of edge effects would depend on whether fragments were grazed by livestock. We measured vegetation structure and rat capture rates at 488 locations ranging from 0-212 m from the forest edge in 15 forest fragments, seven of which were grazed. Contrary to the vast majority of previous studies of edge effects on nest predation, ship rat capture rates increased with increasing distance from the forest edge. For grazed fragments, capture rates were estimated to be 78% lower at the forest edge than 118 m into the forest interior (the farthest distance for grazed fragments). This relationship was similar for ungrazed fragments, with capture rates estimated to be 51% lower at the forest edge than 118 m into the forest interior. A subsequent path analysis suggested that these 'reverse' edge effects were largely or entirely mediated by changes in vegetation structure, implying that edge effects on ship rats can be predicted from the response of vegetation structure to forest edges. We suggest the occurrence, strength, and direction of edge effects on nest predation rates may depend on edge-driven changes in local habitat when the dominant predator is primarily restricted to forest patches.

  19. Adrenergic Receptors From Molecular Structure to in vivo function.

    Science.gov (United States)

    Hein, L; Kobilka, B K

    1997-07-01

    Adrenergic receptors form the interface between the sympathetic nervous system and the cardiovascular system as well as many endocrine and parenchymal tissues. Although several hundred G-protein-coupled receptors have been identified, adrenergic receptors, along with the visual pigment rhodopsin, have been among the most extensively studied members of this family of receptors. This review focuses on recent advances in understanding the molecular structure, function, and regulation of adrenergic receptors using in vitro systems and integrates recent transgenic animal models that were generated to study the adrenergic system in vivo. (Trends Cardiovasc Med 1997;7:137-145). © 1997, Elsevier Science Inc.

  20. Molecular Docking and Structure-Based Drug Design Strategies

    Directory of Open Access Journals (Sweden)

    Leonardo G. Ferreira

    2015-07-01

    Full Text Available Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

  1. Molecular structure and reversible photodegradation in anthraquinone dyes

    CERN Document Server

    Dhakal, Prabodh

    2016-01-01

    Reversible photodegradation is a process that has been observed in several dye molecules, but the underlying mechanisms are not still well understood. In this contribution, we characterize a series of anthraquinone dyes to determine how self-healing depends on molecular structure. Past studies have used probing techniques that rely on linear absorption, two-photon fluorescence, and amplified spontaneous emission. Each of these probes provide an indirect measure of the populations of the damaged and undamaged species, requiring calibrations or assumptions to be made that might affect the accuracy of the results. The present studies use fluorescence as a probe, which is shown to directly measure the undamaged population. It is found that certain anthraquinone classes share common structural features that are associated with self healing. Furthermore, the time and temperature dependence of photodegradation and self-healing is found to be consistent with the domain model of self healing.

  2. Study on multimers and their structures in molecular association mixture

    Institute of Scientific and Technical Information of China (English)

    NI Yi; DOU XiaoMing; ZHAO HaiYing; YIN GuangZhong; YAMAGUCHI Yoshinori; OZAKI Yukihiro

    2007-01-01

    Self-association system of (R)-1,3-butanediol in dilute carbon tetrachloride (CCl4) solution is studied as a model of molecular association mixture. Analysis methods including FSMWEFA (fixed-size moving window evolving factor analysis) combined with PCA (principal component analysis), SIMPLISMA (simple-to-use interactive self-modeling mixture analysis), and ITTFA (iterative target transformation factor analysis) are adopted to resolve infrared spectra of (R)-1,3-butanediol solution. Association number and equilibrium constant are computed. (R)-1,3-butanediol in dilute inert solution is determined as a monomer-trimer equilibrium system. Theoretical investigation of trimer structures is carried out with DFT (density functional theory), and structural factors are analyzed.

  3. Study on multimers and their structures in molecular association mixture

    Institute of Scientific and Technical Information of China (English)

    YAMAGUCHI; Yoshinori; OZAKI; Yukihiro

    2007-01-01

    Self-association system of(R)-1,3-butanediol in dilute carbon tetrachloride(CCl4)solution is studied as a model of molecular association mixture.Analysis methods including FSMWEFA(fixed-size moving window evolving factor analysis)combined with PCA(principal component analysis),SIMPLISMA (simple-to-use interactive self-modeling mixture analysis),and ITTFA(iterative target transformation factor analysis)are adopted to resolve infrared spectra of(R)-1,3-butanediol solution.Association number and equilibrium constant are computed.(R)-1,3-butanediol in dilute inert solution is determined as a monomer-trimer equilibrium system.Theoretical investigation of trimer structures is carried out with DFT(density functional theory),and structural factors are analyzed.

  4. A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site

    CERN Document Server

    Fogarty, Aoife C; Kremer, Kurt

    2016-01-01

    In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the active site to capture the chemistry of substrate binding. Global properties of the rest of the protein also play an essential role, determining the structure and fluctuations of the binding site; however, these can be modelled on a coarser level. Similarly, in the most computationally efficient scheme only the solvent hydrating the active site requires atomistic detail. We present a methodology to couple atomistic and coarse-grained protein models, while solvating the atomistic part of the protein in atomistic water. This allows a free choice of which protein and solvent degrees of freedom to include atomistically, without loss of accuracy in the atomistic description. This multi-resolution methodology can successfully model stable ligand binding, and we furt...

  5. A chloride capturing system via proton-induced structure transformation between opened- and closed-forms of dodecavanadates.

    Science.gov (United States)

    Inoue, Yoshitaka; Kikukawa, Yuji; Kuwajima, Sho; Hayashi, Yoshihito

    2016-05-01

    Chloride-incorporated dodecavanadates show two distinct structures of the monoprotonated-form [HV12O32(Cl)](4-) (closed-V12) with a spherical closed-structure and the opened-form [V12O32(Cl)](5-) (opened-V12). The reaction of closed-V12 with a stoichiometric amount of ethylenediamine drives the structure transformation reaction to opened-V12, quantitatively. From time dependent observations of (51)V NMR, a tube-type intermediate [V12O32(Cl)](5-) (tube-V12) was observed in the transformation process. Isolation of the intermediate was achieved by the deprotonation reaction of closed-V12 with diethylamine, and the structure transformation was confirmed by using the isolated intermediate. The reverse transformation from opened-V12 to closed-V12 was also achieved by addition of trifluoroacetic acid. The geometrical difference between closed-V12 and opened-V12 is reflected in the reactivity difference to the external reagents, and this was demonstrated by examining the chloride removal reaction by using a silver cation. The incorporated chloride was preserved in the closed-V12 cage even in the presence of a silver cation. In contrast, the chloride in opened-V12 was removed as AgCl by the silver cation. In addition, by the reaction of chloride-free opened-V12 with a quantitative amount of {Et4N}Cl retrieved opened-V12, showing the capability of opened-V12 to recapture a guest chloride in the cavity. This transformation between two isomeric dodecavanadate structures is regarded as the movement of a molecular mitt to catch a ball and secure it.

  6. Phenol-formaldehyde resins: A quantitative NMR study of molecular structure and molecular dynamics

    Science.gov (United States)

    Ottenbourgs, Benjamin Tony

    Phenol-formaldehyde (PF) resins have been the subject of this work. 13C liquid-state and solid-state NMR has been used to investigate the molecular structure of mainly novolak and partially of resole resins. 1H wideline in combination with 13C solid-state NMR relaxometry has been applied to study the curing and the molecular dynamics of phenolic resins. It was the intention to provide an insight in the relationship between resin composition, resin structure and subsequent resin properties (by means of the molecular dynamics). An improved 13C liquid-state NMR quantification technique of novolaks in THF-CDCl3 solutions is demonstrated. Full quantitative 13C liquid-state spectra of phenol-formaldehyde resins with high signal- to-noise ratio were obtained by using chromium acetylacetonate under optimized spectral conditions within a few hours spectrometer time. Attached proton test (APT) spectra enabled proper peak assignments in the region with significant overlap. For several novolaks, prepared under different catalytic conditions, the degree of polymerization, degree of branching, number average molecular weight, isomeric distribution, and the number of unreacted ortho and para phenol ring positions was determined with a reduced margin of error, by analyzing and integrating the 13C spectra. The power of 13C solid-state NMR in the analysis of cured PF resins is shown. Particular importance was ascribed to the question of the quantifiability of the experiments when it was desired to measure the degree of conversion by means of a 13C CP/MAS contact time study. The network structure present, and thus also the mechanical properties, is critically dependent upon the final degree of conversion obtained after curing. The degree of conversion, which depended on the cure conditions (cure temperature, cure pressure and cure time), was limited by vitrification as was demonstrated by DSC experiments. Changes in the spin-lattice relaxation time T 1H were observed, providing

  7. A model for the internal structure of molecular cloud cores

    CERN Document Server

    McLaughlin, D E; McLaughlin, Dean E; Pudritz, Ralph E

    1996-01-01

    We generalize the classic Bonnor-Ebert stability analysis of pressure-truncated, self-gravitating gas spheres, to include clouds with arbitrary equations of state. A virial-theorem analysis is also used to incorporate mean magnetic fields into such structures. The results are applied to giant molecular clouds (GMCs), and to individual dense cores, with an eye to accounting for recent observations of the internal velocity-dispersion profiles of the cores in particular. We argue that GMCs and massive cores are at or near their critical mass, and that in such a case the size-linewidth and mass-radius relations between them are only weakly dependent on their internal structures; any gas equation of state leads to essentially the same relations. We briefly consider the possibility that molecular clouds can be described by polytropic pressure-density relations (of either positive or negative index), but show that these are inconsistent with the apparent gravitational virial equilibrium, 2U + W = 0 of GMCs and of ma...

  8. Anti-cancer chalcones: Structural and molecular target perspectives.

    Science.gov (United States)

    Mahapatra, Debarshi Kar; Bharti, Sanjay Kumar; Asati, Vivek

    2015-06-15

    Chalcone or (E)-1,3-diphenyl-2-propene-1-one scaffold remained a fascination among researchers in the 21st century due to its simple chemistry, ease of synthesis and a wide variety of promising biological activities. Several natural and (semi) synthetic chalcones have shown anti-cancer activity due to their inhibitory potential against various targets namely ABCG2/P-gp/BCRP, 5α-reductase, aromatase, 17-β-hydroxysteroid dehydrogenase, HDAC/Situin-1, proteasome, VEGF, VEGFR-2 kinase, MMP-2/9, JAK/STAT signaling pathways, CDC25B, tubulin, cathepsin-K, topoisomerase-II, Wnt, NF-κB, B-Raf and mTOR etc. In this review, a comprehensive study on molecular targets/pathways involved in carcinogenesis, mechanism of actions (MOAs), structure activity relationships (SARs) and patents granted have been highlighted. With the knowledge of molecular targets, structural insights and SARs, this review may be helpful for (medicinal) chemists to design more potent, safe, selective and cost effective anti-cancer chalcones.

  9. Crystal and molecular structures of some organophosphorus insecticides and computer methods for structure determination. [Dissertation

    Energy Technology Data Exchange (ETDEWEB)

    Lapp, R.L.

    1979-01-01

    Molecular structure investigations of a set of organophosphorus insecticides have been carried out in order to acquire the data base to develop correlations between such parameters and their toxicities. The crystal and molecular structures of dimethoate (LD/sub 50/ (rats) = 600 mg/kg), IPAT, and leptophos (LD/sub 50/ (rats) = 90 mg/kg) have been determined via three-dimensional x-ray analysis. The crystal and molecular structure of (-)-..cap alpha..-phenylethylammonium (-)-0-methyl-phenylphosphonothioate was solved by conventional Patterson and Fourier techniques to a final R value of 0.057. The crystal and molecular structures of two crystalline forms of calcium formate were determined. A new least-squares refinement program was written which is much more general and efficient than any previous program. In particular, a new block-diagonal approximation has been devised which is much more economical than full-matrix refinement and appears to work much better than previous block-diagonal methods. A Howells, Phillips and Rogers test for a center of symmetry and a Wilson plot have been programmed into the data collection algorithm. Some approximations and special problems are discussed relative to implementing these routines in a real-time mode on a minicomputer. A mathematical background and program description are included for each program.

  10. Group-selective enrichment and determination of pyrethroid insecticides in aquaculture seawater via molecularly imprinted solid phase extraction coupled with gas chromatography-electron capture detection.

    Science.gov (United States)

    Shi, Xizhi; Liu, Jinghua; Sun, Aili; Li, Dexiang; Chen, Jiong

    2012-03-02

    Two types of molecularly imprinted polymers (MIPs) for the simultaneous determination of six pyrethroid insecticides have been developed using deltamethrin (D-MIPs) and cypermethrin (C-MIPs) as template molecules. A comparison of the performance of D-MIPs, C-MIPs, and the corresponding non-imprinted polymers (NIPs) were conducted. Stronger group-selective interactions between the C-MIPs and the six pyrethroid insecticides were achieved. The MISPE method based on the C-MIPs displayed higher extraction recoveries (86.4-96.0%) with RSD values ranging from 2.4 to 7.8% for the six pyrethroid insecticides in aquaculture seawater. After the C-MIP cartridge procedure, the limits of detection and quantification for fenvalerate, deltamethrin, cypermethrin, cyfluthrin, and bifenthrin were in the 16.6-37.0 and 55.3-109.1 ng L⁻¹ ranges, respectively, and 0.68 and 2.26 μg L⁻¹ for phenothrin, respectively. The proposed MISPE method coupled with gas chromatography-electron capture detection was successfully used for the determination of the six pyrethroid insecticides in aquaculture seawater.

  11. Molecular Modeling and Structural Analysis of Arylesterase of Ancylostoma Duodenale

    Science.gov (United States)

    Panda, Subhamay; Panda, Santamay; Kumari, Leena

    2016-01-01

    Parasitic worm infection of humans is one of the most commonly prevalent helminth infection that has imposed great impact on society and public health in the developing world. The two species of hookworm, namely Ancylostoma duodenale and Necator americanus may be primarily responsible for causing parasitic infections in human beings. The highly prevalent areas for Ancylostoma duodenale infections are mainly India, Middle East, Australia, northern Africa and other parts of the world. The serum arylesterases/paraoxonases are family of enzymes that is involved in the hydrolysis of a number of organophosphorus insecticides to the nontoxic products. The participation of the enzymes in the breakdown of a variety of organophosphate substrates that is generally made up of paraoxon and numerous aromatic carboxylic acid esters (e.g., phenyl acetate), and hence combats the toxic effect of organophosphates. The aim of the present investigation is to evaluate the arylesterases of Ancylostoma duodenale giving special importance to structure generation, validation of the generated models, distribution of secondary structural elements and positive charge distribution over the structure. By the implementation of comparative modeling approach we propose the first molecular model structure of arylesterases of Ancylostoma duodenale. PMID:27642240

  12. Electronic and Magnetic Structure of Octahedral Molecular Sieves

    Science.gov (United States)

    Morey-Oppenheim, Aimee M.

    The major part of this research consists of magnetic and electronic studies of metal doped cryptomelane-type manganese oxide octahedral molecular sieves (KOMS-2). The second part of this study involves the magnetic characterization of cobalt doped MCM-41 before and after use in the synthesis of single walled carbon nanotubes. Manganese oxides have been used widely as bulk materials in catalysis, chemical sensors, and batteries due to the wide range of possible stable oxidation states. The catalytic function of manganese oxides is further tuned by doping the material with numerous transition metals. It is of particular interest the oxidation states of Mn present after doping. New titrations to determine the oxidation state of Mn were investigated. To further examine the structure of KOMS-2, the magnetic contribution of dopant metals was also examined. The KOMS-2 structure having both diamagnetic and paramagnetic metal ions substitutions was studied. MCM-41 with the incorporation of cobalt into the structure was analyzed for its magnetic properties. The material undergoes significant structural change during the synthesis of single walled carbon nanotubes. It was the focus of this portion of the research to do a complete magnetic profile of both the before and after reaction material.

  13. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  14. Genetic structure of Triatoma venosa (Hemiptera: Reduviidae: molecular and morphometric evidence

    Directory of Open Access Journals (Sweden)

    Erika Vargas

    2006-02-01

    Full Text Available Triatoma venosa presents a restricted geographical distribution in America and is considered as a secondary vector of Chagas disease in Colombia and Ecuador. A total of 120 adult insects were collected in domestic and peridomestic habitats in an endemic area of the department of Boyacá, Colombia, in order to determine their genetic structure through morphometric and molecular techniques. The head and wings of each specimen were used for the analyses of size, shape, and sexual dimorphism. A significant sexual dimorphism was found, although no differences in size among the studied groups were detected. Differences were found in the analyzed structures except for male heads. DNA was extracted from the legs in order to carry out the internal transcriber space-2 (ITS-2 amplification and the randon amplified polymorphic DNA (RAPD analyses. Length polymorphisms were not detected in the ITS-2. Fst and Nm values were estimated (0.047 and 3.4, respectively. The high genetic flow found among the insects captured in the domicile and peridomiciliary environment does not permit a genetic differentiation, thus establishing the peridomicile as an important place for epidemiological surveillance.

  15. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations.

    Science.gov (United States)

    Mehere, Prajwalini; Han, Qian; Lemkul, Justin A; Vavricka, Christopher J; Robinson, Howard; Bevan, David R; Li, Jianyong

    2010-11-01

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using α-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 Å resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  16. Tyrosine Aminotransferase: Biochemical and Structural Properties and Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    P Mehere; Q Han; J Lemkul; C Vavricka; H Robinson; D Bevan; J Li

    2011-12-31

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  17. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Mehere, P.; Robinson, H.; Han, Q.; Lemkul, J. A.; Vavricka, C. J.; Bevan, D. R.; Li, J.

    2010-11-01

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  18. Transmission electron microscopy in molecular structural biology: A historical survey.

    Science.gov (United States)

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented.

  19. Molecular and structural antioxidant defenses against oxidative stress in animals.

    Science.gov (United States)

    Pamplona, Reinald; Costantini, David

    2011-10-01

    In this review, it is our aim 1) to describe the high diversity in molecular and structural antioxidant defenses against oxidative stress in animals, 2) to extend the traditional concept of antioxidant to other structural and functional factors affecting the "whole" organism, 3) to incorporate, when supportable by evidence, mechanisms into models of life-history trade-offs and maternal/epigenetic inheritance, 4) to highlight the importance of studying the biochemical integration of redox systems, and 5) to discuss the link between maximum life span and antioxidant defenses. The traditional concept of antioxidant defenses emphasizes the importance of the chemical nature of molecules with antioxidant properties. Research in the past 20 years shows that animals have also evolved a high diversity in structural defenses that should be incorporated in research on antioxidant responses to reactive species. Although there is a high diversity in antioxidant defenses, many of them are evolutionary conserved across animal taxa. In particular, enzymatic defenses and heat shock response mediated by proteins show a low degree of variation. Importantly, activation of an antioxidant response may be also energetically and nutrient demanding. So knowledge of antioxidant mechanisms could allow us to identify and to quantify any underlying costs, which can help explain life-history trade-offs. Moreover, the study of inheritance mechanisms of antioxidant mechanisms has clear potential to evaluate the contribution of epigenetic mechanisms to stress response phenotype variation.

  20. A double molecular disc in NGC 6946: structure and stability

    CERN Document Server

    Romeo, Alessandro B

    2015-01-01

    The late-type spiral galaxy NGC 6946 is a prime example of molecular gas dynamics driven by `bars within bars'. Here we use data from the BIMA SONG and HERACLES surveys to analyse the structure and stability of its molecular disc. Our radial profiles exhibit a clear transition at distance R ~ 1 kpc from the galaxy centre. In particular, the surface density profile breaks at R ~ 0.8 kpc and is well fitted by a double exponential distribution with scale lengths R_1 ~ 200 pc and R_2 ~ 3 kpc, while the 1D velocity dispersion sigma decreases steeply in the central kpc and is approximately constant at larger radii. The fact that we derive and use the full radial profile of sigma rather than a constant value is perhaps the most novel feature of our stability analysis. We show that the profile of the Q stability parameter traced by CO emission is remarkably flat and well above unity, while the characteristic instability wavelength exhibits clear signatures of the nuclear starburst and inner bar within bar. We also sh...

  1. Introductory group theory and its application to molecular structure

    CERN Document Server

    Ferraro, John R

    1975-01-01

    The success of the first edition of this book has encouraged us to revise and update it. In the second edition we have attempted to further clarify por­ tions of the text in reference to point symmetry, keeping certain sections and removing others. The ever-expanding interest in solids necessitates some discussion on space symmetry. In this edition we have expanded the discus­ sion on point symmetry to include space symmetry. The selection rules in­ clude space group selection rules (for k = 0). Numerous examples are pro­ vided to acquaint the reader with the procedure necessary to accomplish this. Recent examples from the literature are given to illustrate the use of group theory in the interpretation of molecular spectra and in the determination of molecular structure. The text is intended for scientists and students with only a limited theoretical background in spectroscopy. For this reason we have presented detailed procedures for carrying out the selection rules and normal coor­ dinate treatment of ...

  2. How does the molecular network structure influence PDMS elastomer wettability?

    Science.gov (United States)

    Melillo, Matthew; Genzer, Jan

    Poly(dimethylsiloxane) (PDMS) is one of the most common elastomers, with applications ranging from medical devices to absorbents for water treatment. Fundamental understanding of how liquids spread on the surface of and absorb into PDMS networks is of critical importance for the design and use of another application - microfluidic devices. We have systematically studied the effects of polymer molecular weight, loading of tetra-functional crosslinker, end-group chemical functionality, and the extent of dilution of the curing mixture on the mechanical and surface properties of end-linked PDMS networks. The gel and sol fractions, storage and loss moduli, liquid swelling ratios, and water contact angles have all been shown to vary greatly based on the aforementioned variables. Similar trends were observed for the commercial PDMS material, Sylgard-184. Our results have confirmed theories predicting the relationships between modulus and swelling. Furthermore, we have provided new evidence for the strong influence that substrate modulus and molecular network structure have on the wettability of PDMS elastomers. These findings will aid in the design and implementation of efficient microfluidics and other PDMS-based materials that involve the transport of liquids.

  3. A new parametrizable model of molecular electronic structure

    CERN Document Server

    Laikov, Dimitri N

    2011-01-01

    A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good dipole polarizabilities and improved intermolecular potentials with dispersion terms. The molecular integrals include up to three-center one-electron and two-center two-electron terms, all in simple analytical forms. A method to extract the effective one-electron Hamiltonian of nonlocal-exchange Kohn-Sham theory from the coupled-cluster one-electron density matrix is designed and used to get its matrix representation in a molecule-intrinsic minimal basis as an input to the paramtrization procedure -- making a direct link...

  4. Effect of processing on carbon molecular sieve structure and performance

    KAUST Repository

    Das, Mita

    2010-11-01

    Sub-micron sized carbon molecular sieve (CMS) materials were produced via ball milling for subsequent use in hybrid material formation. A detailed analysis of the effects of the milling process in the presence of different milling environments is reported. The milling process apparently alters the molecular scale structure and properties of the carbon material. Three cases: unmilled, air milled and nitrogen milled, were analyzed in this work. The property changes were probed using equilibrium sorption experiments with different gases. Furthermore, WAXD and BET results also showed differences between milling processes. Finally in order to improve the interfacial polymer-sieve region of hybrid membranes, the CMS surface was chemically modified with a linkage unit capable of covalently bonding the polymer to the sieve. A published single-wall carbon nanotube (SWCNTs) modification method was adopted to attach a primary aromatic amine to the surface. Several aspects including rigidity, chemical composition, bulky groups and length were considered in selecting the preferred linkage unit. Fortunately kinetic and equilibrium sorption properties of the modified sieves showed very little difference from unmodified samples, suggesting that the linkage unit is not excessively filling or obstructing access to the pores of the CMSs during the modification process. © 2010 Elsevier Ltd. All rights reserved.

  5. Molecular Structures in Hidden Charm Meson and Charmed Baryon Spectrum

    CERN Document Server

    Fernandez, F; Ortega, P G

    2013-01-01

    Using a constituent quark model we study the mass and decay channels of meson meson and meson baryon structures in the charm sector. We show that the $X(3872)$ and $X(3940)$ resonances can be described as mixed charmonium-molecular states with $J^{PC}=1^{++}$, whereas the $X(3915)$ and the $Y(3940)$ can be assigned to similar mixed states with $J^{PC}=0^{++}$. In the baryon spectrum we identify the $\\Lambda^+_c(2940)$ as a $D^*N$ molecule with $(I)J^P=(0)3/2^-$ and the recently reported $X_c(3250)$ as a $D^*\\Delta$ resonance with $(I)J^P=(1)5/2^-$ or $(I)J^P=(2)3/2^-$.

  6. The Physical and Chemical Structure of Hot Molecular Cores

    CERN Document Server

    Nomura, H

    2004-01-01

    We have made self-consistent models of the density and temperature profiles of the gas and dust surrounding embedded luminous objects using a detailed radiative transfer model together with observations of the spectral energy distribution of hot molecular cores. Using these profiles we have investigated the hot core chemistry which results when grain mantles are evaporated, taking into account the different binding energies of the mantle molecules, as well a model in which we assume that all molecules are embedded in water ice and have a common binding energy. We find that most of the resulting column densities are consistent with those observed toward the hot core G34.3+0.15 at a time around 10$^4$ years after central luminous star formation. We have also investigated the dependence of the chemical structure on the density profile which suggests an observational possibility of constraining density profiles from determination of the source sizes of line emission from desorbed molecules.

  7. Molecular dynamics study on the structure I helium hydrate

    Institute of Scientific and Technical Information of China (English)

    CHENG Wei; WU Hucai; YE Xiaoqin; HOU Hongyu

    2004-01-01

    A 368- water molecule structure I gas hydrate, encased by the number of helium (He) molecules ranging from two to twenty-two, are calculated by molecular dynamical simulations. The potential TIP4P (transferable intermolecular potentical with four sites) is used for water interactions and Lennard-Jones for He-He and He-water interactions. He molecules do not affect the water lattice and can stabilize the hydrate when their concentration is small. A trough signature of He encased is found at 80~90 meV in the phonon density of states. He molecules prefer to be more off-center in 51262 cages. Heavier isotope He are energetically favorable to be filled in cages.

  8. Three decades of structure- and property-based molecular design

    DEFF Research Database (Denmark)

    Müller, Klaus

    2014-01-01

    of bioinformatics. It describes the strategic shift to large compound libraries and high-throughput screening with the development of novel compound storage and ultra-high-throughput screening facilities, as well as the strategic return to focused screening of small motif-based compound libraries......Roche has pioneered structure- and property-based molecular design to drug discovery. While this is an ongoing development, the past three decades feature key events that have revolutionized the way drug discovery is conducted in Big Pharma industry. It has been a great privilege to have been...... involved in this transformation process, to have been able to collaborate with, direct, guide, or simply encourage outstanding experts in various disciplines to build and further develop what has become a major pillar of modern small-molecule drug discovery. This article is an account of major events...

  9. Molecular structure and exciton dynamics in organic conjugated polymers

    Science.gov (United States)

    Thomas, Alan K.

    , quenchable, isolated singlet excitations. The structure of J aggregates which leads to isolated excitations, and the role which inter-chain contact sites play in triplet formation from these singlet excitations is revealed. New structure-function relationships were uncovered in poly (3-alkyl-thienylenevinylene) (P3ATV) derivatives using resonance Raman and photocurrent spectroscopies. Time-dependent spectroscopic theory was used to interpret experimental Raman and absorption spectra that revealed the presence of structural polymorphs. These polymorphs provide an explanation of the spectroscopic evidence without presumption of a deactivating dark state in this unusually non-fluorescence material. Photovoltaic devices constructed from blends of poly (2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT) and PCBM blends were examined using Raman and photocurrent imaging techniques. These techniques were used to identify different packing states in blended thin films and correlate photocurrent production with local order. Intensity modulated spectroscopic techniques (IMPS) were then used to locate regions of non-geminate charge recombination at interfaces between amorphous and crystalline regions in working devices. Next, P3HT/PCBM OPV devices were exposed to ionizing radiation in a vacuum chamber. These devices were characterized before and after exposure, using standardized solar cell tests, Raman imaging, wide-field IMPS, and IMVS spectroscopies. An analysis of the spectroscopic data determined that the donor polymer is highly resistant to radiation damage, and that the degradation of device performance is due to an effect (cross-linking or degradation) within aggregates of the acceptor. This dissertation concludes with an interpretation of the significance of the findings contained herein to organic electronics, followed by a brief outlook for future work in these fields. Potential theories to describe and predict molecular interactions for organic polymers in

  10. Derivatives of Ergot-alkaloids: Molecular structure, physical properties, and structure-activity relationships

    Science.gov (United States)

    Ivanova, Bojidarka B.; Spiteller, Michael

    2012-09-01

    A comprehensive screening of fifteen functionalized Ergot-alkaloids, containing bulk aliphatic cyclic substituents at D-ring of the ergoline molecular skeleton was performed, studying their structure-active relationships and model interactions with α2A-adreno-, serotonin (5HT2A) and dopamine D3 (D3A) receptors. The accounted high affinity to the receptors binding loops and unusual bonding situations, joined with the molecular flexibility of the substituents and the presence of proton accepting/donating functional groups in the studied alkaloids, may contribute to further understanding the mechanisms of biological activity in vivo and in predicting their therapeutic potential in central nervous system (CNS), including those related the Schizophrenia. Since the presented correlation between the molecular structure and properties, was based on the comprehensively theoretical computational and experimental physical study on the successfully isolated derivatives, through using routine synthetic pathways in a relatively high yields, marked these derivatives as 'treasure' for further experimental and theoretical studied in areas such as: (a) pharmacological and clinical testing; (b) molecular-drugs design of novel psychoactive substances; (c) development of the analytical protocols for determination of Ergot-alkaloids through a functionalization of the ergoline-skeleton, and more.

  11. Chitosan Molecular Structure as a Function of N-Acetylation

    Energy Technology Data Exchange (ETDEWEB)

    Franca, Eduardo F.; Freitas, Luiz C.; Lins, Roberto D.

    2011-07-01

    Molecular dynamics simulations have been carried out to characterize the structure and solubility of chitosan nanoparticle-like structures as a function of the deacetylation level (0, 40, 60, and 100%) and the spatial distribution of the N-acetyl groups in the particles. The polysaccharide chains of highly N-deacetylated particles where the N-acetyl groups are uniformly distributed present a high flexibility and preference for the relaxed two-fold helix and five-fold helix motifs. When these groups are confined to a given region of the particle, the chains adopt preferentially a two-fold helix with f and w values close to crystalline chitin. Nanoparticles with up to 40% acetylation are moderately soluble, forming stable aggregates when the N-acetyl groups are unevenly distributed. Systems with 60% or higher N-acetylation levels are insoluble and present similar degrees of swelling regardless the distribution of their N-acetyl groups. Overall particle solvation is highly affected by electrostatic forces resulting from the degree of acetylation. The water mobility and orientation around the polysaccharide chains affects the stability of the intramolecular O3- HO3(n) ... O5(n+ 1) hydrogen bond, which in turn controls particle aggregation.

  12. Structural and electronic properties of Diisopropylammonium bromide molecular ferroelectric crystal

    Science.gov (United States)

    Alsaad, A.; Qattan, I. A.; Ahmad, A. A.; Al-Aqtash, N.; Sabirianov, R. F.

    2015-10-01

    We report the results of ab-initio calculations based on Generalized Gradient Approximation (GGA) and hybrid functional (HSE06) of electronic band structure, density of states and partial density of states to get a deep insight into structural and electronic properties of P21 ferroelectric phase of Diisopropylammonium Bromide molecular crystal (DIPAB). We found that the optical band gap of the polar phase of DIPAB is ∼ 5 eV confirming it as a good dielectric. Examination of the density of states and partial density of states reveal that the valence band maximum is mainly composed of bromine 4p orbitals and the conduction band minimum is dominated by carbon 2p, carbon 2s, and nitrogen 2s orbitals. A unique aspect of P21 ferroelectric phase is the permanent dipole within the material. We found that P21 DIPAB has a spontaneous polarization of 22.64 consistent with recent findings which make it good candidate for the creation of ferroelectric tunneling junctions (FTJs) which have the potential to be used as memory devices.

  13. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    Science.gov (United States)

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  14. Photographic images captured while sampling for bald eagles near the Davis Pond freshwater diversion structure in Barataria Bay, Louisiana (2009-10)

    Science.gov (United States)

    Jenkins, Jill A.; Jeske, Clinton W.; Allain, Larry K.

    2011-01-01

    The implementation of freshwater diversions in large-scale coastal restoration schemes presents several scientific and management considerations. Large-scale environmental restructuring necessitates aquatic biomonitoring, and during such field studies, photographs that document animals and habitat may be captured. Among the biomonitoring studies performed in conjunction with the Davis Pond freshwater diversion structure south of New Orleans, Louisiana, only postdiversion study images are readily available, and these are presented here.

  15. Synchrotron-based and globar-sourced molecular (micro)spectroscopy contributions to advances in new hulless barley (with structure alteration) research on molecular structure, molecular nutrition, and nutrient delivery.

    Science.gov (United States)

    Yang, Ling; Yu, Peiqiang

    2017-01-02

    This paper aimed to review synchrotron-based and globar-sourced molecular infrared (micro)spectroscopy contributions to advances in new hulless barley (with structure alteration) research on molecular structure, molecular nutrition, and nutrient delivery in ruminants. It reviewed recent progress in barley varieties, its utilization for animal and human, inherent structure features and chemical make-up, evaluation and research methodology, breeding progress, rumen degradation, and intestinal digestion. The emphasis of this review was focused on the effect of alteration of carbohydrate traits of newly developed hulless barley on molecular structure changes and nutrient delivery and quantification of the relationship between molecular structure features and changes and truly absorbed nutrient supply to ruminants. This review provides an insight into how inherent structure changes on a molecular basis affect nutrient utilization and availability in ruminants.

  16. Structure and molecular modeling of tungsten borotellurate glasses

    Energy Technology Data Exchange (ETDEWEB)

    Rada, S., E-mail: Simona.Rada@phys.utcluj.ro [Department of Physics and Chemistry, Technical University of Cluj-Napoca, Cluj-Napoca 400020 (Romania); Rada, M. [Nat. Inst. for R and D of Isotopic and Molec. Technologies, Cluj-Napoca 400293 (Romania); Culea, E., E-mail: eugen.culea@phys.utcluj.ro [Department of Physics and Chemistry, Technical University of Cluj-Napoca, Cluj-Napoca 400020 (Romania)

    2013-03-05

    Highlights: ► The [WO{sub 6}] structural units are highly deformed. ► EPR spectra reveal the existence of W{sup +5} ions situated in distorted octahedral positions and the oxygen ions defects. ► The presence of W{sup +5} ions confers to the glass colors that change with composition. -- Abstract: Glasses of the xWO{sub 3} (100−x)[3TeO{sub 2}·2B{sub 2}O{sub 3}] system where x = 0–40 mol% WO{sub 3} were synthesized and characterized by investigations on FTIR, UV–VIS, EPR spectroscopy and molecular modeling calculations in order to obtain information about the structural changes of the glass network determined by the evolution of tungsten ions states, glass composition and WO{sub 3} concentration. Our spectroscopic data show that the incorporation of WO{sub 3} into borate–tellurate glasses causes both the formation of Te–O–W as well as B–O–W linkages and the increase of the number of non-bridging oxygens. The accommodation of the network with the excess of oxygen and the higher capacity of migration of the tungsten ions inside the host network can be associated with a change of tungsten coordination, from [WO{sub 4}] to [WO{sub 6}] structural units. This conversion is accompaniment of a large displacement of the tungsten atom from the centre of the octahedral geometry. EPR spectra reveal the existence of two signals associated with the presence of W{sup +5} ions situated in distorted octahedral positions and the oxygen ions defects. The presence of W{sup +5} ions confers to the glass colors that change with composition.

  17. Method of capture and population structure of Aegla georginae Santos and Jara, 2013 (Decapoda: Anomura: Aeglidae in a tributary of the Ibicuí River in southern Brazil

    Directory of Open Access Journals (Sweden)

    C. E. Copatti

    Full Text Available Abstract In the current study, we investigated population aspects of Aegla georginae in the Ibicuí River Basin by considering different capture methods and the implication of these data in the analysis of population dynamics. We sampled 1774 individuals: 1259 males (21 and 97 juveniles and 1029 and 113 adults in trap and handnet, respectively, 512 females (05 and 140 juveniles, 184 and 64 adults, and 81 and 38 ovigerous in trap and handnet, respectively and 03 unsexed individuals (02 and 01 in trap and handnet, respectively. The frequency distribution in size classes shows a bimodal model for both sexes. The carapace length (CL in males and females varied from 3.11 to 26.00 and 3.73 to 22.36 mm, respectively. Males presented significantly larger sizes than females. The relative abundance between males and females was significantly different from 1:1 with more males than females in most sampling periods (p 0.05. Juveniles were recorded in all seasons, and reproduction occurs throughout the year. The population structure is similar to the model known for aeglids, and the capture methods affected the analysis of A. georginae, where the grouped data and trap captures presented greater abundance of individuals than handnet and males predominate in the larger size classes, and females in the intermediary size classes. Therefore, an integrated view of the capture methods is the best model for studying the population dynamics of aeglids.

  18. Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Pabit, Suzette A. [School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA; Katz, Andrea M. [School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA; Tolokh, Igor S. [Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA; Drozdetski, Aleksander [Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA; Baker, Nathan [Pacific Northwest National Laboratory, Richland, Washington 99352, USA; Onufriev, Alexey V. [Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA; Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA; Pollack, Lois [School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA

    2016-05-24

    Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively char- acterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight in understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.

  19. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

    Directory of Open Access Journals (Sweden)

    Wouter A. A. de Steenhuijsen Piters

    2016-03-01

    Full Text Available The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1:e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting.

  20. Death Associated Protein Kinases: Molecular Structure and Brain Injury

    Directory of Open Access Journals (Sweden)

    Claire Thornton

    2013-07-01

    Full Text Available Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1.

  1. Molecular structures of fructans from Agave tequilana Weber var. azul.

    Science.gov (United States)

    Lopez, Mercedes G; Mancilla-Margalli, Norma A; Mendoza-Diaz, Guillermo

    2003-12-31

    Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought.

  2. Modeling Carbon and Hydrocarbon Molecular Structures in EZTB

    Science.gov (United States)

    Lee, Seungwon; vonAllmen, Paul

    2007-01-01

    A software module that models the electronic and mechanical aspects of hydrocarbon molecules and carbon molecular structures on the basis of first principles has been written for incorporation into, and execution within, the Easy (Modular) Tight-Binding (EZTB) software infrastructure, which is summarized briefly in the immediately preceding article. Of particular interest, this module can model carbon crystals and nanotubes characterized by various coordinates and containing defects, without need to adjust parameters of the physical model. The module has been used to study the changes in electronic properties of carbon nanotubes, caused by bending of the nanotubes, for potential utility as the basis of a nonvolatile, electriccharge- free memory devices. For example, in one application of the module, it was found that an initially 50-nmlong carbon, (10,10)-chirality nanotube, which is a metallic conductor when straight, becomes a semiconductor with an energy gap of .3 meV when bent to a lateral displacement of 4 nm at the middle.

  3. Death associated protein kinases: molecular structure and brain injury.

    Science.gov (United States)

    Nair, Syam; Hagberg, Henrik; Krishnamurthy, Rajanikant; Thornton, Claire; Mallard, Carina

    2013-07-04

    Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk) family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1.

  4. Molecular Diversity and Genetic Structure of Durum Wheat Landraces

    Directory of Open Access Journals (Sweden)

    GULNAR SHIKHSEYIDOVA

    2015-06-01

    Full Text Available To determine the genetic diversity of durum wheat, 41 accessions from Morocco, Ethiopia, Turkey, Lebanon, Kazakhstan, China, and Mongolia were analyzed through Inter-Simple Sequence Repeats (ISSR molecular markers. Out of the used twenty primers, 15 primers that included a considerable polymorphism were selected for the analyses. Among the genotypes under study, 163 fragments (73.7% were polymorph. Several indexes were used to determine the most appropriate primers. While UBC812, UBC864, UBC840, and UBC808 primers were among those markers which produced the highest number of bands and polymorphic bands, they also dedicated the highest rate of polymorphic index content (PIC. These primers also possessed the highest amounts of effective multiplex ratio (EMR and marker index (MI. Therefore, these primers can be recommended for genetic evaluation of the durum wheat. The results of cluster analysis and principle component analysis indicated that the observed genetic diversity in wheat materials under study is geographically structured. The results also indicated that the genetic diversity index based on ISSR markers was higher for Turkey, Lebanon, Morocco, and Ethiopia accessions than for other countries. The high level of polymorphism in this collections durum wheat would agree with the suggestion that Fertile Crescent and parts of Africa are first possible diversity center of this crop.

  5. MOLECULAR STRUCTURE OF AMYOTROPHIC LATERAL SCLEROSIS IN RUSSIAN POPULATION

    Directory of Open Access Journals (Sweden)

    N. Yu. Abramycheva

    2016-01-01

    Full Text Available Materials and methods. 285 Russian patients with amyotrophic lateral sclerosis (ALS including 260 patients with a sporadic form and 25 with a familial form were examined for mutations in SOD1, C9orf72, TARDBP,  ANG and other genes and the presence of associations among polymorphic sites in ATXN2 (polyCAG and VEGF (-2578С/А genes.Molecular genetic analysis was performed using direct sequencing, fragment analysis and real-time polymerase chain reaction. On the last stage, rare ALS candidate genes were evaluated using a next generation sequencing (NGS panel.Results. Total rate of the identified mutations in the examined ALS cohort was 9.5 %. The most frequently observed defects were mutations in the SOD1 (24.0 % in familial ALS and 4.6 % in sporadic ALS and C9orf72 (pathological hexanucleotide repeat expansion was identified in 1.8 % cases of ALS, all sporadic genes. The TARDBP gene didn’t contain any mutations, though in the ALS group deletion c.715-126delG located in intron 5 of the TARDBP gene was significantly over-represented – 38.0 % vs. 26.6 % (χ2 = 13.17; р = 0.002. Mutations in the ANG gene were identified in 1.05 % of ALS patients (all cases were sporadic. In 1 (0.35 % sporadic case a G1082A mutation in the DCTN1 gene was identified. The examined group significantly more frequently carried a risk allele of the ATXN2 gene with an “intermediate” (28–33  number of CAG repeats – 5.0 % vs. 1.7 % in the control group (χ2 = 3.89; р = 0.0486. In Russian ALS patients, an association between the disease and the presence of a risk А-allele and homozygote genotype А/А of -2578С/А polymorphism in the VEGF gene was identified (χ2 = 7.14; р = 0.008 and χ2 = 13.46; р = 0.001 for the rates in the ALS population and in the control population, respectively, which is confirmed by the odds ratio.Conclusion. In the current article, molecular structure of ALS in the Russian population was examined, rates of individual genetic forms

  6. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    Energy Technology Data Exchange (ETDEWEB)

    Nagaoka, Masataka [Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan); Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Honmachi, Kawaguchi 332-0012 (Japan); ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520 (Japan)

    2015-12-31

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  7. A Structural and Molecular Approach for the Study Biomarkers

    Science.gov (United States)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  8. Effect of molecular structure and slump loss resistance of polycarboxylate superplasticizers on self-compacting concrete

    Institute of Scientific and Technical Information of China (English)

    LAN Zi-dong

    2016-01-01

    A new kind of polycarboxylate superplasticizer with high slump loss resistance was obtained by designing scheduled molecular structure. The number average molecular mass of the polymer was characterized by thegel permeation chromatography measurements. And chemical structure of the polymer was observed by the Fouriertransform infrared spectroscopy(FT-IR). The results showthat the good workablemaintaining ofself-compacting concretecould be achieved through direct adjustmentof number average molecular mass and different unsaturated monomer in synthetic process. The FT-IR analysis illustrated that the high slump loss resistance of polycarboxylate superplasticizers with ester and carboxyl group and expectations of molecular structure were designed.

  9. Molecular Electronics

    DEFF Research Database (Denmark)

    Jennum, Karsten Stein

    This thesis includes the synthesis and characterisation of organic compounds designed for molecular electronics. The synthesised organic molecules are mainly based on two motifs, the obigo(phenyleneethynylenes) (OPE)s and tetrathiafulvalene (TTF) as shown below. These two scaffolds (OPE and TTF......) are chemically merged together to form cruciform-like structures that are an essential part of the thesis. The cruciform molecules were subjected to molecular conductance measurements to explore their capability towards single-crystal field-effect transistors (Part 1), molecular wires, and single electron......, however, was obtained by a study of a single molecular transistor. The investigated OPE5-TTF compound was captured in a three-terminal experiment, whereby manipulation of the molecule’s electronic spin was possible in different charge states. Thus, we demonstrated how the cruciform molecules could...

  10. Compact structure and proteins of pasta retard in vitro digestive evolution of branched starch molecular structure.

    Science.gov (United States)

    Zou, Wei; Sissons, Mike; Warren, Frederick J; Gidley, Michael J; Gilbert, Robert G

    2016-11-01

    The roles that the compact structure and proteins in pasta play in retarding evolution of starch molecular structure during in vitro digestion are explored, using four types of cooked samples: whole pasta, pasta powder, semolina (with proteins) and extracted starch without proteins. These were subjected to in vitro digestion with porcine α-amylase, collecting samples at different times and characterizing the weight distribution of branched starch molecules using size-exclusion chromatography. Measurement of α-amylase activity showed that a protein (or proteins) from semolina or pasta powder interacted with α-amylase, causing reduced enzymatic activity and retarding digestion of branched starch molecules with hydrodynamic radius (Rh)pasta protects the starch and proteins in the interior of the whole pasta, reducing the enzymatic degradation of starch molecules, especially for molecules with Rh>100nm.

  11. Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L. germplasm

    Directory of Open Access Journals (Sweden)

    Fricano Agostino

    2012-03-01

    Full Text Available Abstract Background The goals of our study were to assess the phylogeny and the population structure of tobacco accessions representing a wide range of genetic diversity; identify a subset of accessions as a core collection capturing most of the existing genetic diversity; and estimate, in the tobacco core collection, the extent of linkage disequilibrium (LD in seven genomic regions using simple sequence repeat (SSR markers. To this end, a collection of accessions were genotyped with SSR markers. Molecular diversity was evaluated and LD was analyzed across seven regions of the genome. Results A genotyping database for 312 tobacco accessions was profiled with 49 SSR markers. Principal Coordinate Analysis (PCoA and Bayesian cluster analysis revealed structuring of the tobacco population with regard to commercial classes and six main clades were identified, which correspond to "Oriental", Flue-Cured", "Burley", "Dark", "Primitive", and "Other" classes. Pairwise kinship was calculated between accessions, and an overall low level of co-ancestry was observed. A set of 89 genotypes was identified that captured the whole genetic diversity detected at the 49 loci. LD was evaluated on these genotypes, using 422 SSR markers mapping on seven linkage groups. LD was estimated as squared correlation of allele frequencies (r2. The pattern of intrachromosomal LD revealed that in tobacco LD extended up to distances as great as 75 cM with r2 > 0.05 or up to 1 cM with r2 > 0.2. The pattern of LD was clearly dependent on the population structure. Conclusions A global population of tobacco is highly structured. Clustering highlights the accessions with the same market class. LD in tobacco extends up to 75 cM and is strongly dependent on the population structure.

  12. Laser pulse induced multiple exciton kinetics in molecular ring structures

    Science.gov (United States)

    Hou, Xiao; Wang, Luxia

    2016-11-01

    Multiple excitons can be formed upon strong optical excitation of molecular aggregates and complexes. Based on a theoretical approach on exciton-exciton annihilation dynamics in supramolecular systems (May et al., 2014), exciton interaction kinetics in ring aggregates of two-level molecules are investigated. Excited by the sub-picosecond laser pulse, multiple excitons keep stable in the molecular ring shaped as a regular polygon. If the symmetry is destroyed by changing the dipole of a single molecule, the excitation of different molecules becomes not identical, and the changed dipole-dipole interaction initiates subsequent energy redistribution. Depending on the molecular distance and the dipole configuration, the kinetics undergo different types of processes, but all get stable within some hundreds of femtoseconds. The study of exciton kinetics will be helpful for further investigations of the efficiency of optical devices based on molecular aggregates.

  13. Molecular evolution, intracellular organization, and the quinary structure of proteins.

    OpenAIRE

    McConkey, E H

    1982-01-01

    High-resolution two-dimensional polyacrylamide gel electrophoresis shows that at least half of 370 denatured polypeptides from hamster cells and human cells are indistinguishable in terms of isoelectric points and molecular weights. Molecular evolution may have been more conservative for this set of proteins than sequence studies on soluble proteins have implied. This may be a consequence of complexities of intracellular organization and the numerous macromolecular interactions in which most ...

  14. Design, synthesis, and evaluation of nonaqueous silylamines for efficient CO2 capture.

    Science.gov (United States)

    Switzer, Jackson R; Ethier, Amy L; Hart, Emily C; Flack, Kyle M; Rumple, Amber C; Donaldson, Jordan C; Bembry, Ashley T; Scott, Owen M; Biddinger, Elizabeth J; Talreja, Manish; Song, Myoung-Geun; Pollet, Pamela; Eckert, Charles A; Liotta, Charles L

    2014-01-01

    A series of silylated amines have been synthesized for use as reversible ionic liquids in the application of post-combustion carbon capture. We describe a molecular design process aimed at influencing industrially relevant carbon capture properties, such as viscosity, temperature of reversal, and enthalpy of regeneration, while maximizing the overall CO2 -capture capacity. A strong structure-property relationship among the silylamines is demonstrated in which minor structural modifications lead to significant changes in the bulk properties of the reversible ionic liquid formed from reaction with CO2 .

  15. Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

    Science.gov (United States)

    Calhoun, Jennifer R; Liu, Weixia; Spiegel, Katrin; Dal Peraro, Matteo; Klein, Michael L; Valentine, Kathleen G; Wand, A Joshua; DeGrado, William F

    2008-02-01

    We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.

  16. Determination of the experimental equilibrium structure of solid nitromethane using path-integral molecular dynamics simulations

    Science.gov (United States)

    Reilly, Anthony M.; Habershon, Scott; Morrison, Carole A.; Rankin, David W. H.

    2010-03-01

    Path-integral molecular dynamics (PIMD) simulations with an empirical interaction potential have been used to determine the experimental equilibrium structure of solid nitromethane at 4.2 and 15 K. By comparing the time-averaged molecular structure determined in a PIMD simulation to the calculated minimum-energy (zero-temperature) molecular structure, we have derived structural corrections that describe the effects of thermal motion. These corrections were subsequently used to determine the equilibrium structure of nitromethane from the experimental time-averaged structure. We find that the corrections to the intramolecular and intermolecular bond distances, as well as to the torsion angles, are quite significant, particularly for those atoms participating in the anharmonic motion of the methyl group. Our results demonstrate that simple harmonic models of thermal motion may not be sufficiently accurate, even at low temperatures, while molecular simulations employing more realistic potential-energy surfaces can provide important insight into the role and magnitude of anharmonic atomic motions.

  17. Effect of valence of lanthanide ion and molecular symmetry in polyoxotungstoborate on the molecular structure and spectrochemical properties

    Science.gov (United States)

    Iijima, Jun; Naruke, Haruo

    2017-01-01

    The compound K9(NH4)H[CeIV(α-BW11O39)(W5O18)]·16H2O (1) was successfully isolated and structurally characterized. The structural investigation revealed that 1 displayed a less molecular distortion, whereas Ln3+-analogs exhibited a large molecular distortion. IR spectroscopy demonstrated that the spectral patterns of 1 and Ce3+-analog were depending on each valence of Ce (IV/III). 11B-NMR spectroscopy showed that a decrease in site symmetry of B atom in the polyoxotungstoborate was related with an increase in a half width of NMR peak. There is a difference in molecular distortion between 1 and Ce3+-analog, but they have similar large half widths because of the same site symmetry of B atom. The 4f electron in Ce atom exhibited less effect on the chemical shift.

  18. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: a non-equilibrium molecular dynamics study

    CERN Document Server

    Lemarchand, Claire A; Todd, Billy D; Daivis, Peter J; Hansen, Jesper S

    2015-01-01

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear is investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity and normal stress differences of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid. The corresponding molecular structure is studied at the same shear rates and temperatures. The Cooee bitumen is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. The nanoaggregates are shown to break up at very high shear rates, leading only to a minor effect on the viscosity of the mixture. At low shear rates, bitumen can be seen as a colloidal suspension of nanoaggregates in a solvent. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified...

  19. Relationship between structural order and water-like anomalies in metastable liquid silicon: Ab initio molecular dynamics

    Science.gov (United States)

    Zhao, G.; Yan, J. L.; Yu, Y. J.; Ding, M. C.; Zhao, X. G.; Wang, H. Y.

    2017-01-01

    The relationship between structural order and water-like anomalies in tetrahedral liquids is still open. Here, first-principle molecular dynamics are performed to study it in metastable liquid Si. It is found that in T-P phase diagram, there indeed exists a structural anomaly region, which encloses density anomaly but not diffusivity anomaly. This is consistent with that of SW Si and BKS SiO2 but different from that of SPC/E water. Two-body excess entropy anomaly can neither capture the diffusivity, structural, and density anomalies, as it can in a two-scale potential fluid. In structural anomaly region, tetrahedrality order qtetra (measuring the extent to which an atom and its four nearest neighbours adopt tetrahedral arrangement) and translational order ttrans (measuring the tendency of two atoms to adopt preferential separation) are not perfectly correlated, which is different from that in SW Si and renders it impossible to use the isotaxis line to quantify the degree of structural order needed for water-like anomalies to occur. Along the isotherm of critical temperature Tc, ttrans/qtetra is approximately linear with pressure. With decreasing pressure along the isotherm below Tc, ttrans/qtetra departs downward from the line, while it is the opposite case above Tc.

  20. Relationship between structural order and water-like anomalies in metastable liquid silicon: Ab initio molecular dynamics

    Science.gov (United States)

    Zhao, G.; Yan, J. L.; Yu, Y. J.; Ding, M. C.; Zhao, X. G.; Wang, H. Y.

    2017-01-01

    The relationship between structural order and water-like anomalies in tetrahedral liquids is still open. Here, first-principle molecular dynamics are performed to study it in metastable liquid Si. It is found that in T-P phase diagram, there indeed exists a structural anomaly region, which encloses density anomaly but not diffusivity anomaly. This is consistent with that of SW Si and BKS SiO2 but different from that of SPC/E water. Two-body excess entropy anomaly can neither capture the diffusivity, structural, and density anomalies, as it can in a two-scale potential fluid. In structural anomaly region, tetrahedrality order qtetra (measuring the extent to which an atom and its four nearest neighbours adopt tetrahedral arrangement) and translational order ttrans (measuring the tendency of two atoms to adopt preferential separation) are not perfectly correlated, which is different from that in SW Si and renders it impossible to use the isotaxis line to quantify the degree of structural order needed for water-like anomalies to occur. Along the isotherm of critical temperature Tc, ttrans/qtetra is approximately linear with pressure. With decreasing pressure along the isotherm below Tc, ttrans/qtetra departs downward from the line, while it is the opposite case above Tc. PMID:28054595

  1. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.

    Science.gov (United States)

    Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-01

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  2. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  3. Graph of atomic orbitals and the molecular structure-descriptors based on it

    Directory of Open Access Journals (Sweden)

    ANDREY A. TOROPOV

    2005-04-01

    Full Text Available The graph of atomic orbitals (GAO is a novel type of molecular graph, recently proposed by one of the authors. Various molecular structure-descriptors computed for GAO are compared with their analogs computed for ordinary molecular graphs. The quality of these structure-descriptors was tested for correlation with the normal boiling points of alkanes and cycloalkanes. In all the studied cases, the results based on GAO are similar to, and usually slightly better than, those obtained by means of ordinary molecular graps.

  4. Relationship between structures of sprite streamers and inhomogeneity of preceding halos captured by high-speed camera during a combined aircraft and ground-based campaign

    Science.gov (United States)

    Takahashi, Y.; Sato, M.; Kudo, T.; Shima, Y.; Kobayashi, N.; Inoue, T.; Stenbaek-Nielsen, H. C.; McHarg, M. G.; Haaland, R. K.; Kammae, T.; Yair, Y.; Lyons, W. A.; Cummer, S. A.; Ahrns, J.; Yukman, P.; Warner, T. A.; Sonnenfeld, R. G.; Li, J.; Lu, G.

    2011-12-01

    The relationship between diffuse glows such as elves and sprite halos and subsequent discrete structure of sprite streamers is considered to be one of the keys to solve the mechanism causing a large variation of sprite structures. However, it's not easy to image at high frame rate both the diffuse and discrete structures simultaneously, since it requires high sensitivity, high spatial resolution and high signal-to-noise ratio. To capture the real spatial structure of TLEs without influence of atmospheric absorption, spacecraft would be the best solution. However, since the imaging observation from space is mostly made for TLEs appeared near the horizon, the range from spacecraft to TLEs becomes large, such as few thousand km, resulting in low spatial resolution. The aircraft can approach thunderstorm up to a few hundred km or less and can carry heavy high-speed cameras with huge size data memories. In the period of June 27 - July 10, 2011, a combined aircraft and ground-based campaign, in support of NHK Cosmic Shore project, was carried with two jet airplanes under collaboration between NHK (Japan Broadcasting Corporation) and universities. On 8 nights out of 16 standing-by, the jets took off from the airport near Denver, Colorado, and an airborne high speed camera captured over 40 TLE events at a frame rate of 8300 /sec. Here we introduce the time development of sprite streamers and the both large and fine structures of preceding halos showing inhomogeneity, suggesting a mechanism to cause the large variation of sprite types, such as crown like sprites.

  5. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve...

  6. Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.

    Directory of Open Access Journals (Sweden)

    Kei Moritsugu

    Full Text Available Molecular dynamics (MD simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a "Motion Tree", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.

  7. Diurnal and circadian rhythm in compound eye of cricket (Gryllus bimaculatus): changes in structure and photon capture efficiency.

    Science.gov (United States)

    Sakura, Midori; Takasuga, Kyo; Watanabe, Mami; Eguchi, Eisuke

    2003-07-01

    Day-night changes in rhabdom size of compound eyes were investigated in three groups of crickets (Gryllus bimaculatus): nymphs and adult males and females. In both adults and nymphs, the rhabdoms were larger at night than during a day. In adults, the mean rhabdom occupation ratios (RORs) of ommatidial retinulae at midnight were about two times greater than the values at midday. This change contributes to control of the photon capture efficiency (PCE) of the eye according to photic environment. The RORs of adult males at midnight were higher than those of both adult females and nymphs. This suggests that the PCE of the compound eye of adult males is the greatest of all groups. Under constant darkness, day-night changes in ROR were detected only in adult males, but neither in adult females nor in nymphs. On the other hand, no day-night changes were detected in any experimental group under constant light. These results suggest that the change in rhabdom size between day and night is an adaptation to the photic environment that is controlled mainly by the light-dark (day-night) cycle. However, the change in male adults is induced by an endogenous circadian clock.

  8. Molecular Dynamics and Protein Structure. Proceedings of a Workshop Held 13-18 May 1984 at Chapel Hill, North Carolina.

    Science.gov (United States)

    Two years ago, when we first proposed to organize a Workship on Molecular Dynamics of Proteins. We desired a format that combined elements of these...students of the field. Molecular Dynamics of Biomolecules; Methods in Molecular Dynamics ; Potential Functions for Simulations of Biomolecules...Statistical Mechanics and Molecular Dynamics ; Molecular Dynamics and Structure Refinement; Simulation of Activated Processes and Reactions; Graphics; Computer

  9. Molecular and structural preservation of dehydrated bio-tissue for THz spectroscopy

    Science.gov (United States)

    Png, Gretel M.; Choi, Jin Wook; Guest, Ian; Ng, Brian W.-H.; Mickan, Samuel P.; Abbott, Derek; Zhang, Xi-Cheng

    2007-12-01

    Terahertz transmission through freshly excised biological tissue is limited by the tissue's high water content. Tissue fixation methods that remove water, such as fixation in Formalin, destroy the structural information of proteins hence are not suitable for THz applications. Dehydration is one possible method for revealing the tissue's underlying molecular structure and components. In this study, we measured the THz responses over time of dehydrating fresh, necrotic and lyophilized rat tissue. Our results show that as expected, THz absorption increases dramatically with drying and tissue freshness can be maintained through lyophilization. Dehydrated biological tissue with retained molecular structure can be useful for future laser-based THz wave molecular analysis.

  10. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    Science.gov (United States)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  11. A Molecular Dynamics Approach to Grain Boundary Structure and Migration

    DEFF Research Database (Denmark)

    Cotterill, R. M. J.; Leffers, Torben; Lilholt, Hans

    1974-01-01

    It has been demonstrated that grain boundary formation from the melt can be simulated by the molecular dynamics method. The space between two mutually-misoriented crystal slabs was filled with atoms in a random manner and this liquid was then cooled until crystallization occurred. The general...

  12. Molecular conformation and structural correlations of liquid D-1-propanol through neutron diffraction

    Indian Academy of Sciences (India)

    A Sahoo; S Sarkar; P S R Krishna; V Bhagat; R N Joarder

    2008-07-01

    An analysis of neutron diffraction data of liquid deuterated 1-propanol at room temperature to extract its molecular conformation is presented. Being a big molecule with twelve atomic sites, the analysis is tricky and needs careful consideration. The resulting molecular parameters are compared with electron diffraction (gas phase), X-ray diffraction (liquid phase) and MD simulation results. Information about the hydrogen-bonded intermolecular structure in liquid is extracted and nature of the probable molecular association suggested.

  13. STRUCTURE AND DYNAMICS OF ALKALI BORATE GLASSES - A MOLECULAR-DYNAMICS STUDY

    NARCIS (Netherlands)

    VERHOEF, AH; DENHARTOG, HW

    1995-01-01

    Structural and dynamical properties of lithium, cesium and mixed alkali (i.e., lithium and cesium) borate glasses have been studied by the molecular dynamics method. The calculations yield glass structures consisting of planar BO3 triangles and BO4 tetrahedrons with no sixfold ring structures at all

  14. Extracting molecular Hamiltonian structure from time-dependent fluorescence intensity data

    OpenAIRE

    Brif, Constantin; Rabitz, Herschel

    2000-01-01

    We propose a formalism for extracting molecular Hamiltonian structure from inversion of time-dependent fluorescence intensity data. The proposed method requires a minimum of \\emph{a priori} knowledge about the system and allows for extracting a complete set of information about the Hamiltonian for a pair of molecular electronic surfaces.

  15. A first-principles density functional theory study of the electronic structural and thermodynamic properties of M2ZrO3 and M2CO3 (M=Na, K) and their capabilities for CO2 capture

    Energy Technology Data Exchange (ETDEWEB)

    Yuhua Duan

    2012-01-01

    Alkali metal zirconates could be used as solid sorbents for CO{sub 2} capture. The structural, electronic, and phonon properties of Na{sub 2}ZrO{sub 3}, K{sub 2}ZrO{sub 3}, Na{sub 2}CO{sub 3}, and K{sub 2}CO{sub 3} are investigated by combining the density functional theory with lattice phonon dynamics. The thermodynamics of CO{sub 2} absorption/desorption reactions of these two zirconates are analyzed. The calculated results show that their optimized structures are in a good agreement with experimental measurements. The calculated band gaps are 4.339 eV (indirect), 3.641 eV (direct), 3.935 eV (indirect), and 3.697 eV (direct) for Na{sub 2}ZrO{sub 3}, K{sub 2}ZrO{sub 3}, Na{sub 2}CO{sub 3}, and K{sub 2}CO{sub 3}, respectively.The calculated phonon dispersions and phonon density of states for M{sub 2}ZrO{sub 3} and M{sub 2}CO{sub 3} (M = K, Na, Li) revealed that from K to Na to Li, their frequency peaks are shifted to high frequencies due to the molecular weight decreased from K to Li. From the calculated reaction heats and relationships of free energy change versus temperatures and CO{sub 2} pressures of the M{sub 2}ZrO{sub 3} (M = K, Na, Li) reacting with CO{sub 2}, we found that the performance of Na{sub 2}ZrO{sub 3} capturing CO{sub 2} is similar to that of Li{sub 2}ZrO{sub 3} and is better than that of K{sub 2}ZrO{sub 3}. Therefore, Na{sub 2}ZrO{sub 3} and Li{sub 2}ZrO{sub 3} are good candidates of high temperature CO{sub 2} sorbents and could be used for post combustion CO{sub 2} capture technologies.

  16. [Cajal bodies and histone locus bodies: molecular structure and function].

    Science.gov (United States)

    Khodiuchenko, T A; Krasikova, A V

    2014-01-01

    The review provides modern classification of evolutionarily conserved coilin-containing nuclear bodies of somatic and germ cells that is based on the characteristic features of their molecular composition and the nature of their functions. The main differences between Cajal bodies and histone locus bodies, which are involved in the biogenesis of small nuclear spliceosomal and nucleolar RNAs and in the 3'-end processing of histone precursor messenger RNA, respectively, are considered. It is shown that a significant contribution to the investigation of the diversity of coilin-containing bodies was made by the studies on the architecture of the RNA processing machinery in oocyte nuclei in a number of model organisms. The characteristics features of the molecular composition of coilin-containing bodies in the nuclei of growing oocytes (the so-called germinal vesicles) of vertebrates, including amphibians and birds, are described.

  17. Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations.

    Science.gov (United States)

    Fang, Jiansong; Pang, Xiaocong; Wu, Ping; Yan, Rong; Gao, Li; Li, Chao; Lian, Wenwen; Wang, Qi; Liu, Ai-lin; Du, Guan-hua

    2016-05-01

    A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2)) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives.

  18. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    Energy Technology Data Exchange (ETDEWEB)

    Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J., E-mail: fwilliams@qi.fcen.uba.ar [INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química-Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EHA (Argentina)

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  19. 3D structure of AcrB: the archetypal multidrug efflux transporter of Escherichia coli likely captures substrates from periplasm.

    Science.gov (United States)

    Elkins, Christopher A; Nikaido, Hiroshi

    2003-02-01

    Recent advances in structural biology have extended our understanding of the multiple drug efflux complex, AcrAB-TolC, of Escherichia coli. This tripartite complex and its homologs are the major mechanisms that give most Gram-negative bacteria their characteristic intrinsic resistance to a variety of lipophilic drugs, dyes, and detergents. Most recently, the structure of the transporter AcrB was elucidated at high resolution [Nature 419(2002)587]. It is a particularly significant achievement since integral membrane proteins are notoriously elusive structures for crystallography. The striking features of this trimeric pump, such as the presence of potential substrate-binding sites in the periplasmic domain and the possibility of direct interaction with the end of TolC tunnel, refine our understanding of the mode of action of this tripartite efflux transport complex.

  20. Puffed rice and the molecular changes that determine its structure

    OpenAIRE

    2003-01-01

    The Rice Krispies™ process consists essentially of the cooking of short or medium rice grains, followed by a mechanical compression between two rolls (bumping), a tempering step and a toasting operation (puffing) which expands the grains into the finished product. The objectives of this project were to clarify which molecular phenomena take place inside the rice grains during the process and to facilitate the improvement and optimisation of the process parameters. The composition and gelatini...

  1. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    Energy Technology Data Exchange (ETDEWEB)

    Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche

    1997-09-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.

  2. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    Science.gov (United States)

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  3. SERS and RAIR for Molecular Structure of Phenylazonaphthalene terminated Self-Assembled Monolayer

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The SAMs of 10-[4-(4-phenylazo)naphth-l-oxyl]-l-decanethiol (Compound 1) on gold were prepared. Their molecular structures were determined by surface enhanced Raman spectroscopy (SERS) and reflection absorption infrared spectroscopy (RAIR).

  4. Molecular Structures and Functional Relationships in Clostridial Neurotoxins

    Energy Technology Data Exchange (ETDEWEB)

    Swaminathan S.

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.

  5. Mapping chemical performance on molecular structures using locally interpretable explanations

    CERN Document Server

    Whitmore, Leanne S; Hudson, Corey M

    2016-01-01

    In this work, we present an application of Locally Interpretable Machine-Agnostic Explanations to 2-D chemical structures. Using this framework we are able to provide a structural interpretation for an existing black-box model for classifying biologically produced fuel compounds with regard to Research Octane Number. This method of "painting" locally interpretable explanations onto 2-D chemical structures replicates the chemical intuition of synthetic chemists, allowing researchers in the field to directly accept, reject, inform and evaluate decisions underlying inscrutably complex quantitative structure-activity relationship models.

  6. Bias-dependent molecular-level structure of electrical double layer in ionic liquid on graphite.

    Science.gov (United States)

    Black, Jennifer M; Walters, Deron; Labuda, Aleksander; Feng, Guang; Hillesheim, Patrick C; Dai, Sheng; Cummings, Peter T; Kalinin, Sergei V; Proksch, Roger; Balke, Nina

    2013-01-01

    Here we report the bias-evolution of the electrical double layer structure of an ionic liquid on highly ordered pyrolytic graphite measured by atomic force microscopy. We observe reconfiguration under applied bias and the orientational transitions in the Stern layer. The synergy between molecular dynamics simulation and experiment provides a comprehensive picture of structural phenomena and long and short-range interactions, which improves our understanding of the mechanism of charge storage on a molecular level.

  7. PREVALENCE OF SOME HELMINTHS IN RODENTS CAPTURED FROM DIFFERENT CITY STRUCTURES INCLUDING POULTRY FARMS AND HUMAN POPULATION OF FAISALABAD, PAKISTAN

    Directory of Open Access Journals (Sweden)

    A. RAFIQUE, S. A. RANA, H. A. KHAN AND A. SOHAIL1

    2009-07-01

    Full Text Available The aim of the present study was to investigate prevalence of zoonotic helminths from human, Rattus rattus (R. rattus, Rattus norvegicus (R. norvegicus and Mus musculus of eight different structures, namely grain shops in grain market, departmental stores, railway godowns, food processing plants (bakeries, poultry farms, houses in kachi-abadies, houses in departmental colonies and posh residences and banglows in Faisalabad city. All the structures were sampled for 2 months each and completed in 16 months. Highest prevalence (70% of Vsmpirolepis spp. was observed in R. rattus sampled from poultry farms, which was significantly higher (P<0.05 than the prevalence of all the helminths recovered from other structures. Hymenolepis nana (H. nana was observed in 60% of the sampled Mus musculus collected from kachi-abadies, which was significantly higher (P<0.05 than all other structures studies for H. nana, except R. rattus from kachi-abadies (55% and R. norvegicus from grain shops in grain market (55%. The rodent’s endo-parasites viz., Hymenolepis nana, Teania taenaeformis, Entrobius spps and Trichuiris spps observed in R. rattus, R. norvegicus and M. musculus at different percentages were also recorded in human stool samples with an incidence of 48, 21, 76 and 10%, respectively.

  8. Capturing coherent structures and turbulent interfaces in wake flows by means of the Organised Eddy Simulation, OES and by Tomo-PIV

    Science.gov (United States)

    Deri, E.; Ouvrard, H.; Braza, M.; Hunt, J.; Hoarau, Y.; Cazin, S.; Cid, E.; Harran, G.

    2011-12-01

    The present study aims at a physical analysis of the coherent and chaotic vortex dynamics in the near wake around a flat plate at incidence, to provide new elements in respect of the flow physics turbulence modelling for high-Reynolds number flows around bodies. This constitutes nowadays a challenge in the aeronautics design. A special attention is paid to capture the thin shear layer interfaces downstream of the separation, responsible for aeroacoustics phenomena related to noise reduction and directly linked to an accurate prediction of the aerodynamic forces. The experimental investigation is carried out by means of tomographic PIV. The interaction of the most energetic coherent structures with the random turbulence is discussed. Furthermore, the POD analysis allowed evaluation of 3D phase averaged dynamics as well as the influence of higher modes associated with the finer-scale turbulence. The numerical study by means of the Organised Eddy Simulation, OES approach ensured a reduced turbulence diffusion that allowed development of the von Karman instability and of capturing of the thin shear-layer interfaces, by using appropriate criteria based on vorticity and dissipation rate of kinetic energy. A comparison between the experiments and the simulations concerning the coherent vortex pattern is carried out.

  9. From electron microscopy to molecular cell biology, molecular genetics and structural biology: intracellular transport and kinesin superfamily proteins, KIFs: genes, structure, dynamics and functions.

    Science.gov (United States)

    Hirokawa, Nobutaka

    2011-01-01

    Cells transport and sort various proteins and lipids following synthesis as distinct types of membranous organelles and protein complexes to the correct destination at appropriate velocities. This intracellular transport is fundamental for cell morphogenesis, survival and functioning not only in highly polarized neurons but also in all types of cells in general. By developing quick-freeze electron microscopy (EM), new filamentous structures associated with cytoskeletons are uncovered. The characterization of chemical structures and functions of these new filamentous structures led us to discover kinesin superfamily molecular motors, KIFs. In this review, I discuss the identification of these new structures and characterization of their functions using molecular cell biology and molecular genetics. KIFs not only play significant roles by transporting various cargoes along microtubule rails, but also play unexpected fundamental roles on various important physiological processes such as learning and memory, brain wiring, development of central nervous system and peripheral nervous system, activity-dependent neuronal survival, development of early embryo, left-right determination of our body and tumourigenesis. Furthermore, by combining single-molecule biophysics with structural biology such as cryo-electrom microscopy and X-ray crystallography, atomic structures of KIF1A motor protein of almost all states during ATP hydrolysis have been determined and a common mechanism of motility has been proposed. Thus, this type of studies could be a good example of really integrative multidisciplinary life science in the twenty-first century.

  10. Effects of molecular structure parameters on ring-openingreaction of benzoxazines

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A colorless monoclinic crystal of dichloro-benzoxazine was obtained and examined bysingle crystal X-ray diffraction analysis. At the same time, molecular modeling analysis of ninebenzoxazine compounds with different substituting groups was performed. Both single crystalX-ray diffraction analysis and molecular modeling analysis provide a detailed picture of molecularstructure on molecular level and show good consistence with each other. On the basis of structuralanalysis, the effects of molecular structure parameters on ring-opening polymerization of ben-zoxazines have been explored.

  11. Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Bibby, Jaclyn [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Keegan, Ronan M. [Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom)

    2013-11-01

    Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

  12. Crystal structural and diffusion property in titanium carbides: A molecular dynamics study

    Science.gov (United States)

    Lv, Yanan; Gao, Weimin

    2016-09-01

    Titanium carbides were studied via molecular dynamics simulation to characterize TiCx structures with respect to the carbon diffusion properties in this study. The effect of carbon concentration on atomic structures of titanium carbides was investigated through discussing the structure variation and the radial distribution functions of carbon atoms in titanium carbides. The carbon diffusion in titanium carbides was also analyzed, focusing on the dependence on carbon concentration and carbide structure. Carbon diffusivity with different carbon concentrations was determined by molecular dynamics (MD) calculations and compared with the available experimental data. The simulation results showed an atomic exchange mechanism for carbon diffusion in titanium carbide.

  13. Extraordinary capture of a Randall's snapper Randallichthys filamentosus in the temperate south-eastern Indian Ocean and its molecular phylogenetic relationship within the Etelinae.

    Science.gov (United States)

    Wakefield, C B; Moore, G I; Bertram, A E; Snow, M; Newman, S J

    2016-02-01

    The capture of a rarely encountered Randall's snapper Randallichthys filamentosus (female, 587 mm fork length) from the upper continental slope (c. 350 m) off the south coast of Western Australia (c. 34·5° S; 122·5° E) in January 2014 represents its first record from the temperate Indian Ocean and a southern range extension. This record suggests that spawning of this predominantly tropical species may probably be occurring in the eastern Indian Ocean, considering the extensive, and unlikely, distance the progeny would have otherwise travelled from its typical distribution in the western and central Pacific Ocean.

  14. Sensitive and label-free biosensing of RNA with predicted secondary structures by a triplex affinity capture method

    Science.gov (United States)

    Carrascosa, Laura G.; Gómez-Montes, S.; Aviñó, A.; Nadal, A.; Pla, M.; Eritja, R.; Lechuga, L. M.

    2012-01-01

    A novel biosensing approach for the label-free detection of nucleic acid sequences of short and large lengths has been implemented, with special emphasis on targeting RNA sequences with secondary structures. The approach is based on selecting 8-aminoadenine-modified parallel-stranded DNA tail-clamps as affinity bioreceptors. These receptors have the ability of creating a stable triplex-stranded helix at neutral pH upon hybridization with the nucleic acid target. A surface plasmon resonance biosensor has been used for the detection. With this strategy, we have detected short DNA sequences (32-mer) and purified RNA (103-mer) at the femtomol level in a few minutes in an easy and level-free way. This approach is particularly suitable for the detection of RNA molecules with predicted secondary structures, reaching a limit of detection of 50 fmol without any label or amplification steps. Our methodology has shown a marked enhancement for the detection (18% for short DNA and 54% for RNA), when compared with the conventional duplex approach, highlighting the large difficulty of the duplex approach to detect nucleic acid sequences, especially those exhibiting stable secondary structures. We believe that our strategy could be of great interest to the RNA field. PMID:22241768

  15. A parity function for studying the molecular electronic structure

    DEFF Research Database (Denmark)

    Schmider, Hartmut

    1996-01-01

    Sections through the molecular Wigner function with zero momentum variable are shown to provide important information about the off-diagonal regions of the spinless one-particle reduced density matrix. Since these regions are characteristic for the bonding situation in molecules, the sections...... are qualitatively even more affected by the presence of chemical bonds than a complementary projection, the reciprocal form factor. In this paper we discuss, on the grounds of a variety of examples, how this rather simple function may aid the understanding of the chemical bond on a one-particle level. (C) 1996...

  16. Molecular structure of the coalescence of liquid interfaces

    Science.gov (United States)

    Koplik, Joel; Banavar, Jayanth R.

    1992-01-01

    When two bodies of liquid merge, their interfaces must also rupture and rearrange into one. Virtually no information is available concerning the small-scale dynamics of this process. Molecular dynamics simulations of coalescence in systems of about 10,000 Lennard-Jones particles have been performed, arranged so as to mimic laboratory experiments on dense liquids. The coalescence event begins when molecules near the boundary of one liquid body thermally fluctuate into the range of attraction of the other, forming a string of mutually attracting molecules. These molecules gradually thicken into a tendril, which continues to thicken as the bodies smoothly combine in a zipper-like merger.

  17. CO2 capture using semi-clathrates of quaternary ammonium salt: structure change induced by CO2 and N2 enclathration.

    Science.gov (United States)

    Chazallon, Bertrand; Ziskind, Michael; Carpentier, Yvain; Focsa, Cristian

    2014-11-26

    Semi-clathrates of tetrabutylammonium bromide (TBAB) are investigated for their potential application in the CO2 capture context based on hydrate technology. The three-phase lines of semi-clathrates of CO2-TBAB-H2O and N2-TBAB-H2O are established simultaneously with their structure using in situ Raman scattering performed at high pressure. The preferred crystal phase obtained at ambient pressure from solutions of 5 and 40 wt % TBAB initial concentrations is shown to change upon enclathration of CO2 or N2, or by applying a higher pressure on the system. Deep in the stability field, metastable hydrate phases are occurring at the onset of the formation and correspond to the ones expected under ambient pressure conditions. Depending on the pressure, they progressively transformed into the most stable ones when approaching equilibrium and dissociation points. Besides, it is shown that a 5 wt % TBAB original solution forms preferentially a mixed structure of both type B and type A at low gas pressure with CO2 as the guest gas. A new structure is spectroscopically characterized at pressures higher than ∼2 MPa CO2. Type A is demonstrated to be stable at 5 wt % initial TBAB concentration with N2 as the guest molecule and pressure between 8 and 12 MPa. These structural data address new insights on the relationship between the hydrophilic-anion and hydrophobic-cation intercalation with a guest gas producing hydrophobic interaction in a distorted water lattice.

  18. Molecular Structure of the Human CFTR Ion Channel.

    Science.gov (United States)

    Liu, Fangyu; Zhang, Zhe; Csanády, László; Gadsby, David C; Chen, Jue

    2017-03-23

    The cystic fibrosis transmembrane conductance regulator (CFTR) is an ATP-binding cassette (ABC) transporter that uniquely functions as an ion channel. Here, we present a 3.9 Å structure of dephosphorylated human CFTR without nucleotides, determined by electron cryomicroscopy (cryo-EM). Close resemblance of this human CFTR structure to zebrafish CFTR under identical conditions reinforces its relevance for understanding CFTR function. The human CFTR structure reveals a previously unresolved helix belonging to the R domain docked inside the intracellular vestibule, precluding channel opening. By analyzing the sigmoid time course of CFTR current activation, we propose that PKA phosphorylation of the R domain is enabled by its infrequent spontaneous disengagement, which also explains residual ATPase and gating activity of dephosphorylated CFTR. From comparison with MRP1, a feature distinguishing CFTR from all other ABC transporters is the helix-loop transition in transmembrane helix 8, which likely forms the structural basis for CFTR's channel function.

  19. Effect of Chemical Structure on Molecular Properties of Hyperbranched Polycarbosilanes

    Institute of Scientific and Technical Information of China (English)

    E.Tarabukina; A.Shpyrkov; A.Amirova; E.Tarasova; N.Shumilkina; A.Filippov; A.Muzafarov

    2007-01-01

    1 Results In spite of the increased interest to the synthesis of hyperbranched polymers,there is a lack of studies of conformational properties of their macromolecules.Structural features of hyperbranched polymers are responsible for new properties that distinguish them from linear compounds and open unique possibilities for their applications.The knowledge of the "structure-properties" relationships is of fundamental value,it also can be helpful when developing new technologies and new materials. The g...

  20. Complex molecular gas structure in the Medusa merger

    CERN Document Server

    Aalto, S

    2000-01-01

    High resolution OVRO aperture synthesis maps of the 12CO 1-0 emission in the `Medusa' galaxy merger (NGC4194) reveal the molecular emission being surprisingly extended. It is distributed on a total scale of 25$''$ (4.7 kpc) - despite the apparent advanced stage of the merger. The complex, striking CO morphology occupies mainly the center and the north-eastern part of the main optical body. The extended 12CO flux is tracing two prominent dust lanes: one which is crossing the central region at right angle and a second which curves to the north-east and then into the beginning of the northern tidal tail. The bulk of the 12CO emission (67%) can be found in a complex starburst region encompassing the central 2kpc. The molecular gas is distributed in five major emission regions of typical size 300pc. About 15% of the total 12CO flux is found in a bright region 1.5'' south of the radio continuum nucleus. We suggest that this region together with the kpc sized central starburst is being fueled by gas flows along the ...

  1. Modelling and enhanced molecular dynamics to steer structure-based drug discovery.

    Science.gov (United States)

    Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe

    2014-05-01

    The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes.

  2. Molecular modeling of mechanosensory ion channel structural and functional features.

    Science.gov (United States)

    Gessmann, Renate; Kourtis, Nikos; Petratos, Kyriacos; Tavernarakis, Nektarios

    2010-09-16

    The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex.

  3. Molecular modeling of mechanosensory ion channel structural and functional features.

    Directory of Open Access Journals (Sweden)

    Renate Gessmann

    Full Text Available The DEG/ENaC (Degenerin/Epithelial Sodium Channel protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1. MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex.

  4. Molecular structural analysis of HPRT mutations induced by thermal and epithermal neutrons in Chinese hamster ovary cells.

    Science.gov (United States)

    Kinashi, Y; Sakurai, Y; Masunaga, S; Suzuki, M; Takagaki, M; Akaboshi, M; Ono, K

    2000-09-01

    Chinese hamster ovary (CHO) cells were exposed to thermal and epithermal neutrons, and the occurrence of mutations at the HPRT locus was investigated. The Kyoto University Research Reactor (KUR), which has been improved for use in neutron capture therapy, was the neutron source. Neutron energy spectra ranging from nearly pure thermal to epithermal can be chosen using the spectrum shifters and thermal neutron filters. To determine mutant frequency and cell survival, cells were irradiated with thermal and epithermal neutrons under three conditions: thermal neutron mode, mixed mode with thermal and epithermal neutrons, and epithermal neutron mode. The mutagenicity was different among the three irradiation modes, with the epithermal neutrons showing a mutation frequency about 5-fold that of the thermal neutrons and about 1.5-fold that of the mixed mode. In the thermal neutron and mixed mode, boron did not significantly increase the frequency of the mutants at the same dose. Therefore, the effect of boron as used in boron neutron capture therapy (BNCT) is quantitatively minimal in terms of mutation induction. Over 300 independent neutron-induced mutant clones were isolated from 12 experiments. The molecular structure of HPRT mutations was determined by analysis of all nine exons by multiplex polymerase chain reaction. In the thermal neutron and mixed modes, total and partial deletions were dominant and the fraction of total deletions was increased in the presence of boron. In the epithermal neutron mode, more than half of the mutations observed were total deletions. Our results suggest that there are clear differences between thermal and epithermal neutron beams in their mutagenicity and in the structural pattern of the mutants that they induce. Mapping of deletion breakpoints of 173 partial-deletion mutants showed that regions of introns 3-4, 7/8-9 and 9-0 are sensitive to the induction of mutants by neutron irradiation.

  5. The Molecular Structure of the Liquid Ordered Phase

    Science.gov (United States)

    Lyman, Edward

    2014-03-01

    Molecular dynamics simulations reveal substructures within the liquid-ordered phase of lipid bilayers. These substructures, identified in a 10 μsec all-atom trajectory of liquid-ordered/liquid-disordered coexistence (Lo/Ld) , are composed of saturated hydrocarbon chains packed with local hexagonal order, and separated by interstitial regions enriched in cholesterol and unsaturated chains. Lipid hydrocarbon chain order parameters calculated from the Lo phase are in excellent agreement with 2H NMR measurements; the local hexagonal packing is also consistent with 1H-MAS NMR spectra of the Lo phase, NMR diffusion experiments, and small angle X-ray- and neutron scattering. The balance of cholesterol-rich to local hexagonal order is proposed to control the partitioning of membrane components into the Lo regions. The latter have been frequently associated with formation of so-called rafts, platforms in the plasma membranes of cells that facilitate interaction between components of signaling pathways.

  6. Introductory group theory and its application to molecular structure

    CERN Document Server

    Ferraro, John R

    1969-01-01

    This volume is a consequence of a series of seminars presented by the authors at the Infrared Spectroscopy Institute, Canisius College, Buffalo, New York, over the last nine years. Many participants on an intermediate level lacked a sufficient background in mathematics and quantum mechan­ ics, and it became evident that a non mathematical or nearly nonmathe­ matical approach would be necessary. The lectures were designed to fill this need and proved very successful. As a result of the interest that was developed in this approach, it was decided to write this book. The text is intended for scientists and students with only limited theore­ tical background in spectroscopy, but who are sincerely interested in the interpretation of molecular spectra. The book develops the detailed selection rules for fundamentals, combinations, and overtones for molecules in several point groups. Detailed procedures used in carrying out the normal coordinate treatment for several molecules are also presented. Numerous examples...

  7. Molecular and Electronic Structure of n-Alkyl Cyanobiphenyl Nematogens

    Energy Technology Data Exchange (ETDEWEB)

    Risser, Steven M.(TEXAS A and M UNIVERSITY); Ferris, Kim F.(BATTELLE (PACIFIC NW LAB))

    2001-12-01

    First principle electronic structure calculations (ab-initio and density functional) were performed on a series of substituted cyanobiphenyls to examine the structural and electronic properties as a function of the alkyl tail length and changes in torsion angle about the central bond connecting the rings. We find good agreement between our results and previous electronic structure studies for the optimized torsion angle between phenyls in the cyanobiphenyls, and changes in dipole moment for the cyanobiphenyls. We also find the torsion angle and rotational barriers in cyanobiphenyls to be similar to that in simple biphenyl. However, we find large discrepancies with the recent density functional calculations that reported a much smaller torsion angle in the syanobiphenyls.

  8. The Structural, Functional and Molecular Organization of the Brainstem

    Directory of Open Access Journals (Sweden)

    Rudolf eNieuwenhuys

    2011-06-01

    Full Text Available According to Wilhelm His (1891, 1893 the brainstem consists of two longitudinal zones, the dorsal alar plate (sensory in nature and the ventral basal plate (motor in nature. Johnston and Herrick indicated that both plates can be subdivided into separate somatic and visceral zones, distinguishing somatosensory and viscerosensory zones within the alar plate, and visceromotor and somatomotor zones within the basal plate. To test the validity of this ‘four-functional-zones’ concept, I developed a topological procedure, surveying the spatial relationships of the various cell masses in the brainstem in a single figure. Brainstems of 16 different anamniote species were analyzed, and revealed that the brainstems are clearly divisible into four morphological zones, which correspond largely with the functional zones of Johnston and Herrick. Exceptions include (1 the magnocellular vestibular nucleus situated in the viscerosensory zone; (2 the basal plate containing a number of evidently non-motor centres (superior and inferior olives. Nevertheless the ‘functional zonal model’ has explanatory value. Thus, it is possible to interpret certain brain specializations related to particular behavioural profiles, as ‘local hypertrophies’ of one or two functional columns. Recent developmental molecular studies on brains of birds and mammals confirmed the presence of longitudinal zones, and also showed molecularly defined transverse bands or neuromeres throughout development. The intersecting boundaries of the longitudinal zones and the transverse bands appeared to delimit radially arranged histogenetic domains. Because neuromeres have been observed in embryonic and larval stages of numerous anamniote species, it may be hypothesized that the brainstems of all vertebrates share a basic organizational plan, in which intersecting longitudinal and transverse zones form fundamental histogenetic and genoarchitectonic units.

  9. Loading Actinides in Multilayered Structures for Nuclear Waste Treatment: The First Case Study of Uranium Capture with Vanadium Carbide MXene.

    Science.gov (United States)

    Wang, Lin; Yuan, Liyong; Chen, Ke; Zhang, Yujuan; Deng, Qihuang; Du, Shiyu; Huang, Qing; Zheng, Lirong; Zhang, Jing; Chai, Zhifang; Barsoum, Michel W; Wang, Xiangke; Shi, Weiqun

    2016-06-29

    Efficient nuclear waste treatment and environmental management are important hurdles that need to be overcome if nuclear energy is to become more widely used. Herein, we demonstrate the first case of using two-dimensional (2D) multilayered V2CTx nanosheets prepared by HF etching of V2AlC to remove actinides from aqueous solutions. The V2CTx material is found to be a highly efficient uranium (U(VI)) sorbent, evidenced by a high uptake capacity of 174 mg g(-1), fast sorption kinetics, and desirable selectivity. Fitting of the sorption isotherm indicated that the sorption followed a heterogeneous adsorption model, most probably due to the presence of heterogeneous adsorption sites. Density functional theory calculations, in combination with X-ray absorption fine structure characterizations, suggest that the uranyl ions prefer to coordinate with hydroxyl groups bonded to the V-sites of the nanosheets via forming bidentate inner-sphere complexes.

  10. Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle.

    Science.gov (United States)

    Cavalli, Andrea; Camilloni, Carlo; Vendruscolo, Michele

    2013-03-07

    In order to characterise the dynamics of proteins, a well-established method is to incorporate experimental parameters as replica-averaged structural restraints into molecular dynamics simulations. Here, we justify this approach in the case of interproton distance information provided by nuclear Overhauser effects by showing that it generates ensembles of conformations according to the maximum entropy principle. These results indicate that the use of replica-averaged structural restraints in molecular dynamics simulations, given a force field and a set of experimental data, can provide an accurate approximation of the unknown Boltzmann distribution of a system.

  11. The molecular structural features controlling stickiness in cooked rice, a major palatability determinant

    Science.gov (United States)

    Li, Hongyan; Fitzgerald, Melissa A.; Prakash, Sangeeta; Nicholson, Timothy M.; Gilbert, Robert G.

    2017-03-01

    The stickiness of cooked rice is important for eating quality and consumer acceptance. The first molecular understanding of stickiness is obtained from leaching and molecular structural characteristics during cooking. Starch is a highly branched glucose polymer. We find (i) the molecular size of leached amylopectin is 30 times smaller than that of native amylopectin while (ii) that of leached amylose is 5 times smaller than that of native amylose, (iii) the chain-length distribution (CLD: the number of monomer units in a chain on the branched polymer) of leached amylopectin is similar to native amylopectin while (iv) the CLD of leached amylose is much narrower than that of the native amylose, and (v) mainly amylopectin, not amylose, leaches out of the granule and rice kernel during cooking. Stickiness is found to increase with decreasing amylose content in the whole grain, and, in the leachate, with increasing total amount of amylopectin, the proportion of short amylopectin chains, and amylopectin molecular size. Molecular adhesion mechanisms are put forward to explain this result. This molecular structural mechanism provides a new tool for rice breeders to select cultivars with desirable palatability by quantifying the components and molecular structure of leached starch.

  12. Effect of Molecular Structure on the Performance of Polyacrylic Acid Superplasticizer

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rongguo; GUO Huiling; LEI Jiaheng; ZHANG Anfu; GU Huajun

    2007-01-01

    The effects of structure parameters, such as molecular structure, segment kinds, molecular weight, and organic functional groups, on the performance of polyacrylic acid superplasticizer were discussed. According to the differences of chain sections, functional groups, etc, polyacrylic acid superplasticizer could be divided into A, B, C three parts. Among them, A chain section included sulfonic acid groups, B chain section carboxyl groups, C chain section polyester. Polyacrylic acid superplasticizers with different matching of A, B, C chain sections, different length of C chain section and different molecular weights were synthesized by acrylic acid, polyethylene glycol, sodium methyl allylsulfonate; the relation between the molecular structure and performance was also studied. The expetimental results indicate that the water-reduction ratio increases obviously with the increment of the proportion of sodium methyl allylsulfonate chain section in the molecular; the slump retention increases greatly with the increment of the proportion of acrylic acid chain section; the dispersion of cement particles increases with the increment of the chain length of polyethylene glycol; when the molecular weight is in the range of 5000, the dispersion and slump retentibity increase with the increment of the average molecular weight of polymers.

  13. Molecular dynamics simulations on the relationship between the elastic parameters and the molecular structures of nano-hybrid POSS materials

    Institute of Scientific and Technical Information of China (English)

    ZENG Fan-lin; SUN Yi; HU Li-jiang

    2006-01-01

    To research the relationship between the elastic parameters and the molecular structures of nano hybrid polyhedral oligomeric silsesquioxanes (POSS) materials, the mechanical properties at different temperatures for three POSS polymers with different molecular architectures, polymerlized norbornene POSS homopolymer (PNPOSS, pedant architecture), γ - (2, 3 glycidoxy) propyl diaminoethane POSS polymer (GPDP, catena architecture) and trimethoxysilylcyclopentyl POSS polymer (TSCP, cage -cage network architecture) were obtained by molecular dynamics simulations based on the Compass force-field. Results indicate that the molecular architectures of the POSS polymers have great influence on the reinforced effects. The effect of the cage-cage network architecture is best, while that of the catena architecture takes second place and the pedant architecture has the least influence comparatively. The reinforced effects of the POSS monomers were examined. The influences of the temperatures on these effects were analyzed also. It may provide some basis for the reasonable applications of the excellent mechanical properties of the organic-inorganic nano-hybrid materials. It may also provide references for exploitation and design of the POSS materials.

  14. Molecular flexibility and structural instabilities in crystalline L-methionine

    NARCIS (Netherlands)

    Fischer, Jennifer; Lima, Jose A.; Freire, Paulo T. C.; Melo, Francisco E. A.; Havenith, Remco W. A.; Mendes Filho, Josue; Broer, Ria; Eckert, Juergen; Bordallo, Heloisa N.

    2013-01-01

    We have investigated the dynamics in polycrystalline samples of L-methionine related to the structural transition at about 307 K by incoherent inelastic and quasielastic neutron scattering, X-ray powder diffraction as well as ab-initio calculations. L-Methionine is a sulfur amino acid which can be c

  15. Structure and properties of sodium aluminosilicate glasses from molecular dynamics simulations

    DEFF Research Database (Denmark)

    Xiang, Ye; Du, Jincheng; Smedskjær, Morten Mattrup;

    2013-01-01

    the recent Corning® Gorilla® Glass. In this paper, the structures of sodium aluminosilicate glasses with a wide range of Al/Na ratios (from 1.5 to 0.6) have been studied using classical molecular dynamics simulations in a system containing around 3000 atoms, with the aim to understand the structural role...

  16. Molecular conformation and liquid structure of 2-propanol through neutron diffraction

    Indian Academy of Sciences (India)

    A Sahoo; S Sarkar; P S R Krishna; R N Joarder

    2010-05-01

    The neutron diffraction data analysis of deuterated liquid 2-propanol at room temperature to define its molecular conformation is presented. 2-Propanol being a large molecule with twelve atomic sites, the conformation analysis is tricky and an improved method of data analysis is given. The intermolecular structural correlations, i.e., hydrogen-bonded liquid structure, can be modelled accurately to extract the nature of the average hydrogen-bonded molecular association in liquid state at room temperature. Like other alcohols these are mostly hexamer ring chain (HRC) clusters. The cluster analysis of recent X-ray data available in the literature also support the same liquid structure.

  17. A holistic molecular docking approach for predicting protein-protein complex structure

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure selection.This article explains the detailed steps and applications for CAPRI Target 39.The CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

  18. NATO Advanced Study Institute on Electronic Structure of Polymers and Molecular Crystals

    CERN Document Server

    Ladik, János

    1975-01-01

    The NATO Advanced Study Institute on "Electronic Structure of Polymers and Molecular Crystals" was held at the Facultes Universi­ taires de Namur (F.U.N.) from September 1st till September 14th, 1974. We wish to express our appreciation to the NATO Scientific Affairs Division whose generous support made this Institute possible and to the Facultes Universitaires de Namur and the Societe Chimique de Belgique which provided fellowships and travel grants to a number of students. This volume contains the main lectures about the basic principles of the field and about different recent developments of the theory of the electronic structure of polymers and molecular crystals. The school started with the presentation of the basic SCF-LCAO theory of the electronic structure of periodic polymers and molecular crystals (contributions by Ladik, Andre & Delhalle) showing how a combination of quantum chemical and solid state physical methods can provide band structures for these systems. The numerical aspects of these ...

  19. Revealing structural and dynamical properties of high density lipoproteins through molecular simulations

    DEFF Research Database (Denmark)

    Koivuniemi, A.; Vattulainen, I.

    2012-01-01

    The structure and function of high density lipoprotein (HDL) particles have intrigued the scientific community for decades because of their crucial preventive role in coronary heart disease. However, it has been a taunting task to reveal the precise molecular structure and dynamics of HDL. Further......, because of the complex composition of HDL, understanding the impact of its structure and dynamics on the function of HDL in reverse cholesterol transport has also been a major issue. Recent progress in molecular simulation methodology and computing power has made a difference, as it has enabled...... essentially atomistic considerations of HDL particles over microsecond time scales, thereby proving substantial added value to experimental research. In this article, we discuss recent highlights concerning the structure and dynamics of HDL particles as revealed by atomistic and coarse-grained molecular...

  20. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    Energy Technology Data Exchange (ETDEWEB)

    Eisenberg, David S.

    2008-07-15

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  1. Molecular and supra-molecular structure of waxy starches developed from cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Rolland-Sabaté, Agnès; Sanchez, Teresa; Buléon, Alain; Colonna, Paul; Ceballos, Hernan; Zhao, Shan-Shan; Zhang, Peng; Dufour, Dominique

    2013-02-15

    The aim of this work was to characterize the amylopectin of low amylose content cassava starches obtained from transgenesis comparatively with a natural waxy cassava starch (WXN) discovered recently in CIAT (International Center for Tropical Agriculture). Macromolecular features, starch granule morphology, crystallinity and thermal properties of these starches were determined. M¯(w) of amylopectin from the transgenic varieties are lower than WXN. Branched and debranched chain distributions analyses revealed slight differences in the branching degree and structure of these amylopectins, principally on DP 6-9 and DP>37. For the first time, a deep structural characterization of a series of transgenic lines of waxy cassava was carried out and the link between structural features and the mutated gene expression approached. The transgenesis allows to silenced partially or totally the GBSSI, without changing deeply the starch granule ultrastructure and allows to produce clones with similar amylopectin as parental cassava clone.

  2. Molecular Structure of Humin and Melanoidin via Solid State NMR

    OpenAIRE

    Herzfeld, Judith; Rand, Danielle; Matsuki, Yoh; Daviso, Eugenio; Mak-Jurkauskas, Melody; Mamajanov, Irena

    2011-01-01

    Sugar-derived humins and melanoidins figure significantly in food chemistry, agricultural chemistry, biochemistry and prebiotic chemistry. Despite wide interest and significant experimental attention, the amorphous and insoluble nature of the polymers has made them resistant to conventional structural characterization. Here we make use of solid-state NMR methods, including selective 13C substitution, 1H-dephasing, and double quantum filtration. The spectra, and their interpretation, are simpl...

  3. Do Giant Molecular Clouds Care About the Galactic Structure?

    CERN Document Server

    Fujimoto, Yusuke; Wakayama, Mariko; Habe, Asao

    2014-01-01

    We investigate the impact of galactic environment on the properties of simulated giant molecular clouds formed in a M83-type barred spiral galaxy. Our simulation uses a rotating stellar potential to create the grand design features and resolves down to 1.5 pc. From the comparison of clouds found in the bar, spiral and disc regions, we find that the typical GMC is environment independent, with a mass of 5e+5 Msun and radius 11 pc. However, the fraction of clouds in the property distribution tails varies between regions, with larger, more massive clouds with a higher velocity dispersion being found in greatest proportions in the bar, spiral and then disc. The bar clouds also show a bimodality that is not reflected in the spiral and disc clouds except in the surface density, where all three regions show two distinct peaks. We identify these features as being due to the relative proportion of three cloud types, classified via the mass-radius scaling relation, which we label A, B and C. Type A clouds have the typi...

  4. Molecular modeling of the ion channel-like nanotube structure of amyloid β-peptide

    Institute of Scientific and Technical Information of China (English)

    JIAO Yong; YANG Pin

    2007-01-01

    The ion channel-like nanotube structure of the oligomers of amyloid β-peptide (Aβ) was first investigated by molecular modeling. The results reveal that the hydrogen bond net is one of the key factors to stabilize the structure. The hydrophobicity distribution mode of the side chains is in favor of the structure inserting into the bilayers and forming a hydrophilic pore. The lumen space is under the control of the negative potential, weaker but spreading continuously, to which the cation selectivity attributes; meanwhile, the alternate distribution of the stronger positive and negative potentials makes the electrostatic distribution of the structure framework balance, which is also one of the key factors stabilizing the structure. The results lay the theoretical foundation for illuminating the structure stability and the ion permeability, and give a clue to elucidating the molecular mechanism of Alzheimer's disease (AD) and designing novel drugs to prevent or reverse AD at the root.

  5. Advances in Rosetta structure prediction for difficult molecular-replacement problems

    Energy Technology Data Exchange (ETDEWEB)

    DiMaio, Frank, E-mail: dimaio@u.washington.edu [University of Washington, UW Box 357350, Seattle, WA 98195 (United States)

    2013-11-01

    Modeling advances using Rosetta structure prediction to aid in solving difficult molecular-replacement problems are discussed. Recent work has shown the effectiveness of structure-prediction methods in solving difficult molecular-replacement problems. The Rosetta protein structure modeling suite can aid in the solution of difficult molecular-replacement problems using templates from 15 to 25% sequence identity; Rosetta refinement guided by noisy density has consistently led to solved structures where other methods fail. In this paper, an overview of the use of Rosetta for these difficult molecular-replacement problems is provided and new modeling developments that further improve model quality are described. Several variations to the method are introduced that significantly reduce the time needed to generate a model and the sampling required to improve the starting template. The improvements are benchmarked on a set of nine difficult cases and it is shown that this improved method obtains consistently better models in less running time. Finally, strategies for best using Rosetta to solve difficult molecular-replacement problems are presented and future directions for the role of structure-prediction methods in crystallography are discussed.

  6. FlaME: Flash Molecular Editor - a 2D structure input tool for the web

    Directory of Open Access Journals (Sweden)

    Dallakian Pavel

    2011-02-01

    Full Text Available Abstract Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME. In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol( and setMol(. In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application and the HTML elements on a web page, using JavaScript functions.

  7. Evolving Molecular Cloud Structure and the Column Density Probability Distribution Function

    CERN Document Server

    Ward, Rachel L; Sills, Alison

    2014-01-01

    The structure of molecular clouds can be characterized with the probability distribution function (PDF) of the mass surface density. In particular, the properties of the distribution can reveal the nature of the turbulence and star formation present inside the molecular cloud. In this paper, we explore how these structural characteristics evolve with time and also how they relate to various cloud properties as measured from a sample of synthetic column density maps of molecular clouds. We find that, as a cloud evolves, the peak of its column density PDF will shift to surface densities below the observational threshold for detection, resulting in an underlying lognormal distribution which has been effectively lost at late times. Our results explain why certain observations of actively star-forming, dynamically older clouds, such as the Orion molecular cloud, do not appear to have any evidence of a lognormal distribution in their column density PDFs. We also study the evolution of the slope and deviation point ...

  8. A circumstellar molecular gas structure associated with the massive young star Cepheus A-HW 2

    Science.gov (United States)

    Torrelles, Jose M.; Rodriguez, Luis F.; Canto, Jorge; Ho, Paul T. P.

    1993-01-01

    We report the detection via VLA-D observations of ammonia of a circumstellar high-density molecular gas structure toward the massive young star related to the object Cepheus A-HW 2, a firm candidate for the powering source of the high-velocity molecular outflow in the region. We suggest that the circumstellar molecular gas structure could be related to the circumstellar disk previously suggested from infrared, H2O, and OH maser observations. We consider as a plausible scenario that the double radio continuum source of HW 2 could represent the ionized inner part of the circumstellar disk, in the same way as proposed to explain the double radio source in L1551. The observed motions in the circumstellar molecular gas can be produced by bound motions (e.g., infall or rotation) around a central mass of about 10-20 solar masses (B0.5 V star or earlier).

  9. A Quantitative Structure Property Relationship for Prediction of Flash Point of Alkanes Using Molecular Connectivity Indices

    Institute of Scientific and Technical Information of China (English)

    Morteza Atabati; Reza Emamalizadeh

    2013-01-01

    Many structure-property/activity studies use graph theoretical indices,which are based on the topological properties of a molecule viewed as a graph.Since topological indices can be derived directly from the molecular structure without any experimental effort,they provide a simple and straightforward method for property prediction.In this work the flash point of alkanes was modeled by a set of molecular connectivity indices (x),modified molecular connectivity indices (mx(1)h) and valance molecular connectivity indices (mxv),with mxv calculated using the hydrogen perturbation.A stepwise Multiple Linear Regression (MLR) method was used to select the best indices.The predicted flash points are in good agreement with the experimental data,with the average absolute deviation 4.3 K.

  10. Structure of beryllium isotopes in fermionic molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Torabi, Bahram Ramin

    2009-02-16

    Modern theoretical nuclear physics faces two major challenges. The first is finding a suitable interaction, which describes the forces between nucleons. The second challenge is the solution of the nuclear many-body problem for a given nucleus while applying a realistic potential. The potential used in the framework of this thesis is based on the Argonne AV18 potential. It was transformed by means of the Unitary Correlation Operator Method (UCOM) to optimize convergence. The usual phenomenological corrections were applied to improve the potential for the Hilbert space used in Fermionic Molecular Dynamics (FMD). FMD is an approach to solve the nuclear many-body problem. It uses a single-particle basis which is a superposition of Gaussian distributions in phase-space. The most simple many-body state is the antisymmetric product of the singleparticle states: a Slater determinant, the so called intrinsic state. This intrinsic state is projected on parity, total angular momentum and a center of mass momentum zero. The Hilbert space is spanned by several of these projected states. The states are obtained by minimizing their energy while demanding certain constraints. The expectation values of Slater determinants, parity projected and additionally total angular momentum projected Slater determinants are used. The states that are relevant in the low energy regime are obtained by diagonalization. The lowest moments of the mass-, proton- or neutron-distribution and the excitation in proton- and neutron-shells of a harmonic oscillator are some of the used constraints. The low energy regime of the Beryllium isotopes with masses 7 to 14 is calculated by using these states. Energies, radii, electromagnetic transitions, magnetic moments and point density distributions of the low lying states are calculated and are presented in this thesis. (orig.)

  11. Gas-phase doubly charged complexes of cyclic peptides with copper in +1, +2 and +3 formal oxidation states: formation, structures and electron capture dissociation.

    Science.gov (United States)

    Afonso, Carlos; Tabet, Jean-Claude; Giorgi, Gianluca; Tureček, František

    2012-02-01

    Copper complexes with a cyclic D-His-β-Ala-L-His-L-Lys and all-L-His-β-Ala-His-Lys peptides were generated by electrospray which were doubly charged ions that had different formal oxidation states of Cu(I), Cu(II) and Cu(III) and different protonation states of the peptide ligands. Electron capture dissociation showed no substantial differences between the D-His and L-His complexes. All complexes underwent peptide cross-ring cleavages upon electron capture. The modes of ring cleavage depended on the formal oxidation state of the Cu ion and peptide protonation. Density functional theory (DFT) calculations, using the B3LYP with an effective core potential at Cu and M06-2X functionals, identified several precursor ion structures in which the Cu ion was threecoordinated to pentacoordinated by the His and Lys side-chain groups and the peptide amide or enolimine groups. The electronic structure of the formally Cu(III) complexes pointed to an effective Cu(I) oxidation state with the other charge residing in the peptide ligand. The relative energies of isomeric complexes of the [Cu(c-HAHK + H)](2+) and [Cu(c-HAHK - H)](2+) type with closed electronic shells followed similar orders when treated by the B3LYP and M06-2X functionals. Large differences between relative energies calculated by these methods were obtained for open-shell complexes of the [Cu(c-HAHK)](2+) type. Charge reduction resulted in lowering the coordination numbers for some Cu complexes that depended on the singlet or triplet spin state being formed. For [Cu(c-HAHK - H)](2+) complexes, solution H/D exchange involved only the N-H protons, resulting in the exchange of up to seven protons, as established by ultra-high mass resolution measurements. Contrasting the experiments, DFT calculations found the lowest energy structures for the gas-phase ions that were deprotonated at the peptide C(α) positions.

  12. Extensional orogenic collapse captured by strike-slip tectonics: Constraints from structural geology and Usbnd Pb geochronology of the Pinhel shear zone (Variscan orogen, Iberian Massif)

    Science.gov (United States)

    Fernández, Rubén Díez; Pereira, Manuel Francisco

    2016-11-01

    The late Paleozoic collision between Gondwana and Laurussia resulted in the polyphase deformation and magmatism that characterizes the Iberian Massif of the Variscan orogen. In the Central Iberian Zone, initial continental thickening (D1; folding and thrusting) was followed by extensional orogenic collapse (D2) responsible for the exhumation of high-grade rocks coeval to the emplacement of granitoids. This study presents a tectonometamorphic analysis of the Trancoso-Pinhel region (Central Iberian Zone) to explain the processes in place during the transition from an extension-dominated state (D2) to a compression-dominated one (D3). We reveal the existence of low-dipping D2 extensional structures later affected by several pulses of subhorizontal shortening, each of them typified by upright folds and strike-slip shearing (D3, D4 and D5, as identified by superimposition of structures). The D2 Pinhel extensional shear zone separates a low-grade domain from an underlying high-grade domain, and it contributed to the thermal reequilibration of the orogen by facilitating heat advection from lower parts of the crust, crustal thinning, decompression melting, and magma intrusion. Progressive lessening of the gravitational disequilibrium carried out by this D2 shear zone led to a switch from subhorizontal extension to compression and the eventual cessation and capture of the Pinhel shear zone by strike-slip tectonics during renewed crustal shortening. High-grade domains of the Pinhel shear zone were folded together with low-grade domains to define the current upright folded structure of the Trancoso-Pinhel region, the D3 Tamames-Marofa-Sátão synform. New dating of syn-orogenic granitoids (SHRIMP Usbnd Pb zircon dating) intruding the Pinhel shear zone, together with the already published ages of early extensional fabrics constrain the functioning of this shear zone to ca. 331-311 Ma, with maximum tectonomagmatic activity at ca. 321-317 Ma. The capture and apparent cessation

  13. Molecular structure and biological function of proliferating cell nuclear antigen

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Proliferating cell nuclear antigen (PCNA) is the core component of replication complex in eukaryote.As a processive factor of DNA polymerase delta, PCNA coordinates the replication process by interacting with various replication proteins. PCNA appears to play an essential role in many cell events, such as DNA damage repair, cell cycle regulation, and apoptosis, through the coordination or organization of different partners. PCNA is an essential factor in cell proliferation, and has clinical significance in tumor research. In this article we review the functional structure of PCNA, which acts as a function switch in different cell events.

  14. Crystal and molecular structure of N-(-nitrobenzylidene)-3-chloro-4-fluoroaniline

    Indian Academy of Sciences (India)

    K V Arjuna Gowda; M K Kokila; Puttaraja; M V Kulkarni; N C Shivaprakash

    2000-09-01

    The crystal structure of N-(-nitrobenzylidene)-3-chloro-4-fluoroaniline (II) has been determined by X-ray structure analysis. This belongs to a class of benzylidene anilines. The structure was solved by direct method. The molecular packing of the non-planar molecules are held by Van der Waals and F$\\cdots\\cdot$H7, O$\\cdots\\cdot$Cl, F$\\cdots\\cdot$F and N$\\cdots\\cdot$H interactions.

  15. Effect of structural parameters on the electron capture dissociation and collision-induced dissociation pathways of copper(II)-peptide complexes.

    Science.gov (United States)

    Chen, Xiangfeng; Wang, Ze; Li, Wan; Wong, Y L Elaine; Chan, T-W Dominic

    2015-01-01

    The gas-phase dissociation pathways of proteins/peptides are usually affected by the nature of the charge carrier and the sequence of amino acid residues. The effects of peptide structural parameters, including peptide composition, chain length and amide hydrogen, on the gas-phase dissociation of Cu(II)-model peptide complexes were explored in this study. Polyglycine peptides with flexible frames were used as probes to reduce the complexity of the system and illustrate the mechanism. Results revealed that the types of fragment ions generated in the electron capture dissociation (ECD) of Cu(II)-adducted peptides changed according to the basic amino acid residue composition. Charged or neutral tryptophan side-chain losses were observed in the collision-induced dissociation (CID) of Cu(II)-peptide complexes. Internal electron transfer between tryptophan and metal ion within the complex occurred during the CID reaction, leaving the charge-reduced Cu(+) as a closed d-shell stable electron configuration. The choice of the reaction channel was then determined by the gas-phase basicity of the peptide. Amide hydrogen was critical in the formation of metalated b-/y-ions in the ECD process as determined through mutation of the backbone amide group. Increasing the chain length suppressed the ECD of Cu-metalated peptide species. Our results indicate that the structural parameters of peptides play important roles in the gas-phase dissociation processes of Cu-peptide complexes.

  16. A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders

    Science.gov (United States)

    Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

    2016-10-01

    In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

  17. Molecular Clouds in the North American and Pelican Nebulae: Structures

    CERN Document Server

    Zhang, Shaobo; Yang, Ji

    2013-01-01

    We present observations of 4.25 square degree area toward the North American and Pelican Nebulae in the $J = 1-0$ transitions of $^{12}$CO, $^{13}$CO, and C$^{18}$O. Three molecules show different emission area with their own distinct structures. These different density tracers reveal several dense clouds with surface density over 500 $M_\\odot$ pc$^{-2}$ and a mean H$_2$ column density of 5.8, 3.4, and 11.9$\\times10^{21}$ cm$^{-2}$ for $^{12}$CO, $^{13}$CO, and C$^{18}$O, respectively. We obtain a total mass of $5.4\\times10^4 M_\\odot$ ($^{12}$CO), $2.0\\times10^4 M_\\odot$ ($^{13}$CO), and $6.1\\times10^3 M_\\odot$ (C$^{18}$O) in the complex. The distribution of excitation temperature shows two phase of gas: cold gas ($\\sim$10 K) spreads across the whole cloud; warm gas ($>$20 K) outlines the edge of cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud including t...

  18. Molecular Determinants of Staphylococcal Biofilm Dispersal and Structuring

    Directory of Open Access Journals (Sweden)

    Katherine Y Le

    2014-11-01

    Full Text Available Staphylococci are frequently implicated in human infections, and continue to pose a therapeutic dilemma due to their ability to form deeply seated microbial communities, known as biofilms, on the surfaces of implanted medical devices and host tissues. Biofilm development has been proposed to occur in three stages: 1 attachment, 2 proliferation/structuring, and 3 detachment/dispersal. Although research within the last several decades has implicated multiple molecules in the roles as effectors of staphylococcal biofilm proliferation/structuring and detachment/dispersal, to date, only phenol soluble modulins (PSMs have been consistently demonstrated to serve in this role under both in-vitro and in-vivo settings. PSMs are regulated directly through a density-dependent manner by the accessory gene regulator (Agr system. They disrupt the non-covalent forces holding the biofilm extracellular matrix together, which is necessary for the formation of channels, a process essential for the delivery of nutrients to deeper biofilm layers, and for dispersal/dissemination of clusters of biofilm to distal organs in acute infection. Given their relevance in both acute and chronic biofilm-associated infections, the Agr system and the psm genes hold promise as potential therapeutic targets.

  19. Allyl strontium compounds: synthesis, molecular structure and properties.

    Science.gov (United States)

    Jochmann, Phillip; Davin, Julien P; Maslek, Stefanie; Spaniol, Thomas P; Sarazin, Yann; Carpentier, Jean-Francois; Okuda, Jun

    2012-08-14

    The synthesis and attempted isolation of neutral bis(allyl)strontium [Sr(C(3)H(5))(2)] (1) resulted in the isolation of potassium tris(allyl)strontiate K[Sr(C(3)H(5))(3)] (2). In situ generated 1 shows a pronounced Brønsted basicity, inducing polymerisation of THF. Ate complex 2 crystallises as [K(THF)(2){Sr(C(3)H(5))(3)}(THF)](∞) (2·(THF)(3)). The salt-like solid state structure of 2·(THF)(3) comprises a two-dimensional network of (μ(2)-η(3):η(3)-C(3)H(5))(-) bridged potassium and strontium centres. Synthesis of allyl complexes 1 and 2 utilised SrI(2), [Sr(TMDS)(2)] (3) (TMDS = tetramethyldisilazanide), and [Sr(HMDS)(2)] (HMDS = hexamethyldisilazanide) as strontium precursors. The solid state structure of previously reported [Sr(TMDS)(2)] (3) was established by X-ray single crystal analysis as a dissymmetric dimer of [Sr(2)(TMDS)(4)(THF)(3)] (3·(THF)(3)) with multiple Si-HSr agostic interactions. The presence of ether ligands (THF, 18-crown-6) influenced the Si-HSr resonances in the NMR spectra of the amido complex 3.

  20. Structured attachment of bacterial molecular motors for defined microflow induction

    Directory of Open Access Journals (Sweden)

    Woerdemann Mike

    2014-01-01

    Full Text Available Bacterial rotational motor complexes that propel flagellated bacteria possess unique properties like their size of a few nanometres and the ability of selfreproduction that have led to various exciting applications including biohybrid nano-machines. One mandatory prerequisite to utilize bacterial nano motors in fluid applications is the ability to transfer force and torque to the fluid, which usually can be achieved by attachment of the bacterial cell to adequate surfaces. Additionally, for optimal transfer of force or torque, precise control of the position down to the single cell level is of utmost importance. Based on a PIV (particle image velocimetry evaluation of the induced flow of single bacteria,we propose and demonstrate attachment of arbitrary patterns of motile bacterial cells in a fast light-based two-step process for the first time to our knowledge. First, these cells are pre-structured by holographic optical tweezers and then attached to a homogeneous, polystyrene-coated surface. In contrast to the few approaches that have been implemented up to now and which rely on pre-structured surfaces, our scheme allows for precise control on a single bacterium level, is versatile, interactive and has low requirements with respect to the surface preparation.

  1. Structural studies of molecular and metallic overlayers using angle- resolved photoemission extended fine structure

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Z.

    1992-10-01

    Angle-resolved photoemission extended fine structure (ARPEFS) was used to study molecular and metallic overlayers on metal surfaces through analysis of p2mg(2[times]1)CO/Ni(110) and the p(2[times]2)K/Ni(111) adsorption. For the dense p2mg(2[times]1)CO/Ni(110) surface layer, photoemission intensities from C 1s level were measured in three directions at photoelectron kinetic energies 60-400 eV. Using multiple-scattering spherical-wave (MSSW) modeling, it was found that CO molecules are adsorbed on short-bridge sites, with adjacent CO along the [110] direction displaced alternatively in opposite directions towards the [001] azimuths to form a zigzag chain geometry. The tilt angle is 16[plus minus]2[degree] from the surface normal for the direction linking the C atom and the center of the Ni bridge. The carbon C-Ni interatomic distance was determined to be 1.94[plus minus]0.02[Angstrom]. The first- to second-layer spacing of Ni is 1.27[plus minus]0.04[Angstrom], up from 1.10[Angstrom] for the clean Ni(110) surface, but close to the 1.25[Angstrom] Ni interlayer spacing in the bulk. The C-O bond length and tilt angle were varied within small ranges (1.10--1.20[Angstrom] and 15--23[degrees]) in our MSSW simulations. Best agreement between experiment and simulations was achieved at 1.16[Angstrom] and 19[degrees]. This yields an O-O distance of 2.95[Angstrom] for the two nearest CO molecules, (van der Waals' radius [approximately] 1.5 [Angstrom] for oxygen). Two different partial-wave phase-shifts were used in MSSW, and structural results from both are in very good agreement. For the p(2[times]2)K/Ni(111) overlayer, ARPEFS [chi](k) curves from K 1s level measured along [111] and [771] at 130K showed that the K atoms are preferentially adsorbed on the atop sites, in agreement with a LEED study of the same system.

  2. Structural studies of molecular and metallic overlayers using angle- resolved photoemission extended fine structure

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Z.

    1992-10-01

    Angle-resolved photoemission extended fine structure (ARPEFS) was used to study molecular and metallic overlayers on metal surfaces through analysis of p2mg(2{times}1)CO/Ni(110) and the p(2{times}2)K/Ni(111) adsorption. For the dense p2mg(2{times}1)CO/Ni(110) surface layer, photoemission intensities from C 1s level were measured in three directions at photoelectron kinetic energies 60-400 eV. Using multiple-scattering spherical-wave (MSSW) modeling, it was found that CO molecules are adsorbed on short-bridge sites, with adjacent CO along the [110] direction displaced alternatively in opposite directions towards the [001] azimuths to form a zigzag chain geometry. The tilt angle is 16{plus_minus}2{degree} from the surface normal for the direction linking the C atom and the center of the Ni bridge. The carbon C-Ni interatomic distance was determined to be 1.94{plus_minus}0.02{Angstrom}. The first- to second-layer spacing of Ni is 1.27{plus_minus}0.04{Angstrom}, up from 1.10{Angstrom} for the clean Ni(110) surface, but close to the 1.25{Angstrom} Ni interlayer spacing in the bulk. The C-O bond length and tilt angle were varied within small ranges (1.10--1.20{Angstrom} and 15--23{degrees}) in our MSSW simulations. Best agreement between experiment and simulations was achieved at 1.16{Angstrom} and 19{degrees}. This yields an O-O distance of 2.95{Angstrom} for the two nearest CO molecules, (van der Waals` radius {approximately} 1.5 {Angstrom} for oxygen). Two different partial-wave phase-shifts were used in MSSW, and structural results from both are in very good agreement. For the p(2{times}2)K/Ni(111) overlayer, ARPEFS {chi}(k) curves from K 1s level measured along [111] and [771] at 130K showed that the K atoms are preferentially adsorbed on the atop sites, in agreement with a LEED study of the same system.

  3. Thermodynamic Stability of Structure H Hydrates Based on the Molecular Properties of Large Guest Molecules

    Directory of Open Access Journals (Sweden)

    Ryo Ohmura

    2012-02-01

    Full Text Available This paper report analyses of thermodynamic stability of structure-H clathrate hydrates formed with methane and large guest molecules in terms of their gas phase molecular sizes and molar masses for the selection of a large guest molecule providing better hydrate stability. We investigated the correlation among the gas phase molecular sizes, the molar masses of large molecule guest substances, and the equilibrium pressures. The results suggest that there exists a molecular-size value for the best stability. Also, at a given molecule size, better stability may be available when the large molecule guest substance has a larger molar mass.

  4. EFFECTS OF MATRIX MOLECULAR WEIGHT ON STRUCTURE AND REINFORCEMENT OF HIGH DENSITY POLYETHYLENE/MICA COMPOSITES

    Institute of Scientific and Technical Information of China (English)

    Li Chen; Yu-fang Xiang; Ke Wang; Qin Zhang; Rong-ni Du; Qiang Fu

    2011-01-01

    Three types of high-density polyethylene (HDPE) with different molecular weights (high, medium and Iow) were adopted to evaluate the influence of matrix molecular weight on the structure-property relation of injection-molded HDPE/mica composites through a combination of SEM, 2d-WAXS, DSC, DMA and tensile testing. Various structural factors including orientation, filler dispersion, interfacial interaction between HDPE and mica, etc., which can impact the macroscopic mechanics, were compared in detail among the three HDPE/mica composites. The transcrystallization of HDPE on the mica surface was observed and it exhibited strong matrix molecular weight dependence. Obvious transcrystalline structure was found in the composite with Iow molecular weight HDPE, whereas it was hard to be detected in the composites with increased HDPE molecular weight. The best reinforcement effect in the composite with low molecular weight HDPE can be understood as mainly due to substantially improved interracial adhesion between matrix and mica filler, which arises from the transerystallization mechanism.

  5. Prevalence and molecular characterizations of Toxoplasma gondii and Babesia microti from small mammals captured in Gyeonggi and Gangwon Provinces, Republic of Korea.

    Science.gov (United States)

    Hong, Sung-Hee; Lee, Sang-Eun; Jeong, Young-Il; Kim, Heung-Chul; Chong, Sung-Tae; Klein, Terry A; Song, Jin-Won; Gu, Se Hun; Cho, Shin-Hyeong; Lee, Won-Ja

    2014-10-15

    A survey was conducted to determine the distribution and prevalence of Toxoplasma gondii and Babesia microti infections in small mammals captured in Gyeonggi and Gangwon Provinces, Republic of Korea (ROK). The serological prevalence of T. gondii (ELISA) and B. microti (IFAT) was 2.3% (15/667) and 2.1% (14/667), respectively. DNA extracts from small mammal heart tissues were screened by PCR for T. gondii and B. microti targeting regions of the GRA5 gene and the 18S rRNA and β-tubulin genes, respectively. Only 0.17% (1/578) of Apodemus agrarius was positive of T. gondii by PCR, while 0.52% (3/578) was positive of B. microti. All other small mammal species [Micromys minutus (16), Mus musculus (3), Myodes regulus (22), Microtus fortis (6), and Crocidura lasiura (42)] were negative for both T. gondii and B. microti. Based on sequence polymorphism and phylogenetic analysis, T. gondii closely aligned with Type I, a highly virulent strain, while B. microti positive samples closely aligned with US-type B. microti and others observed in the ROK, Russia, and Japan. These results indicate that A. agrarius is a reservoir for both T. gondii and B. microti in the ROK.

  6. Coalescence of silver unidimensional structures by molecular dynamics simulation; Coalescencia de estructuras unidimensionales de plata por simulacion dinamica molecular

    Energy Technology Data Exchange (ETDEWEB)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G. [ININ, 52750 La Marquesa, Estado de Mexico (Mexico); Arenas, J. [IFUNAM, 04510 Mexico D.F. (Mexico)

    2007-07-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  7. Molecular tools for investigating ANME community structure and function

    Energy Technology Data Exchange (ETDEWEB)

    Hallam, Steven J.; Page, Antoine P.; Constan, Lea; Song, Young C.; Norbeck, Angela D.; Brewer, Heather M.; Pasa-Tolic, Ljiljana

    2011-05-20

    Methane production and consumption in anaerobic marine sediments 1 is catalyzed by a series of reversible tetramethanopterin (H4MPT)-linked C1 transfer reactions. Although many of these reactions are conserved between one-carbon compound utilizing microorganisms, two remain diagnostic for archaeal methane metabolism. These include reactions catalyzed by N5-methyltetrahydromethanopterin: coenzyme M methyltransferase and methyl coenzyme M reductase. The latter enzyme is central to C-H bond formation and cleavage underlying methanogenic and reverse methanogenic phenotypes. Here we describe a set of novel tools for the detection and functional analysis of H4MPT-linked C1 transfer reactions mediated by uncultivated anaerobic methane oxidizing archaea (ANME). These tools include polymerase chain reaction primers targeting ANME methyl coenzyme M reductase subunit A subgroups and protein extraction methods from marine sediments compatible with high-resolution mass spectrometry for profiling population structure and functional dynamics. [910, 1,043

  8. Molecular Structure and Reactivity in the Pyrolysis of Aldehydes

    Science.gov (United States)

    Sias, Eric; Cole, Sarah; Sowards, John; Warner, Brian; Wright, Emily; McCunn, Laura R.

    2016-06-01

    The effect of alkyl chain structure on pyrolysis mechanisms has been investigated in a series of aldehydes. Isovaleraldehyde, CH_3CH(CH_3)CH_2CHO, and pivaldehyde, (CH_3)_3CCHO, were subject to thermal decomposition in a resistively heated SiC tubular reactor at 800-1200 °C. Matrix-isolation FTIR spectroscopy was used to identify pyrolysis products. Carbon monoxide and isobutene were major products from each of the aldehydes, which is consistent with what is known from previous studies of unbranched alkyl-chain aldehydes. Other products observed include vinyl alcohol, propene, acetylene, and ethylene, revealing complexities to be considered in the pyrolysis of large, branched-chain aldehydes.

  9. Searching molecular structure databases with tandem mass spectra using CSI:FingerID

    Science.gov (United States)

    Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian

    2015-01-01

    Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. We present a method for searching molecular structure databases using tandem MS data of small molecules. Our method computes a fragmentation tree that best explains the fragmentation spectrum of an unknown molecule. We use the fragmentation tree to predict the molecular structure fingerprint of the unknown compound using machine learning. This fingerprint is then used to search a molecular structure database such as PubChem. Our method is shown to improve on the competing methods for computational metabolite identification by a considerable margin. PMID:26392543

  10. Theoretical study on molecular packing and electronic structure of bi-1,3,4-oxadiazole derivatives

    KAUST Repository

    Wang, Haitao

    2014-01-01

    The molecular aggregation structure of 5,5′-bis(naphthalen-2-yl)-2,2′-bi(1,3,4-oxadiazole) (BOXD-NP) was studied by computing the intermolecular interaction potential energy surface (PES) at density functional theory level based on a dimer model. All B3LYP, CAM-B3LYP and M062x functionals can yield a reliable isolated molecular geometry. The conformation of BOXD-NP obtained with all methods is perfectly planar, indicating good conjugation ability between oxadiazole and naphthalene rings. The vibrational frequencies of BOXD-NP were also calculated using the B3LYP/6-311+G∗∗ method, which showed great consistency with the experimental observations and makes the assignments of the IR spectra more solid. It was revealed that the lowest excited state of BOXD-NP should be assigned as a highly allowed π-π∗ state by TD-DFT calculation. Considering the non-covalent interactions in molecular aggregates, the M062x functional was applied in the construction of the PES. Besides the packing structure found in the crystals, PES also predicted several stable structures, indicating that PES has great ability in guiding molecular self-assembly. Symmetry Adapted Perturbation Theory (SAPT) analysis on these energy-minimum molecular stacking structures revealed that London dispersion forces are the strongest attractive component in the binding. This journal is

  11. Hierarchical QSAR technology based on the Simplex representation of molecular structure

    Science.gov (United States)

    Kuz'min, V. E.; Artemenko, A. G.; Muratov, E. N.

    2008-06-01

    This article is about the hierarchical quantitative structure-activity relationship technology (HiT QSAR) based on the Simplex representation of molecular structure (SiRMS) and its application for different QSAR/QSP(property)R tasks. The essence of this technology is a sequential solution (with the use of the information obtained on the previous steps) to the QSAR problem by the series of enhanced models of molecular structure description [from one dimensional (1D) to four dimensional (4D)]. It is a system of permanently improved solutions. In the SiRMS approach, every molecule is represented as a system of different simplexes (tetratomic fragments with fixed composition, structure, chirality and symmetry). The level of simplex descriptors detailing increases consecutively from the 1D to 4D representation of the molecular structure. The advantages of the approach reported here are the absence of "molecular alignment" problems, consideration of different physical-chemical properties of atoms (e.g. charge, lipophilicity, etc.), the high adequacy and good interpretability of obtained models and clear ways for molecular design. The efficiency of the HiT QSAR approach is demonstrated by comparing it with the most popular modern QSAR approaches on two representative examination sets. The examples of successful application of the HiT QSAR for various QSAR/QSPR investigations on the different levels (1D-4D) of the molecular structure description are also highlighted. The reliability of developed QSAR models as predictive virtual screening tools and their ability to serve as the base of directed drug design was validated by subsequent synthetic and biological experiments, among others. The HiT QSAR is realized as a complex of computer programs known as HiT QSAR software that also includes a powerful statistical block and a number of useful utilities.

  12. Hierarchical QSAR technology based on the Simplex representation of molecular structure.

    Science.gov (United States)

    Kuz'min, V E; Artemenko, A G; Muratov, E N

    2008-01-01

    This article is about the hierarchical quantitative structure-activity relationship technology (HiT QSAR) based on the Simplex representation of molecular structure (SiRMS) and its application for different QSAR/QSP(property)R tasks. The essence of this technology is a sequential solution (with the use of the information obtained on the previous steps) to the QSAR problem by the series of enhanced models of molecular structure description [from one dimensional (1D) to four dimensional (4D)]. It is a system of permanently improved solutions. In the SiRMS approach, every molecule is represented as a system of different simplexes (tetratomic fragments with fixed composition, structure, chirality and symmetry). The level of simplex descriptors detailing increases consecutively from the 1D to 4D representation of the molecular structure. The advantages of the approach reported here are the absence of "molecular alignment" problems, consideration of different physical-chemical properties of atoms (e.g. charge, lipophilicity, etc.), the high adequacy and good interpretability of obtained models and clear ways for molecular design. The efficiency of the HiT QSAR approach is demonstrated by comparing it with the most popular modern QSAR approaches on two representative examination sets. The examples of successful application of the HiT QSAR for various QSAR/QSPR investigations on the different levels (1D-4D) of the molecular structure description are also highlighted. The reliability of developed QSAR models as predictive virtual screening tools and their ability to serve as the base of directed drug design was validated by subsequent synthetic and biological experiments, among others. The HiT QSAR is realized as a complex of computer programs known as HIT QSAR: software that also includes a powerful statistical block and a number of useful utilities.

  13. Crystal and mol-ecular structure of aflatrem.

    Science.gov (United States)

    Lenta, Bruno N; Ngatchou, Jules; Kenfack, Patrice T; Neumann, Beate; Stammler, Hans-Georg; Sewald, Norbert

    2015-11-01

    The crystal structure of the title compound, C32H39NO4, confirms the absolute configuration of the seven chiral centres in the mol-ecule. The molecule has a 1,1-dimethylprop-2-enyl substituent on the indole nucleus and this nucleus shares one edge with the five-membered ring which is, in turn, connected to a sequence of three edge-shared fused rings. The skeleton is completed by the 7,7-trimethyl-6,8-dioxabi-cyclo-[3.2.1]oct-3-en-2-one group connected to the terminal cyclohexene ring. The two cyclohexane rings adopt chair and half-chair conformations, while in the dioxabi-cyclo-[3.2.1]oct-3-en-2-one unit, the six-membered ring has a half-chair conformation. The indole system of the mol-ecule exhibits a tilt of 2.02 (1)° between its two rings. In the crystal, O-H⋯O hydrogen bonds connect mol-ecules into chains along [010]. Weak N-H⋯π inter-actions connect these chains, forming sheets parallel to (10-1).

  14. Molecular Structure, Theoretical Calculation and Thermodynamic Properties of Tebuconazole

    Institute of Scientific and Technical Information of China (English)

    MA Haixia; SONG Jirong; HUANG Ting; LU Xingqiang; XU Kangzhen; SUN Xiaohong

    2009-01-01

    Single crystals of 5-(4-chlorophenyl)-2,2-dimethyl-3-(1,2,4-triazol-1-ylmethyl)-pentom-3-ol (tebuconazole) were obtained in toluene. The single-crystal X-ray diffraction studies showed that it crystallized in the monoclinic system, with space group P2(1)/c and crystal parameters of a= 1.1645(1) nm, b= 1.6768(2) nm, c= 1.7478(2) nm,β=92.055(2)°, Dc= 1.199 g/cm3, Z=4 and F(000)= 1312. Density functional theory (DFT) B3LYP was employed to optimize the structure and calculate the frequencies of tebuconazole. The calculated geometrical parameters are close to the corresponding experimental ones. The specific heat capacity of the title compound was determined with continuous Cp mode of a mircocalorimeter. In the determining temperature range from 283 to 353 K, the special heat capacity of the title compound presents good linear relation with temperature. Using the determined relation-ship of Cp with temperature T, thermodynamic functions (enthalpy, entropy and Gibbs free energy) of the title compound between 283 and 353 K, relative to the standard temperature 298.15 K, were derived through thermody-namic relationship.

  15. Can we predict lattice energy from molecular structure?

    Science.gov (United States)

    Ouvrard, Carole; Mitchell, John B O

    2003-10-01

    By using simply the numbers of occurrences of different atom types as descriptors, a conceptually transparent and remarkably accurate model for the prediction of the enthalpies of sublimation of organic compounds has been generated. The atom types are defined on the basis of atomic number, hybridization state and bonded environment. Models of this kind were applied firstly to aliphatic hydrocarbons, secondly to both aliphatic and aromatic hydrocarbons, thirdly to a wide range of non-hydrogen-bonding molecules, and finally to a set of 226 organic compounds including 70 containing hydrogen-bond donors and acceptors. The final model gives squared correlation coefficients of 0.925 for the 226 compounds in the training set and 0.937 for an independent test set of 35 compounds. The success of such a simple model implies that the enthalpy of sublimation can be predicted accurately without knowledge of the crystal packing. This hypothesis is in turn consistent with the idea that, rather than being determined by the particular features of the lowest-energy packing, the lattice energy is similar for a number of hypothetical alternative crystal structures of a molecule.

  16. Amylopectin molecular structure reflected in macromolecular organization of granular starch.

    Science.gov (United States)

    Vermeylen, Rudi; Goderis, Bart; Reynaers, Harry; Delcour, Jan A

    2004-01-01

    For lintners with negligible amylose retrogradation, crystallinity related inversely to starch amylose content and, irrespective of starch source, incomplete removal of amorphous material was shown. The latter was more pronounced for B-type than for A-type starches. The two predominant lintner populations, with modal degrees of polymerization (DP) of 13-15 and 23-27, were best resolved for amylose-deficient and A-type starches. Results indicate a more specific hydrolysis of amorphous lamellae in such starches. Small-angle X-ray scattering showed a more intense 9-nm scattering peak for native amylose-deficient A-type starches than for their regular or B-type analogues. The experimental evidence indicates a lower contrasting density within the "crystalline" shells of the latter starches. A higher density in the amorphous lamellae, envisaged by the lamellar helical model, explains the relative acid resistance of linear amylopectin chains with DP > 20, observed in lintners of B-type starches. Because amylopectin chain length distributions were similar for regular and amylose-deficient starches of the same crystal type, we deduce that the more dense (and ordered) packing of double helices into lamellar structures in amylose-deficient starches is due to a different amylopectin branching pattern.

  17. Computational nanochemistry study of the molecular structure and properties of ethambutol.

    Science.gov (United States)

    Salgado-Morán, Guillermo; Ruiz-Nieto, Samuel; Gerli-Candia, Lorena; Flores-Holguín, Norma; Favila-Pérez, Alejandra; Glossman-Mitnik, Daniel

    2013-09-01

    The M06 family of density functionals was employed to calculate the molecular structure and properties of the ethambutol molecule. Besides determination of molecular structures, UV-vis spectra were computed using TD-DFT in the presence of a solvent and the results compared with available experimental data. The chemical reactivity descriptors were calculated through conceptual DFT. The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to Fukui function indices. A comparison between the descriptors calculated through vertical energy values and those arising from Koopmans' theorem approximation were performed in order to check the validity of the latter procedure.

  18. Structure-Activity Relationships on the Molecular Descriptors Family Project at the End

    Directory of Open Access Journals (Sweden)

    Lorentz JÄNTSCHI

    2007-12-01

    Full Text Available Molecular Descriptors Family (MDF on the Structure-Activity Relationships (SAR, a promising approach in investigation and quantification of the link between 2D and 3D structural information and the activity, and its potential in the analysis of the biological active compounds is summarized. The approach, attempts to correlate molecular descriptors family generated and calculated on a set of biological active compounds with their observed activity. The estimation as well as prediction abilities of the approach are presented. The obtained MDF SAR models can be used to predict the biological activity of unknown substrates in a series of compounds.

  19. Spectroscopic study of molecular structure, antioxidant activity and biological effects of metal hydroxyflavonol complexes

    Science.gov (United States)

    Samsonowicz, Mariola; Regulska, Ewa

    2017-02-01

    Flavonols with varied hydroxyl substitution can act as strong antioxidants. Thanks to their ability to chelate metals as well as to donate hydrogen atoms they have capacity to scavenge free radicals. Their metal complexes are often more active in comparison with free ligands. They exhibit interesting biological properties, e.g. anticancer, antiphlogistic and antibacterial. The relationship between molecular structure and their biological properties was intensively studied using spectroscopic methods (UV-Vis, IR, Raman, NMR, ESI-MS). The aim of this paper is review on spectroscopic analyses of molecular structure and biological activity of hydroxyflavonol metal complexes.

  20. Effect of molecular weight on the vibronic structure of a diketopyrrolopyrrole polymer

    KAUST Repository

    Hayes, Sophia C.

    2016-09-27

    Resonance Raman Spectroscopy (RRS) is employed in this study to examine the influence of molecular weight on the optical response of a diketopyrrolopyrrole polymer (DPP-TT-T) in solution. The vibronic structure observed for the ground state absorption of this polymer is found to vary with molecular weight and solvent. Resonance Raman Intensity Analysis (RRIA) revealed that the absorption spectra can be described by at least two dipole-allowed transitions and the vibronic structure variation is due to differing contributions from linear and curved segments of the polymer.

  1. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

    Science.gov (United States)

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-12-10

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

  2. Molecular Structures of Isolevuglandin-Protein Cross-Links.

    Science.gov (United States)

    Bi, Wenzhao; Jang, Geeng-Fu; Zhang, Lei; Crabb, John W; Laird, James; Linetsky, Mikhail; Salomon, Robert G

    2016-10-17

    Isolevuglandins (isoLGs) are stereo and structurally isomeric γ-ketoaldehydes produced through free radical-induced oxidation of arachidonates. Some isoLG isomers are also generated through enzymatic cyclooxygenation. Post-translational modification of proteins by isoLGs is associated with loss-of-function, cross-linking and aggregation. We now report that a low level of modification by one or two molecules of isoLG has a profound effect on the activity of a multi subunit protease, calpain-1. Modification of one or two key lysyl residues apparently suffices to abolish catalytic activity. Covalent modification of calpain-1 led to intersubunit cross-linking. Hetero- and homo-oligomers of the catalytic and regulatory subunits of calpain-1 were detected by SDS-PAGE with Western blotting. N-Acetyl-glycyl-lysine methyl ester and β-amyloid(11-17) peptide EVHHQKL were used as models for characterizing the cross-linking of protein lysyl residues resulting from adduction of iso[4]LGE2. Aminal, bispyrrole, and trispyrrole cross-links of these two peptides were identified and fully characterized by mass spectrometry. Aminal and bispyrrole dimers were both detected. Furthermore, a complex mixture of derivatives of the bispyrrole cross-link containing one or more additional atoms of oxygen was found. Interesting differences are evident in the predominant cross-link type generated in the reaction of iso[4]LGE2 with these peptides. More aminal cross-links versus bispyrrole are formed during the reaction of the dipeptide with iso[4]LGE2. In contrast, more bispyrrole versus aminal cross-links are formed during the reaction of EVHHQKL with iso[4]LGE2. It is tempting to speculate that the EVHHQKL peptide-pyrrole modification forms noncovalent aggregates that favor the production of covalent bispyrrole cross-links because β-amyloid(11-17) tends to spontaneously oligomerize.

  3. Structure enhancement methodology using theory and experiment: gas-phase molecular structures using a dynamic interaction between electron diffraction, molecular mechanics, and ab initio data.

    Science.gov (United States)

    Kafka, Graeme R; Masters, Sarah L; Rankin, David W H

    2007-07-01

    A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).

  4. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    Science.gov (United States)

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.

  5. Profiling of the molecular weight and structural isomer abundance of macroalgae-derived phlorotannins.

    Science.gov (United States)

    Heffernan, Natalie; Brunton, Nigel P; FitzGerald, Richard J; Smyth, Thomas J

    2015-01-16

    Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4-12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

  6. Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins

    Directory of Open Access Journals (Sweden)

    Natalie Heffernan

    2015-01-01

    Full Text Available Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis. Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW phlorotannins were found to have a molecular weight range equivalent to 4–12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs. These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

  7. A Structured Approach to Capture the Lived Experience of Spinal Cord Injury: Data Model and Questionnaire of the International Spinal Cord Injury Community Survey.

    Science.gov (United States)

    Fekete, Christine; Post, Marcel W M; Bickenbach, Jerome; Middleton, James; Prodinger, Birgit; Selb, Melissa; Stucki, Gerold

    2017-02-01

    The International Spinal Cord Injury (InSCI) community survey has been developed to collect internationally comparable data on the lived experience of persons with spinal cord injury (SCI) in all 6 WHO regions. The InSCI survey provides a crucial first step to generate evidence on functioning, health maintenance, and subjective well-being in persons with SCI globally. A major challenge in setting up the InSCI community survey was to develop a data model and questionnaire that comprehensively captures what matters to people and, at the same time, is feasible and parsimonious in terms of participant's burden. This paper outlines the components of the InSCI data model and presents the question selection to operationalize the data model along the 4 guiding principles of efficiency, feasibility, comparability, and truth and discrimination. The data model consists of 6 components operationalized with 125 questions including functioning (n = 28 body functions and structures; n = 42 activities and participation), contextual factors (n = 26 environmental; n = 19 personal factors), lesion characteristics (n = 2), and appraisal of health and well-being (n = 8). The InSCI questionnaire presents an efficient and feasible solution with satisfying comparability to other populations; however, its validity and reliability still needs to be confirmed.

  8. Video Screen Capture Basics

    Science.gov (United States)

    Dunbar, Laura

    2014-01-01

    This article is an introduction to video screen capture. Basic information of two software programs, QuickTime for Mac and BlueBerry Flashback Express for PC, are also discussed. Practical applications for video screen capture are given.

  9. Synthesis and X-ray Crystal Structure of a New Molecular Clip

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The synthesis and X-ray crystal structure of a new molecular clip 2 was reported.It (C24H24N4O2, Mr = 400.47) crystallizes in the space group C2/c with a = 15.587(2), b =8.5805(12), c = 15.259(2)(A),β= 102.448(3)°, V = 1992.9 (5)(A)3, Z= 4, Dc = 1.335 g/cm3,μ= 0.087mm-1 and F(000) = 848.It remains monomeric in the crystal and a tape-like structure is formed in the crystal structure of molecular clip.The most unusual structural feature of 2 is the boat conformation of its cyclohexyl ring imposed by the ring fusion at C(9)-C(9a).

  10. De Novo generation of molecular structures using optimization to select graphs on a given lattice

    DEFF Research Database (Denmark)

    Bywater, R.P.; Poulsen, Thomas Agersten; Røgen, Peter;

    2004-01-01

    A recurrent problem in organic chemistry is the generation of new molecular structures that conform to some predetermined set of structural constraints that are imposed in an endeavor to build certain required properties into the newly generated structure. An example of this is the pharmacophore...... model, used in medicinal chemistry to guide de novo design or selection of suitable structures from compound databases. We propose here a method that efficiently links up a selected number of required atom positions while at the same time directing the emergent molecular skeleton to avoid forbidden...... positions. The linkage process takes place on a lattice whose unit step length and overall geometry is designed to match typical architectures of organic molecules. We use an optimization method to select from the many different graphs possible. The approach is demonstrated in an example where crystal...

  11. Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics

    Science.gov (United States)

    Whitfield, T. W.; Crain, J.; Martyna, G. J.

    2006-03-01

    In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.

  12. Molecular Structures and Mechanical Properties of Microbe Rapid Coagulation Natural Rubber

    Institute of Scientific and Technical Information of China (English)

    LIANG Yue; HUANG Mao-Fang; ZENG Zong-Qiang

    2011-01-01

    In this work,molecular structures,dynamic mechanical properties and glass transition temperatures of microbe coagulated natural rubber(NR) samples were analyzed by using pyrolysis gas chromatography-mass spectrometry(py-GC/MS),rubber process analyzer(RPA) and dynamic mechanical thermal analysis(DMA).And the cross-linked network structures and mechanical properties of the corresponding NR vulcanizates were further determined by using nuclear magnetic resonance(NMR) crosslink density spectrometer(XLDS-15) and universal testing machines.The results show that NR raw rubber produced by rapidly coagulated with microorganism exhibits a simple molecular structure composition and good dynamic mechanical properties,and the corresponding NR vulcanizates possess the aggregation structure of high cross-linked density,a high glass transition temperature of-61.5 ℃ and high mechanical properties(tensile strength reaches 25.2 MPa),as compared with that coagulated with acetic acid.

  13. Density functional theory study of the structural, electronic, lattice dynamical, and thermodynamic properties of Li4SiO4 and its capability for CO2 capture

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Yuhua; Parlinski, K.

    2011-01-01

    The structural, electronic, lattice dynamical, optical, thermodynamic, and CO{sub 2} capture properties of monoclinic and triclinic phases of Li{sub 4}SiO{sub 4} are investigated by combining density functional theory with phonon lattice dynamics calculations. We found that these two phases have some similarities in their bulk and thermodynamic properties. The calculated bulk modulus and the cohesive energies of these two phases are close to each other. Although both of them are insulators, the monoclinic phase of Li{sub 4}SiO{sub 4} has a direct band gap of 5.24 eV while the triclinic Li{sub 4}SiO{sub 4} phase has an indirect band gap of 4.98 eV. In both phases of Li{sub 4}SiO{sub 4}, the s orbital of O mainly contributes to the lower-energy second valence band (VB{sub 2}) and the p orbitals contribute to the fist valence band (VB{sub 1}) and the conduction bands (CBs). The s orbital of Si mainly contributes to the lower portions of the VB1 and VB{sub 2}, and Si p orbitals mainly contribute to the higher portions of the VB{sub 1} and VB{sub 2}. The s and p orbitals of Li contribute to both VBs and to CBs, and Li p orbitals have a higher contribution than the Li s orbital. There is possibly a phonon soft mode existing in triclinic {gamma}-Li{sub 4}SiO{sub 4}; in the monoclinic Li{sub 4}SiO{sub 4}, there are three phonon soft modes, which correspond to the one type of Li disordered over a few sites. Their LO-TO splitting indicates that both phases of Li{sub 4}SiO{sub 4} are polar anisotropic materials. The calculated infrared absorption spectra for LO and TO modes are different for these two phases of Li{sub 4}SiO{sub 4}. The calculated relationships of the chemical potential versus temperature and CO{sub 2} pressure for reaction of Li{sub 4}SiO{sub 4} with CO{sub 2} shows that Li{sub 4}SiO{sub 4} could be a good candidate for a high-temperature CO{sub 2} sorbent while used for postcombustion capture technology.

  14. NATO Advanced Research Workshop on Vectorization of Advanced Methods for Molecular Electronic Structure

    CERN Document Server

    1984-01-01

    That there have been remarkable advances in the field of molecular electronic structure during the last decade is clear not only to those working in the field but also to anyone else who has used quantum chemical results to guide their own investiga­ tions. The progress in calculating the electronic structures of molecules has occurred through the truly ingenious theoretical and methodological developments that have made computationally tractable the underlying physics of electron distributions around a collection of nuclei. At the same time there has been consider­ able benefit from the great advances in computer technology. The growing sophistication, declining costs and increasing accessibi­ lity of computers have let theorists apply their methods to prob­ lems in virtually all areas of molecular science. Consequently, each year witnesses calculations on larger molecules than in the year before and calculations with greater accuracy and more com­ plete information on molecular properties. We can surel...

  15. Molecular dynamics simulation study on zwitterionic structure to maintain the normal conformations of Glutathione

    Institute of Scientific and Technical Information of China (English)

    YAN; Han; ZHU; HaoMiao; SHEN; Jian

    2007-01-01

    Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The results showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".

  16. Nodal structure of the wave function for a two-dimensionalhydrogen molecular ion

    Institute of Scientific and Technical Information of China (English)

    段宜武; 周光辉; 鲍诚光; 袁建民

    1996-01-01

    Under the Born-Oppenheimer approximation, the exact solution of the Schrodinger equation for a two-dimensional hydrogen molecular ion is obtained through separation of variables. The inter-quantum numbers and the modes of internal motion are determined by analysing the nodal structure of the wavefunction. The eigenstates are classified and the classical periodic orbits corresponding to the modes of internal motion are found. two-center molecule, nodal structure, mode of internal motion.

  17. Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces.

    OpenAIRE

    Evans, E; Ritchie, K; Merkel, R.

    1995-01-01

    Adhesion and cytoskeletal structure are intimately related in biological cell function. Even with the vast amount of biological and biochemical data that exist, little is known at the molecular level about physical mechanisms involved in attachments between cells or about consequences of adhesion on the material structure. To expose physical actions at soft biological interfaces, we have combined an ultrasensitive transducer and reflection interference microscopy to image submicroscopic displ...

  18. Optimization of large amorphous silicon and silica structures for molecular dynamics simulations of energetic impacts

    Energy Technology Data Exchange (ETDEWEB)

    Samela, Juha, E-mail: juha.samela@helsinki.fi [Department of Physics and Helsinki Institute of Physics, University of Helsinki, P.O. Box 43, FI-00014 University of Helsinki (Finland); Norris, Scott A. [Southern Methodist University, Dallas, TX 75205 (United States); Nordlund, Kai [Department of Physics and Helsinki Institute of Physics, University of Helsinki, P.O. Box 43, FI-00014 University of Helsinki (Finland); Aziz, Michael J. [School of Engineering and Applied Sciences, Harvard University, 29 Oxford St., Cambridge, MA 02138 (United States)

    2011-07-15

    A practical method to create optimized amorphous silicon and silica structures for molecular dynamics simulations is developed and tested. The method is based on the Wooten, Winer, and Weaire algorithm and combination of small optimized blocks to larger structures. The method makes possible to perform simulations of either very large cluster hypervelocity impacts on amorphous targets or small displacements induced by low energy ion impacts in silicon.

  19. Molecular basis of classic galactosemia from the structure of human galactose 1-phosphate uridylyltransferase

    OpenAIRE

    McCorvie, Thomas J; Kopec, Jolanta; Angel L Pey; Fitzpatrick, Fiona; Patel, Dipali; Chalk, Rod; Shrestha, Leela; Yue, Wyatt W.

    2016-01-01

    Classic galactosemia is a potentially lethal disease caused by the dysfunction of galactose 1-phosphate uridylyltransferase (GALT). Over 300 disease-associated GALT mutations have been reported, with the majority being missense changes, although a better understanding of their underlying molecular effects has been hindered by the lack of structural information for the human enzyme. Here, we present the 1.9 Å resolution crystal structure of human GALT (hGALT) ternary complex, revealing a homod...

  20. Molecular Modeling of Rigid-Rod Polymers Structures Dominated by Electrostatic Interactions

    Science.gov (United States)

    2005-11-01

    the structure in solutions of PBO in strong acids . The role of the dielectric properties of the medium ( dielectric constant) and counterions. 1...morphology which the polymer adopts. We propose to undertake a molecular modeling study of the effect of strong acids on the structure and properties of PBO...methane sulphonic and chlorine sulphonic acids [5], (protons are connected with oxygen atoms as well). Besides we have considered also patially protonated

  1. Refinement of homology-based protein structures by molecular dynamics simulation techniques

    NARCIS (Netherlands)

    Fan, H; Mark, AE

    2004-01-01

    The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to asses

  2. Origami: A Versatile Modeling System for Visualising Chemical Structure and Exploring Molecular Function

    Science.gov (United States)

    Davis, James; Leslie, Ray; Billington, Susan; Slater, Peter R.

    2010-01-01

    The use of "Origami" is presented as an accessible and transferable modeling system through which to convey the intricacies of molecular shape and highlight structure-function relationships. The implementation of origami has been found to be a versatile alternative to conventional ball-and-stick models, possessing the key advantages of being both…

  3. Structural Dynamics of Overcrowded Alkene-Based Molecular Motors during Thermal Isomerization

    NARCIS (Netherlands)

    Cnossen, Arjen; Kistemaker, Jos C. M.; Kojima, Tatsuo; Feringa, Ben L.

    2014-01-01

    Synthetic light-driven rotary molecular motors show complicated structural dynamics during the rotation process. A combination of DFT calculations and various spectroscopic techniques is employed to study the effect of the bridging group in the lower half of the molecule on the conformational dynami

  4. Molecular Docking of Enzyme Inhibitors: A Computational Tool for Structure-Based Drug Design

    Science.gov (United States)

    Rudnitskaya, Aleksandra; Torok, Bela; Torok, Marianna

    2010-01-01

    Molecular docking is a frequently used method in structure-based rational drug design. It is used for evaluating the complex formation of small ligands with large biomolecules, predicting the strength of the bonding forces and finding the best geometrical arrangements. The major goal of this advanced undergraduate biochemistry laboratory exercise…

  5. Structural investigation of bistrifluron using x-ray crystallography, NMR spectroscopy, and molecular modeling

    CERN Document Server

    Moon, J K; Rhee, S K; Kim, G B; Yun, H S; Chung, B J; Lee, S S; Lim, Y H

    2002-01-01

    A new insecticide, bistrifluron acts as an inhibitor of insect development and interferes with the cuticle formation of insects. Since it shows low acute oral and dermal toxicities, it can be one of potent insecticides. Based on X-ray crystallography, NMR spectroscopy and molecular modeling, the structural studies of bistrifluron have been carried out.

  6. Formation, Molecular Structure, and Morphology of Humins in Biomass Conversion : Influence of Feedstock and Processing Conditions

    NARCIS (Netherlands)

    van Zandvoort, Ilona; Wang, Yuehu; Rasrendra, Carolus B.; van Eck, Ernst R. H.; Bruijnincx, Pieter C. A.; Heeres, Hero J.; Weckhuysen, Bert M.

    2013-01-01

    Neither the routes through which humin byproducts are formed, nor their molecular structure have yet been unequivocally established. A better understanding of the formation and physicochemical properties of humins, however, would aid in making biomass conversion processes more efficient. Here, an ex

  7. Fine tuning of the rotary motion by structural modification in light-driven unidirectional molecular motors

    NARCIS (Netherlands)

    Vicario, J; Walko, M; Meetsma, A; Feringa, Ben L.

    2006-01-01

    The introduction of bulky substituents at the stereogenic center of light-driven second-generation molecular motors results in an acceleration of the speed of rotation. This is due to a more strained structure with elongated C=C bonds and a higher energy level of the ground state relative to the tra

  8. (TMTSF)2X materials and structural implications for low-dimensional polymeric and disordered molecular semiconductors

    DEFF Research Database (Denmark)

    Bechgaard, Klaus; Nielsen, Martin Meedom; Krebs, Frederik C

    2000-01-01

    The structural characteristics and the relation to the electronic properties of three types of molecular materials are discussed. In TMTSF2X salts a triclinic unit cell it suggested to be important in avoiding a 2k(F) Peierls distortion. In polythiophenes appropriate ordering of microcrystallites...

  9. Linear hydrogen adsorbate structures on graphite induced by self-assembled molecular monolayers

    DEFF Research Database (Denmark)

    Nilsson, Louis; Sljivancanin, Zeljko; Balog, Richard

    2012-01-01

    Combined scanning tunnelling microscopy measurements and density functional theory calculations reveal a method to induce linear structures of hydrogen adsorbates on graphite by covering the surface with a self-assembled molecular monolayer of cyanuric acid and exposing it to atomic hydrogen...

  10. Probing the evolution of molecular cloud structure II: From chaos to confinement

    CERN Document Server

    Kainulainen, J; Banerjee, R; Federrath, C; Henning, T

    2011-01-01

    We present an analysis of the large-scale molecular cloud structure and of the stability of clumpy structures in nearby molecular clouds. In our recent work, we identified a structural transition in molecular clouds by studying the probability distributions of gas column densities in them. In this paper, we further examine the nature of this transition. The transition takes place at the visual extinction of A_V^tail = 2-4 mag, or equivalently, at \\Sigma^tail = 40-80 Ms pc^{-2}. The clumps identified above this limit have wide ranges of masses and sizes, but a remarkably constant mean volume density of n = 10^3 cm^{-3}. This is 5-10 times larger than the density of the medium surrounding the clumps. By examining the stability of the clumps, we show that they are gravitationally unbound entities, and that the external pressure from the parental molecular cloud is a significant source of confining pressure for them. Then, the structural transition at A_V^tail may be linked to a transition between this population...

  11. Looking beyond Lewis Structures: A General Chemistry Molecular Modeling Experiment Focusing on Physical Properties and Geometry

    Science.gov (United States)

    Linenberger, Kimberly J.; Cole, Renee S.; Sarkar, Somnath

    2011-01-01

    We present a guided-inquiry experiment using Spartan Student Version, ready to be adapted and implemented into a general chemistry laboratory course. The experiment provides students an experience with Spartan Molecular Modeling software while discovering the relationships between the structure and properties of molecules. Topics discussed within…

  12. Study of the Molecular Geometry, Electronic Structure, and Thermal Stability of Phosphazene and Heterophosphazene Rings with ab Initio Molecular Orbital Calculations

    NARCIS (Netherlands)

    Jaeger, C.R.; Debowski, M.A.; Manners, I.; Vancso, G.J.

    1999-01-01

    Ab initio molecular orbital calculations at the MP2/6-31G* level of theory have been used to study the molecular geometry, electronic structure, and the thermal stability of six-membered phosphazene and heterophosphazene rings. The studies included the phosphazene ring [NPCl2]3, the carbophosphazene

  13. Determining molecular structures and conformations directly from electron diffraction using a genetic algorithm.

    Science.gov (United States)

    Habershon, Scott; Zewail, Ahmed H

    2006-02-13

    A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all-trans retinal and p-coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data.

  14. Boron neutron capture therapy of EGFR or EGFRvIII positive gliomas using either boronated monoclonal antibodies or epidermal growth factor as molecular targeting agents

    Energy Technology Data Exchange (ETDEWEB)

    Yang, W. [Department of Pathology, Ohio State University, 165 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210 (United States); Barth, R.F. [Department of Pathology, Ohio State University, 165 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210 (United States)], E-mail: rolf.barth@osumc.edu; Wu, G. [Department of Pathology, Ohio State University, 165 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210 (United States); Tjarks, W. [College of Pharmacy, Ohio State University, Columbus, OH 43210 (United States); Binns, P.; Riley, K. [Nuclear Reactor Laboratory and Department of Nuclear Engineering, Massachusetts Institute of Technology, Cambridge, MA 02215 (United States)

    2009-07-15

    In the present report we have summarized studies carried out over the past five years on molecular targeting of the epidermal growth factor receptor (EGFR) and its mutant isoform, EFGRvIII, for BNCT of genetically engineered F98 rat gliomas, expressing either wildtype (F98{sub EGFR}) or mutant receptors (F98{sub npEGFRvIII}). EGF or the monoclonal antibodies (mAbs), cetuximab (IMC-C225) and L8A4, which recognize wildtype EGFR and EGFRvIII, respectively, were heavily boronated using polyamidoamine (PAMAM) dendrimers (BD) linked to the targeting vehicles by means of heterobifunctional reagents. Boronated EGF or mAbs, alone or in combination with i.v. boronophenylalanine (BPA), were administered intracerebrally (i.c.) by either intratumoral (i.t.) injection or convection enhanced delivery (CED) to rats bearing F98 gliomas following which BNCT was initiated. The best survival data were obtained in rats bearing F98{sub npEGFRvIII} gliomas that had received CED of BD-L8A4 either alone or in combination with i.v. boronophenylalanine (BPA). Studies carried out in rats bearing composite tumors (F98{sub EGFR}/F98{sub npEGFRvIII}) demonstrated that it was essential to target both tumor cell populations in order to obtain an optimal therapeutic effect. Based on these observations, we have concluded that EGFR targeting vehicles are useful, but not stand-alone boron delivery agents due to the heterogeneity of receptor expression in brain tumors. They could, however, be quite useful in combination with the two drugs that currently are being used clinically, BPA and sodium borocaptate (BSH) for BNCT of either brain tumors or head and neck cancers.

  15. Capture Their Attention: Capturing Lessons Using Screen Capture Software

    Science.gov (United States)

    Drumheller, Kristina; Lawler, Gregg

    2011-01-01

    When students miss classes for university activities such as athletic and academic events, they inevitably miss important class material. Students can get notes from their peers or visit professors to find out what they missed, but when students miss new and challenging material these steps are sometimes not enough. Screen capture and recording…

  16. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: A non-equilibrium molecular dynamics study

    Science.gov (United States)

    Lemarchand, Claire A.; Bailey, Nicholas P.; Todd, Billy D.; Daivis, Peter J.; Hansen, Jesper S.

    2015-06-01

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. At a fixed temperature, the shear-shinning behavior is related not only to the inter- and intramolecular alignments of the solvent molecules but also to the decrease of the average size of the nanoaggregates at high shear rates. The variation of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex systems such as colloidal suspensions, polymer solutions, and associating polymer networks is discussed.

  17. The effect of molecular mass on the polymorphism and crystalline structure of isotactic polypropylene

    Directory of Open Access Journals (Sweden)

    2010-02-01

    Full Text Available This study is devoted to the investigation of the effect of molecular mass on the α-, β- and γ-crystallization tendency of isotactic polypropylene (iPP. The crystalline structure was studied by wide angle X-ray scattering (WAXS and by polarised light microscopy (PLM. The melting and crystallization characteristics were determined by differential scanning calorimetry (DSC. The results indicate clearly that iPP with low molecular mass crystallizes essentially in α-modification. However, it crystallizes in β-form in the presence of a highly efficient and selective β-nucleating agent. The α- and β-modifications form in wide molecular mass range. The decreasing molecular mass results in increased structural instability in both α- and β-modifications and consequently enhanced inclination to recrystallization during heating. The formation of γ-modification could not be observed, although some literature sources report that γ-form develops in iPP with low molecular mass.

  18. Structure of the thermolabile mutant aldolase B, A149P: molecular basis of hereditary fructose intolerance.

    Science.gov (United States)

    Malay, Ali D; Allen, Karen N; Tolan, Dean R

    2005-03-18

    Hereditary fructose intolerance (HFI) is a potentially lethal inborn error in metabolism caused by mutations in the aldolase B gene, which is critical for gluconeogenesis and fructose metabolism. The most common mutation, which accounts for 53% of HFI alleles identified worldwide, results in substitution of Pro for Ala at position 149. Structural and functional investigations of human aldolase B with the A149P substitution (AP-aldolase) have shown that the mutation leads to losses in thermal stability, quaternary structure, and activity. X-ray crystallography is used to reveal the structural basis of these perturbations. Crystals of AP-aldolase are grown at two temperatures (4 degrees C and 18 degrees C), and the structure solved to 3.0 angstroms resolution, using the wild-type structure as the phasing model. The structures reveal that the single residue substitution, A149P, causes molecular disorder around the site of mutation (residues 148-159), which is propagated to three adjacent beta-strand and loop regions (residues 110-129, 189-199, 235-242). Disorder in the 110-129-loop region, which comprises one subunit-subunit interface, provides an explanation for the disrupted quaternary structure and thermal instability. Greater structural perturbation, particularly at a Glu189-Arg148 salt bridge in the active-site architecture, is observed in the structure determined at 18 degrees C, which could explain the temperature-dependent loss in activity. The disorder revealed in these structures is far greater than that predicted by homology modeling and underscores the difficulties in predicting perturbations of protein structure and function by homology modeling alone. The AP-aldolase structure reveals the molecular basis of a hereditary disease and represents one of only a few structures known for mutant proteins at the root of the thousands of other inherited disorders.

  19. Molecular dynamics simulations of H2 adsorption in tetramethyl ammonium lithium phthalocyanine crystalline structures.

    Science.gov (United States)

    Lamonte, Kevin; Gómez Gualdrón, Diego A; Cabrales-Navarro, Fredy A; Scanlon, Lawrence G; Sandi, Giselle; Feld, William; Balbuena, Perla B

    2008-12-11

    Tetramethyl ammonium lithium phthalocyanine is explored as a potential material for storage of molecular hydrogen. Density functional theory calculations are used to investigate the molecular structure and the dimer conformation. Additional scans performed to determine the interactions of a H2 molecule located at various distances from the molecular sites are used to generate a simple force field including dipole-induced-dipole interactions. This force field is employed in molecular dynamics simulations to calculate adsorption isotherms at various pressures. The regions of strongest adsorption are quantified as functions of temperature, pressure, and separation between molecules in the adsorbent phase, and compared to the regions of strongest binding energy as given by the proposed force field. It is found that the total adsorption could not be predicted only from the spatial distribution of the strongest binding energies; the available volume is the other contributing factor even if the volume includes regions of much lower binding energy. The results suggest that the complex anion is primarily involved in the adsorption process with molecular hydrogen, whereas the cation serves to provide access for hydrogen adsorption in both sides of the anion molecular plane, and spacing between the planes.

  20. Structural characterization of interfacial n-octanol and 3-octanol using molecular dynamic simulations.

    Science.gov (United States)

    Napoleon, Raeanne L; Moore, Preston B

    2006-03-01

    Structurally isomeric octanol interfacial systems, water/vapor, 3-octanol/vapor, n-octanol/vapor, 3-octanol/water, and n-octanol/water are investigated at 298 K using molecular dynamics simulation techniques. The present study is intended to investigate strongly associated liquid/liquid interfaces and probe the atomistic structure of these interfaces. The octanol and water molecules were initially placed randomly into a box and were equilibrated using constant pressure techniques to minimize bias within the initial conditions as well as to fully sample the structural conformations of the interface. An interface formed via phase separation during equilibration and resulted in a slab geometry with a molecularly sharp interface. However, some water molecules remained within the octanol phase with a mole fraction of 0.12 after equilibration. The resulting "wet" octanol interfaces were analyzed using density profiles and orientational order parameters. Our results support the hypothesis of an ordered interface only 1 or 2 molecular layers deep before bulk properties are reached for both the 3-octanol and water systems. However, in contrast to most other interfacial systems studied by molecular dynamics simulations, the n-octanol interface extends for several molecular layers. The octanol hydroxyl groups form a hydrogen-bonding network with water which orders the surface molecules toward a preferred direction and produces a hydrophilic/hydrophobic layering. The ordered n-octanol produces an oscillating low-high density of oxygen atoms out of phase with a high-low density of carbon atoms, consistent with an oscillating dielectric. In contrast, the isomeric 3-octanol has only a single carbon-rich layer directly proximal to the interface, which is a result of the different molecular topology. Both 3-octanol and n-octanol roughen the water interface with respect to the water/vapor interface. The "wet" octanol phases, in the octanol/water systems reach bulk properties in a

  1. Similarity boosted quantitative structure-activity relationship--a systematic study of enhancing structural descriptors by molecular similarity.

    Science.gov (United States)

    Girschick, Tobias; Almeida, Pedro R; Kramer, Stefan; Stålring, Jonna

    2013-05-24

    The concept of molecular similarity is one of the most central in the fields of predictive toxicology and quantitative structure-activity relationship (QSAR) research. Many toxicological responses result from a multimechanistic process and, consequently, structural diversity among the active compounds is likely. Combining this knowledge, we introduce similarity boosted QSAR modeling, where we calculate molecular descriptors using similarities with respect to representative reference compounds to aid a statistical learning algorithm in distinguishing between different structural classes. We present three approaches for the selection of reference compounds, one by literature search and two by clustering. Our experimental evaluation on seven publicly available data sets shows that the similarity descriptors used on their own perform quite well compared to structural descriptors. We show that the combination of similarity and structural descriptors enhances the performance and that a simple stacking approach is able to use the complementary information encoded by the different descriptor sets to further improve predictive results. All software necessary for our experiments is available within the cheminformatics software framework AZOrange.

  2. Novel aldehyde and thiosemicarbazone derivatives: Synthesis, spectroscopic characterization, structural studies and molecular docking studies

    Science.gov (United States)

    Karakurt, Tuncay; Tahtaci, Hakan; Subasi, Nuriye Tuna; Er, Mustafa; Ağar, Erbil

    2016-12-01

    In this study our purpose is that, synthesis and characterization of compounds containing the aldehyde and thiosemicarbazone groups and comparison of the theoretical results with the experimental results. The structures of all synthesized compounds were elucidated by IR, 1H NMR, 13C NMR, elemental analyses techniques. The structure of compound (4) (C9H8N4O2S) was also elucidated by X-ray diffraction analysis. In addition, the theoretical IR spectrum, 1H NMR and 13C NMR chemical shift values, frontier molecular orbital values (FMO) of these molecules were analyzed by using Becke-3- Lee-Yang-Parr (B3LYP) method with LanL2DZ basis set. Finally, molecular docking studies were performed on synthesized compounds using the 4DKI beta-lactam protein structure to determine the potential binding mode of inhibitors.

  3. Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

    CERN Document Server

    Singh, Raghvendra Pratap; Cleri, Fabrizio

    2013-01-01

    We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to...

  4. Correlating Molecular Structures with Transport Dynamics in High-Efficiency Small-Molecule Organic Photovoltaics.

    Science.gov (United States)

    Peng, Jiajun; Chen, Yani; Wu, Xiaohan; Zhang, Qian; Kan, Bin; Chen, Xiaoqing; Chen, Yongsheng; Huang, Jia; Liang, Ziqi

    2015-06-24

    Efficient charge transport is a key step toward high efficiency in small-molecule organic photovoltaics. Here we applied time-of-flight and organic field-effect transistor to complementarily study the influences of molecular structure, trap states, and molecular orientation on charge transport of small-molecule DRCN7T (D1) and its analogue DERHD7T (D2). It is revealed that, despite the subtle difference of the chemical structures, D1 exhibits higher charge mobility, the absence of shallow traps, and better photosensitivity than D2. Moreover, charge transport is favored in the out-of-plane structure within D1-based organic solar cells, while D2 prefers in-plane charge transport.

  5. Kinked structures of isolated nicotinic receptor M2 helices: a molecular dynamics study.

    Science.gov (United States)

    Sankararamakrishnan, R; Samsom, M S

    1994-12-01

    The pore-lining M2 helix of the nicotinic acetylcholine receptor exhibits a pronounced kink when the corresponding ion channel is in a closed conformation [N. Unwin (1993) Journal of Molecular Biology, Vol. 229, pp. 1101-1124]. We have performed molecular dynamics simulations of isolated 22-residue M2 helices in order to identify a possible molecular origin of this kink. In order to sample a wide range of conformational space, a simulated annealing protocol was used to generate five initial M2 helix structures, each of which was subsequently used as the basis of 300 ps MD simulations. Two helix sequences (M2 alpha and M2 delta) were studied in this manner, resulting in a total of ten 300 ps trajectories. Kinked helices present in the trajectories were identified and energy minimized to yield a total of five different stable kinked structures. For comparison, a similar molecular dynamics simulation of a Leu23 helix yielded no stable kinked structures. In four of the five kinked helices, the kink was stabilized by H bonds between the helix backbone and polar side-chain atoms. Comparison with data from the literature on site-directed mutagenesis of M2 residues suggests that such polar side-chain to main-chain H bonds may also contribute to kinking of M2 helices in the intact channel protein.

  6. Establishing whether the structural feature controlling the mechanical properties of starch films is molecular or crystalline.

    Science.gov (United States)

    Li, Ming; Xie, Fengwei; Hasjim, Jovin; Witt, Torsten; Halley, Peter J; Gilbert, Robert G

    2015-03-06

    The effects of molecular and crystalline structures on the tensile mechanical properties of thermoplastic starch (TPS) films from waxy, normal, and high-amylose maize were investigated. Starch structural variations were obtained through extrusion and hydrothermal treatment (HTT). The molecular and crystalline structures were characterized using size-exclusion chromatography and X-ray diffractometry, respectively. TPS from high-amylose maize showed higher elongation at break and tensile strength than those from normal maize and waxy maize starches when processed with 40% plasticizer. Within the same amylose content, the mechanical properties were not affected by amylopectin molecular size or the crystallinity of TPS prior to HTT. This lack of correlation between the molecular size, crystallinity and mechanical properties may be due to the dominant effect of the plasticizer on the mechanical properties. Further crystallization of normal maize TPS by HTT increased the tensile strength and Young's modulus, while decreasing the elongation at break. The results suggest that the crystallinity from the remaining ungelatinized starch granules has less significant effect on the mechanical properties than that resulting from starch recrystallization, possibly due to a stronger network from leached-out amylose surrounding the remaining starch granules.

  7. History, Classification, Molecular Structure and Properties of Dendrimers which are a New Concept in Textile

    Directory of Open Access Journals (Sweden)

    Osman NAMIRTI

    2011-02-01

    Full Text Available Over the last 20 years polymer chemistry has created a number of non-lineer structures and introduction of a large number of branches during the polymer synthesis leads to obtain molecules with many end groups. Two types of these polymers are regularly branched "dendrimers" and "hyperbranched polymers" where branching is formed randomly. In this article knowledge about history, classification, molecular structure and properties of dendrimers which have found various application areas also in textile due to their special structures is given.

  8. Molecules and Models The molecular structures of main group element compounds

    CERN Document Server

    Haaland, Arne

    2008-01-01

    This book provides a systematic description of the molecular structures and bonding in simple compounds of the main group elements with particular emphasis on bond distances, bond energies and coordination geometries. The description includes the structures of hydrogen, halogen and methyl derivatives of the elements in each group, some of these molecules are ionic, some polar covalent. The survey of molecules whose structures conform to well-established trends is followed byrepresentative examples of molecules that do not conform. We also describe electron donor-acceptor and hydrogen bonded co

  9. Molecular design chemical structure generation from the properties of pure organic compounds

    CERN Document Server

    Horvath, AL

    1992-01-01

    This book is a systematic presentation of the methods that have been developed for the interpretation of molecular modeling to the design of new chemicals. The main feature of the compilation is the co-ordination of the various scientific disciplines required for the generation of new compounds. The five chapters deal with such areas as structure and properties of organic compounds, relationships between structure and properties, and models for structure generation. The subject is covered in sufficient depth to provide readers with the necessary background to understand the modeling

  10. Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

    DEFF Research Database (Denmark)

    Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob;

    2002-01-01

    , the simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width......The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations...

  11. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    Directory of Open Access Journals (Sweden)

    Yajiang Hao

    2015-07-01

    Full Text Available We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.

  12. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    CERN Document Server

    Hao, Yajiang; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-01-01

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.

  13. Carbohydrate compositions and molecular structure of dextrins in enzymatic high maltose syrups

    Energy Technology Data Exchange (ETDEWEB)

    Nebesny, E. (Politechnika Lodzka, Lodz (Poland). Dept. of Food Technology)

    1990-11-01

    Investigations of the potato starch hydrolysis during bacterial {alpha}-amylase liquefaction and saccharification with barley {beta}-amylase itself and with cooperation with pullulanase were carried out. In adequate conditions at different enzyme dosages hydrolyzates of the maltose content of 60 to about 85% in DS with significantly (6-10 times) lower maltotriose and minimal glucose content could be obtained. Investigations comprised both carbohydrate contents in hydrolyzates changing with hydrolyze course and dextrine molecular structure in hydrolyzates. It was found out that decreasing dextrine molecular weight and the number of branchings was accompanied by charateristic changes of the viscosity of hydrolyzate solutions. (orig.).

  14. Theoretical Study of Copper Complexes: Molecular Structure, Properties, and Its Application to Solar Cells

    Directory of Open Access Journals (Sweden)

    Jesus Baldenebro-Lopez

    2013-01-01

    Full Text Available We present a theoretical investigation of copper complexes with potential applications as sensitizers for solar cells. The density functional theory (DFT and time-dependent DFT were utilized, using the M06 hybrid meta-GGA functional with the LANL2DZ (D95V on first row and DZVP basis sets. This level of calculation was used to find the optimized molecular structure, the absorption spectra, the molecular orbitals energies, and the chemical reactivity parameters that arise from conceptual DFT. Solvent effects have been taken into account by an implicit approach, namely, the polarizable continuum model (PCM, using the nonequilibrium version of the IEF-PCM model.

  15. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow

    DEFF Research Database (Denmark)

    Lemarchand, Claire; Bailey, Nicholas; Daivis, Peter

    2015-01-01

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear...... rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates...

  16. The cluster structure of dilute aqueous-alcoholic solutions and molecular light scattering in them

    Science.gov (United States)

    Malomuzh, N. P.; Slinchak, E. L.

    2007-11-01

    The structures, equations of state, and character of fluctuations of dilute water-glycerol solutions are discussed. Two or three glycerol and about ten water molecules were found to form a fairly stable molecular complex. We call this complex elementary cluster (pseudoparticle). In a certain region of state parameters, the system could be considered a solution of pseudoparticles (clusters). Its properties were modeled by the van der Waals equation. The character of interactions between clusters was analyzed. An anomalous increase in concentration and molecular light scattering fluctuations was caused by the approach to the solution “pseudospinodal.” The experimental data were found to be in quite satisfactory agreement with theoretical estimates.

  17. Molecular Beam Epitaxial Growth, Characterization, and Devices of Modulated Semiconductor Structures

    Science.gov (United States)

    1990-02-28

    on reverse if necessary and identify by block number) Key Words: Molecular Beam Epitaxv, X-ray diffraction, RHEED, GeSn , AlGaSb, Surface Structure iLb...equipment so far has been used in the study of metastable GeSn alloys grown on InP and GaSb substrates, and in analysis of the (Al, Ga)Sb material system...Homma, "Molecular beam epitaxial 6 growth of metastable GeSn alloys", Sept. 13-15, 1989, North Carolina State University, Raleigh, N.C. Also to be

  18. A Study on the Structure and Photodetachment Dynamics of Copper Based Molecular Anions Using Photoelectron Spectroscopy

    Science.gov (United States)

    Holtgrewe, Nicholas Stephen

    This dissertation represents a study of the effects of electron molecule interactions in the detachment and dissociation dynamics of copper based molecular anions. Results are presented on the photodetachment of small copper oxide CuOn-- (n = 1, 2) and copper fluoride CuFn-- (n = 1, 2) molecular anions. Effects of different resonances are explored using the photoelectron angular distributions (PADs) and the relative intensity variations in vibrational channel cross sections. The specific resonances studied include dipole bound resonances, in which the electric dipole moment of the neutral molecule captures the outgoing electron, and electronic Feshbach resonances, in which the anion undergoes absorption to an excited anion state (lying energetically above the neutral) followed by relaxation via autodetachment into the electronic continuum. In addition to electron scattering resonances, the effects of dissociation dynamics on linear CuO2-- are studied, wherein the linear anion isomer was found to dissociate to Cu-- fragments. This dissociation process is interpreted with experimental data acquired from nanosecond photoelectron images and a femtosecond time resolved study.

  19. Probing the evolution of molecular cloud structure. II. From chaos to confinement

    Science.gov (United States)

    Kainulainen, J.; Beuther, H.; Banerjee, R.; Federrath, C.; Henning, T.

    2011-06-01

    We present an analysis of the large-scale molecular cloud structure and of the stability of clumpy structures in nearby molecular clouds. In our recent work, we identified a structural transition in molecular clouds by studying the probability distributions of their gas column densities. In this paper, we further examine the nature of this transition. The transition takes place at the visual extinction of A_V^tail = 2{-4} mag, or equivalently, at Σtail ≈ 40-80 M⊙ pc-2. The clumps identified above this limit have wide ranges of masses and sizes, but a remarkably constant mean volume density of overline{n ≈ 10^3} cm-3. This is 5-10 times higher than the density of the medium surrounding the clumps. By examining the stability of the clumps, we show that they are gravitationally unbound entities, and that the external pressure from the parental molecular cloud is a significant source of confining pressure for them. Then, the structural transition at A_V^tail may be linked to a transition between this population and the surrounding medium. The star-formation rates in the clouds correlate strongly with the total mass in the clumps, i.e., with the mass above A_V^tail, and drops abruptly below that threshold. These results imply that the formation of pressure-confined clumps introduces a prerequisite for star formation. Furthermore, they give a physically motivated explanation for the recently reported relation between the star-formation rates and the amount of dense material in molecular clouds. Likewise, they give rise to a natural threshold for star formation at A_V^tail.

  20. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

    Science.gov (United States)

    Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Dror, Ron O; Shaw, David E

    2012-08-01

    Accurate computational prediction of protein structure represents a longstanding challenge in molecular biology and structure-based drug design. Although homology modeling techniques are widely used to produce low-resolution models, refining these models to high resolution has proven difficult. With long enough simulations and sufficiently accurate force fields, molecular dynamics (MD) simulations should in principle allow such refinement, but efforts to refine homology models using MD have for the most part yielded disappointing results. It has thus far been unclear whether MD-based refinement is limited primarily by accessible simulation timescales, force field accuracy, or both. Here, we examine MD as a technique for homology model refinement using all-atom simulations, each at least 100 μs long-more than 100 times longer than previous refinement simulations-and a physics-based force field that was recently shown to successfully fold a structurally diverse set of fast-folding proteins. In MD simulations of 24 proteins chosen from the refinement category of recent Critical Assessment of Structure Prediction (CASP) experiments, we find that in most cases, simulations initiated from homology models drift away from the native structure. Comparison with simulations initiated from the native structure suggests that force field accuracy is the primary factor limiting MD-based refinement. This problem can be mitigated to some extent by restricting sampling to the neighborhood of the initial model, leading to structural improvement that, while limited, is roughly comparable to the leading alternative methods.

  1. A tetraphenylethylene core-based 3D structure small molecular acceptor enabling efficient non-fullerene organic solar cells.

    Science.gov (United States)

    Liu, Yuhang; Mu, Cheng; Jiang, Kui; Zhao, Jingbo; Li, Yunke; Zhang, Lu; Li, Zhengke; Lai, Joshua Yuk Lin; Hu, Huawei; Ma, Tingxuan; Hu, Rongrong; Yu, Demei; Huang, Xuhui; Tang, Ben Zhong; Yan, He

    2015-02-01

    A tetraphenylethylene core-based small molecular acceptor with a unique 3D molecular structure is developed. Bulk-heterojunction blend films with a small feature size (≈20 nm) are obtained, which lead to non-fullerene organic solar cells (OSCs) with 5.5% power conversion efficiency. The work provides a new molecular design approach to efficient non-fullerene OSCs based on 3D-structured small-molecule acceptors.

  2. Construction of a novel coarse grain model for simulations of HIV capsid assembly to capture the backbone structure and inter-domain motions in solution

    Directory of Open Access Journals (Sweden)

    Xin Qiao

    2015-12-01

    Full Text Available We show the construction of a novel coarse grain model for simulations of HIV capsid assembly based on four structural models of HIV capsid proteins: isolated hexamer 3H47.pdb, tubular assembly 3J34.pdb, isolated pentamer 3P05.pdb and C-terminus dimer 2KOD.pdb. The data demonstrates the derivation of inter-domain motions from all atom Molecular Dynamics simulations and comparison with the motions derived from the analysis of solution NMR results defined in 2M8L.pdb. Snapshots from a representative Monte Carlo simulation with 128 dimeric subunit proteins based on 3J34.pdb are shown in addition to the quantitative analysis of its assembly pathway. Movies of the assembly process are compiled with snapshots of representative simulations of four structural models. The methods and data in this article were utilized in Qiao et al. (in press [1] to probe the mechanism of polymorphism and curvature control of HIV capsid assembly.

  3. Fine- and hyperfine-structure effects in molecular photoionization: II. Resonance-enhanced multiphoton ionization and hyperfine-selective generation of molecular cations

    CERN Document Server

    Germann, Matthias

    2016-01-01

    Resonance-enhanced multiphoton ionization (REMPI) is a widely used technique for studying molecular photoionization and producing molecular cations for spectroscopy and dynamics studies. Here, we present a model for describing hyperfine-structure effects in the REMPI process and for predicting hyperfine populations in molecular ions produced by this method. This model is a generalization of our model for fine- and hyperfine- structure effects in one-photon ionization of molecules presented in the preceding companion article. This generalization is achieved by covering two main aspects: (1) treatment of the neutral bound-bound transition including hyperfine structure that makes up the first step of the REMPI process and (2) modification of our ionization model to account for anisotropic populations resulting from this first excitation step. Our findings may be used for analyzing results from experiments with molecular ions produced by REMPI and may serve as a theoretical background for hyperfine-selective ioni...

  4. Molecular structure and spectral (FT-IR, Raman) investigations of 3-aminocoumarin

    Science.gov (United States)

    Dereli, Ömer

    2016-05-01

    The molecular structure of 3-Aminocoumarin was determined by conformational analysis. Conformational space was scanned by conformer distribution option of Spartan 08 program package using Merck Molecular Force Field (MMFF) method. Then obtained conformers were optimized by B3LYP/6-311++ G( d, p) and B3LYP/6-311 G( d, p) levels of Density Functional Theory. As a result of these calculations, only one conformer was determined. Vibrational frequencies of this conformer were calculated by Gaussian 03 program package using the same levels of geometry optimizations. The FT-IR and Raman spectra of 3-Aminocoumarin were recorded and compared with the calculated values. Consequently, a good agreement between experimental and the calculated values were founded. Molecular electrostatic potentials (MEPs), HOMO-LUMO energies, thermodynamic properties and Mulliken atomic charges were also covered in this study.

  5. Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.

    Science.gov (United States)

    Koromyslova, Anna D; Chugunov, Anton O; Efremov, Roman G

    2014-04-28

    Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them--protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.

  6. Changes of carbohydrates and molecular structure of dextrins during enzymatic liquefaction of starch

    Energy Technology Data Exchange (ETDEWEB)

    Nebesny, E. (Dept. of Food Technology, Technical Univ. Lodz (Poland))

    1992-10-01

    Investigations of potato starch hydrolysis during bacterial [alpha]-amylase 'Amylogal CS' liquefaction to a different dextrose equivalent were carried out at 85deg C and pH 6,5. DE-values, carbohydrate compositions and molecular structure of dextrins were investigated in starch hydrolyzate samples taken at DE-values from 3,4 to 20,6. In the progress of liquefaction, that is at increasing DE-values, changes in carbohydrate compositions, and there the decrease only of maltoheptaose and dextrins content in hydrolyzate were observed. Simultaneously, it was found that molecular weight and number of dextrin branchings decreased particularly rapidly to a significant degree of nearly 3,4 DE. At further increase of DE-value during starch liquefaction the decrease of dextrins molecular weight and the number of branchings was lower and not that significant. (orig.).

  7. Molecular early main group metal hydrides: synthetic challenge, structures and applications.

    Science.gov (United States)

    Harder, Sjoerd

    2012-11-25

    Within the general area of early main group metal chemistry, the controlled synthesis of well-defined metal hydride complexes is a rapidly developing research field. As group 1 and 2 metal complexes are generally highly dynamic and lattice energies for their [MH](∞) and [MH(2)](∞) salts are high, the synthesis of well-defined soluble hydride complexes is an obvious challenge. Access to molecular early main group metal hydrides, however, is rewarding: these hydrocarbon-soluble metal hydrides are highly reactive, have found use in early main group metal catalysis and are potentially also valuable molecular model systems for polar metal hydrides as a hydrogen storage material. The article focusses specifically on alkali and alkaline-earth metal hydride complexes and discusses the synthetic challenge, molecular structures, reactivity and applications.

  8. Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

    Energy Technology Data Exchange (ETDEWEB)

    Sidhu, Navdeep S. [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Schreiber, Kathrin [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); Pröpper, Kevin [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Becker, Stefan [Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany); Usón, Isabel [Instituto de Biologia Molecular de Barcelona (IBMB–CSIC), Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); Sheldrick, George M. [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Gärtner, Jutta; Krätzner, Ralph, E-mail: rkraetz@gwdg.de; Steinfeld, Robert, E-mail: rkraetz@gwdg.de [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany)

    2014-05-01

    Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.

  9. Molecular dynamics simulation of the structure and dynamics of 5-HT3 serotonin receptor

    Science.gov (United States)

    Antonov, M. Yu.; Popinako, A. V.; Prokopiev, G. A.

    2016-10-01

    In this work, we investigated structure, dynamics and ion transportation in transmembrane domain of the 5-HT3 serotonin receptor. High-resolution (0.35 nm) structure of the 5-HT3 receptor in complex with stabilizing nanobodies was determined by protein crystallography in 2014 (Protein data bank (PDB) code 4PIR). Transmembrane domain of the structure was prepared in complex with explicit membrane environment (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC)) and solvent (TIP3P water model). Molecular dynamics protocols for simulation and stabilization of the transmembrane domain of the 5-HT3 receptor model were developed and 60 ns simulation of the structure was conducted in order to explore structural parameters of the system. We estimated the mean force profile for Na+ ions using umbrella sampling method.

  10. Correlation between Molecular Structures and Relative Electrophoretic Mobility in Capillary Electrophoresis: Alkylpyridines

    Institute of Scientific and Technical Information of China (English)

    YAO, Xiao-Jun; FAN, Bo-Tao; DOUCET, J. P.; PANAYE, A.; LIU, Man-Cang; ZHANG, Rui-Sheng; HU, Zhi-De

    2003-01-01

    The quantitative relationship between relative electrophoretic mobility in capillary electrophoresis for a series of 31 closely related alkylpyridines and their molecular structures was studied by using CODESSA. According to the t-test on the results, we found that the three most important descriptors affecting the mobility are the relative number of rings (NR), Min e-n attraction for a C-N bond (MEN) and average complementary information index (ACIC). With these structure descriptors a good three-parameter linear model was developed to correlate the mobility of these compounds with their structures. This model can not only correctly predict the migration behavior of these compounds, but also find the structural factors which are responsible for the migration behavior of these compounds,thus can help to explain the separation mechanism of these compounds. The method used in this work can also be extended to the mobility-structure relationship research of other compounds.

  11. DFT study of the molecular and crystal structure and vibrational analysis of cisplatin

    Science.gov (United States)

    Georgieva, I.; Trendafilova, N.; Dodoff, N.; Kovacheva, D.

    2017-04-01

    DFT and periodic-DFT (PAW-PBE method, code VASP) calculations have been performed to study the structural and vibrational characteristics of cis-diamminedichloroplatinum(II) (cisplatin) at molecular and outside molecular level. To estimate the effect of the intermolecular interactions in crystal on the structural and vibrational properties of cisplatin, three theoretical models are considered in the present study: monomer (isolated molecule), hydrogen bonded dimer and periodic solid state structures. The work focused on the role of the theoretical models for correct modeling and prediction of geometrical and vibrational parameters of cisplatin. It has been found that the elaborate three-dimensional intermolecular hydrogen bonding network in the crystalline cisplatin significantly influences the structural and vibrational pattern of cisplatin and therefore the isolated cisplatin molecule is not the correct computational model regardless of the theoretical level used. To account for the whole intermolecular hydrogen bonding network in direction of both a and c axis and for more reliable calculations of structural and vibrational parameters periodic DFT calculations were carried out in the full crystalline periodic environment with the known lattice parameters for each cisplatin polymorph phase. The model calculations performed both at molecular level and for the periodic structures of alpha and beta cisplatin polymorph forms revealed the decisive role of the extended theoretical model for reliable prediction of the structural and vibrational characteristics of cisplatin. The powder diffraction pattern and the calculated IR and Raman spectra predicted beta polymorph form of our cisplatin sample freshly synthesized for the purposes of the present study using the Dhara's method. The various rotamers realized in the polymorph forms of cisplatin were explained by the low population of the large number of rotamers in solution as well as with the high rotamer

  12. Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair

    Science.gov (United States)

    Zhang, Yuchen; Alsop, Richard J.; Soomro, Asfia; Yang, Fei-Chi

    2015-01-01

    The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3–90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers. PMID:26557428

  13. Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair.

    Science.gov (United States)

    Zhang, Yuchen; Alsop, Richard J; Soomro, Asfia; Yang, Fei-Chi; Rheinstädter, Maikel C

    2015-01-01

    The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3-90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.

  14. Photophysical and electrochemical properties, and molecular structures of organic dyes for dye-sensitized solar cells.

    Science.gov (United States)

    Ooyama, Yousuke; Harima, Yutaka

    2012-12-21

    Dye-sensitized solar cells (DSSCs) based on organic dyes adsorbed on oxide semiconductor electrodes, such as TiO(2), ZnO, or NiO, which have emerged as a new generation of sustainable photovoltaic devices, have attracted much attention from chemists, physicists, and engineers because of enormous scientific interest in not only their construction and operational principles, but also in their high incident-solar-light-to-electricity conversion efficiency and low cost of production. To develop high-performance DSSCs, it is important to create efficient organic dye sensitizers, which should be optimized for the photophysical and electrochemical properties of the dyes themselves, with molecular structures that provide good light-harvesting features, good electron communication between the dye and semiconductor electrode and between the dye and electrolyte, and to control the molecular orientation and arrangement of the dyes on a semiconductor surface. The aim of this Review is not to make a list of a number of organic dye sensitizers developed so far, but to provide a new direction in the epoch-making molecular design of organic dyes for high photovoltaic performance and long-term stability of DSSCs, based on the accumulated knowledge of their photophysical and electrochemical properties, and molecular structures of the organic dye sensitizers developed so far.

  15. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of mannitol.

    Science.gov (United States)

    Moorthi, P P; Gunasekaran, S; Swaminathan, S; Ramkumaar, G R

    2015-02-25

    A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of mannitol. The FT-IR and FT-Raman spectra of mannitol were recorded in the solid phase. The molecular geometry, vibrational frequencies, thermodynamic functions and atomic charges of mannitol in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking cc-pVDZ basis set. The complete vibrational assignments were performed on the basis of Total Energy Distribution (TED) of the vibrational modes. The UV absorption spectra of the title compound dissolved in water. Natural bond orbital analysis has been carried out to explain the charge transfer or delocalization of charge due to the intra-molecular interactions. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO methods. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of mannitol are calculated using B3LYP/cc-pVDZ and HF/cc-pVDZ methods on the finite-field approach. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP) have been investigated using theoretical calculations, the calculated HOMO and LUMO energies shows that the charge transfer within the molecule.

  16. Raman spectroscopy as an advanced structural nanoprobe for conjugated molecular semiconductors

    Science.gov (United States)

    Wood, Sebastian; Razzell Hollis, Joseph; Kim, Ji-Seon

    2017-02-01

    Raman spectroscopy has emerged as a powerful and important characterisation tool for probing molecular semiconducting materials. The useful optoelectronic properties of these materials arise from the delocalised π-electron density in the conjugated core of the molecule, which also results in large Raman scattering cross-sections and a strong coupling between its electronic states and vibrational modes. For this reason, Raman spectroscopy offers a unique insight into the properties of molecular semiconductors, including: chemical structure, molecular conformation, molecular orientation, and fundamental photo- and electro-chemical processes—all of which are critically important to the performance of a wide range of optical and electronic organic semiconductor devices. Experimentally, Raman spectroscopy is non-intrusive, non-destructive, and requires no special sample preparation, and so is suitable for a wide range of in situ measurements, which are particularly relevant to issues of thermal and photochemical stability. Here we review the development of the family of Raman spectroscopic techniques, which have been applied to the study of conjugated molecular semiconductors. We consider the suitability of each technique for particular circumstances, and the unique insights it can offer, with a particular focus on the significance of these measurements for the continuing development of stable, high performance organic electronic devices.

  17. Neutron Capture Nucleosynthesis

    CERN Document Server

    Kiss, Miklos

    2016-01-01

    Heavy elements (beyond iron) are formed in neutron capture nucleosynthesis processes. We have proposed a simple unified model to investigate the neutron capture nucleosynthesis in arbitrary neutron density environment. We have also investigated what neutron density is required to reproduce the measured abundance of nuclei assuming equilibrium processes. We found both of these that the medium neutron density has a particularly important role at neutron capture nucleosynthesis. About these results most of the nuclei can formed at medium neutron capture density environment e.g. in some kind of AGB stars. Besides these observations our model is capable to use educational purpose.

  18. Basic Research Needs for Carbon Capture: Beyond 2020

    Energy Technology Data Exchange (ETDEWEB)

    Alivisatos, Paul [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Buchanan, Michelle [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2010-03-04

    these technologies. Workshop attendees were then given the charge to identify high-priority basic research directions that could provide revolutionary new concepts to form the basis for separation technologies in 2020 and beyond. The participants were divided into three major panels corresponding to different approaches for separating gases to reduce carbon emissions—liquid absorption, solid adsorption, and membrane separations. Two other panels were instructed to attend each of these three technology panels to assess crosscutting issues relevant to characterization and computation. At the end of the workshop, a final plenary session was convened to summarize the most critical research needs identified by the workshop attendees in each of the three major technical panels and from the two cross-cutting panels. The reports of the three technical panels included a set of high level Priority Research Directions meant to serve as inspiration to researchers in multiple disciplines—materials science, chemistry, biology, computational science, engineering, and others—to address the huge scientific challenges facing this nation and the world as we seek technologies for large-scale carbon capture beyond 2020. These Priority Research Directions were clustered around three main areas, all tightly coupled: Understand and control the dynamic atomic-level and molecular-level interactions of the targeted species with the separation media. Discover and design new materials that incorporate designed structures and functionalities tuned for optimum separation properties. Tailor capture/release processes with alternative driving forces, taking advantage of a new generation of materials. In each of the technical panels, the participants identified two major crosscutting research themes. The first was the development of new analytical tools that can characterize materials structure and molecular processes across broad spatial and temporal scales and under realistic conditions that

  19. Capturing RNA-dependent pathways for cryo-EM analysis

    Directory of Open Access Journals (Sweden)

    Deborah F Kelly

    2012-04-01

    Full Text Available Cryo-Electron Microscopy (EM is a powerful technique to visualize biological processes at nanometer resolution. Structural studies of macromolecular assemblies are typically performed on individual complexes that are biochemically isolated from their cellular context. Here we present a molecular imaging platform to capture and view multiple components of cellular pathways within a functionally relevant framework. We utilized the bacterial protein synthesis machinery as a model system to develop our approach. By using modified Affinity Grid surfaces, we were able to recruit multiple protein assemblies bound to nascent strands of mRNA. The combined use of Affinity Capture technology and single particle electron microscopy provide the basis for visualizing RNA-dependent pathways in a remarkable new way.

  20. Validity boundary of orbital-free molecular dynamics method corresponding to thermal ionization of shell structure

    Science.gov (United States)

    Gao, Chang; Zhang, Shen; Kang, Wei; Wang, Cong; Zhang, Ping; He, X. T.

    2016-11-01

    With 6LiD as an example, we show that the applicable region of the orbital-free molecular dynamics (OFMD) method in a large temperature range is determined by the thermal ionization process of bound electrons in shell structures. The validity boundary of the OFMD method is defined roughly by the balance point of the average thermal energy of an electron and the ionization energy of the lowest localized electronic state. This theoretical proposition is based on the observation that the deviation of the OFMD method originates from its less accurate description to the charge density in partially ionized shells, as compared with the results of the extended first-principles molecular dynamics method, which well reproduces the charge density of shell structures.

  1. Regularizing the molecular potential in electronic structure calculations. II. Many-body methods

    Energy Technology Data Exchange (ETDEWEB)

    Bischoff, Florian A., E-mail: florian.bischoff@hu-berlin.de [Institut für Chemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin (Germany)

    2014-11-14

    In Paper I of this series [F. A. Bischoff, “Regularizing the molecular potential in electronic structure calculations. I. SCF methods,” J. Chem. Phys. 141, 184105 (2014)] a regularized molecular Hamilton operator for electronic structure calculations was derived and its properties in SCF calculations were studied. The regularization was achieved using a correlation factor that models the electron-nuclear cusp. In the present study we extend the regularization to correlated methods, in particular the exact solution of the two-electron problem, as well as second-order many body perturbation theory. The nuclear and electronic correlation factors lead to computations with a smaller memory footprint because the singularities are removed from the working equations, which allows coarser grid resolution while maintaining the precision. Numerical examples are given.

  2. A nitrogen-vacancy spin based molecular structure microscope using multiplexed projection reconstruction

    CERN Document Server

    Lazariev, Andrii

    2015-01-01

    Methods and techniques to measure and image beyond the state-of-the-art have always been influential in propelling basic science and technology. Because current technologies are venturing into nanoscopic and molecular-scale fabrication, atomic-scale measurement techniques are inevitable. One such emerging sensing method uses the spins associated with nitrogen-vacancy (NV) defects in diamond. The uniqueness of this NV sensor is its atomic size and ability to perform precision sensing under ambient conditions conveniently using light and microwaves (MW). These advantages have unique applications in nanoscale sensing and imaging of magnetic fields from nuclear spins in single biomolecules. During the last few years, several encouraging results have emerged towards the realization of an NV spin-based molecular structure microscope. Here, we present a projection-reconstruction method that retrieves the three-dimensional structure of a single molecule from the nuclear spin noise signatures. We validate this method ...

  3. Quantum chemistry study of molecular structure and vibrational spectrum of naproxen.

    Science.gov (United States)

    Liu, Lekun; Gao, Hongwei

    2012-02-01

    The purpose of this research was to compare the performance of different DFT methods at different basis sets in predicting geometry and vibrational spectrum of naproxen. The molecular structure and infrared spectrum of naproxen was studied. Quantum chemical calculations using density functional theory (DFT) with functions LSDA, B3LYP, B3PW91, BPV86, mPW1PW91 and PBEPBE at various basis set levels (LANL2DZ, SDD, 3-21G, 6-31G, 6-311G and STO-3G) were performed. The computed result indicates that LSDA/6-311G level is distinctly superior to all the remaining DFT methods in predicting molecular structure of naproxen. The vibrational spectral analysis indicates the LSDA/3-21G level and LSDA/6-311G level are both better than the other methods at all the remaining basis sets.

  4. Crystal and Molecular Structure of N-(Pyridin-2-yl- carbonyl)-2-ethoxycarbonyl-benzene sulfonamide

    Institute of Scientific and Technical Information of China (English)

    姜林; 李正名; 翁林红; 冷雪冰

    2002-01-01

    The crystal and molecular structures of the title compound (C15H14N2O5S, Mr = 334.34) were determined by X-ray diffraction. The crystal structure is of triclinic, space group P ī with a = 7.306(1), b = 7.933(1), c =14.146(2) ? , ( = 81.95, ( = 80.28, ( = 72.92°, V = 768.9(2) ?3, Z = 2, Dc = 1.444 g/cm3 , μ= 0.238mm-1, F(000) = 348, S = 1.033, the final R = 0.0453 and wR = 0.1181 for 2704 observed reflections with I >2((I). In the molecule there are three different planes. In each of them a conjugated system is formed. The intra-molecular hydrogen bond between N and H atoms was ascertained and a five-membered ring including hydrogen bond is formed.

  5. Molecular Weight and Proposed Structure of the Angelica sinensis Polysaccharide-iron Complex

    Institute of Scientific and Technical Information of China (English)

    WANG,Kai-Ping; CHEN,Zhi-Xiang; ZHANG,Yu; WANG,Pei-Pei; WANG,Ji-Hong; DAI,Li-Quan

    2008-01-01

    The molecular weight and the proposed structure of the Angelica sinensis polysaccharide-iron complex (APIC) were studied.Fourier transform infrared spectroscopy,X-ray powder diffraction,differential scanning calorimetry,transmission electron microscopy,electron paramagnetic resonance,thermogravimetric analysis,atomic force microscopy,and gel filtration chromatography were used to characterize APIC,which is a macromolecule complex composed of Angelica sinensis polysaccharide (ASP) and iron.The structure of APIC was proposed to be a polynuclear ferrihydrite core chelated firmly by an encircling framework of ASP chains,forming a core molecule,which is surrounded by a removable outer protective sheath of colloidal ASP.And the molecular formula of APIC was proposed to be { [(Fe2O3·2.2H2O)1043(ASP)32](ASP)12 },with MW=270000 Da.

  6. Analysis of the effect of core structure upon dineutron correlation using antisymmetrized molecular dynamics

    CERN Document Server

    Kobayashi, Fumiharu

    2015-01-01

    We extend the method of antisymmetrized molecular dynamics to investigate dineutron correlation. We apply this method to $^{10}$Be as an example and investigate the motion of two neutrons around a largely deformed $^8$Be core by analyzing the two-neutron overlap function around the core. We show that the core structure plays an important role in dineutron formation and expansion from the core and that the present framework is effective for the studies of dineutron correlation.

  7. Chemical descriptors, convexity and structure of density matrices in molecular systems

    CERN Document Server

    Bochicchio, Roberto C

    2015-01-01

    The electron energy and density matrices in molecular systems are convex in respect of the number of particles. So that, the chemical descriptors based on their derivatives present the hamper of discontinuities for isolated systems and consequently higher order derivatives are undefined. The introduction of the interaction between the physical domain with an environment induces a coherent structure for the density matrix in the grand-canonical formulation suppressing the discontinuities leading to the proper definitions of the descriptors.

  8. Molecular structure and polymorphism of a cyclohexanediol: trans-1,4-cyclohexanedimethanol

    OpenAIRE

    Rosado, Mário T. S.; Maria, Teresa M. R.; Castro, Ricardo A. E.; Canotilho, João; Silva, Manuela Ramos; Eusébio,M. Ermelinda S.

    2014-01-01

    This study aims to investigate the molecular structure and polymorphism of trans-1,4-cyclohexanedimethanol, including the bi-axial/bi-equatorial equilibrium and the nature of the intermolecular H-bond networks in condensed phases created by the hydroxyl group torsions. The full conformational space of the single molecule was explored by MP2 calculations, showing that the optimized bi-equatorial conformers have similar stability and the bi-axial ones have much higher energies. The ...

  9. Efficient 3D Kinetic Monte Carlo Method for Modeling of Molecular Structure and Dynamics

    DEFF Research Database (Denmark)

    Panshenskov, Mikhail; Solov'yov, Ilia; Solov'yov, Andrey V.

    2014-01-01

    Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with...... the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system....

  10. The Research Progress of CO2 Capture with Ionic Liquids

    Institute of Scientific and Technical Information of China (English)

    赵志军; 董海峰; 张香平

    2012-01-01

    Due to their negligible volatility, reasonable thermal stability, strong dissolubility, wide liquid range and tunability of structure and property, ionic liquids have been regarded as emerging candidate reagents for CO2 cap- ture from industries gases. In this review, the research progresses in CO2 capture using conventional ionic liquids,functionalized ionic liquids, supported ionic-liquids membranes, polymerized ionic liquids and mixtures of ionic liquids with some molecular solvents were investigated and reviewed. Discussion of relevant research fields was presented and the future developments were suggested.

  11. Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding.

    Directory of Open Access Journals (Sweden)

    Alessandro Marchiori

    Full Text Available Bitter molecules in humans are detected by ∼25 G protein-coupled receptors (GPCRs. The lack of atomic resolution structure for any of them is complicating an in depth understanding of the molecular mechanisms underlying bitter taste perception. Here, we investigate the molecular determinants of the interaction of the TAS2R38 bitter taste receptor with its agonists phenylthiocarbamide (PTC and propylthiouracil (PROP. We use the recently developed hybrid Molecular Mechanics/Coarse Grained (MM/CG method tailored specifically for GPCRs. The method, through an extensive exploration of the conformational space in the binding pocket, allows the identification of several residues important for agonist binding that would have been very difficult to capture from the standard bioinformatics/docking approach. Our calculations suggest that both agonists bind to Asn103, Phe197, Phe264 and Trp201, whilst they do not interact with the so-called extra cellular loop 2, involved in cis-retinal binding in the GPCR rhodopsin. These predictions are consistent with data sets based on more than 20 site-directed mutagenesis and functional calcium imaging experiments of TAS2R38. The method could be readily used for other GPCRs for which experimental information is currently lacking.

  12. Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding.

    Science.gov (United States)

    Marchiori, Alessandro; Capece, Luciana; Giorgetti, Alejandro; Gasparini, Paolo; Behrens, Maik; Carloni, Paolo; Meyerhof, Wolfgang

    2013-01-01

    Bitter molecules in humans are detected by ∼25 G protein-coupled receptors (GPCRs). The lack of atomic resolution structure for any of them is complicating an in depth understanding of the molecular mechanisms underlying bitter taste perception. Here, we investigate the molecular determinants of the interaction of the TAS2R38 bitter taste receptor with its agonists phenylthiocarbamide (PTC) and propylthiouracil (PROP). We use the recently developed hybrid Molecular Mechanics/Coarse Grained (MM/CG) method tailored specifically for GPCRs. The method, through an extensive exploration of the conformational space in the binding pocket, allows the identification of several residues important for agonist binding that would have been very difficult to capture from the standard bioinformatics/docking approach. Our calculations suggest that both agonists bind to Asn103, Phe197, Phe264 and Trp201, whilst they do not interact with the so-called extra cellular loop 2, involved in cis-retinal binding in the GPCR rhodopsin. These predictions are consistent with data sets based on more than 20 site-directed mutagenesis and functional calcium imaging experiments of TAS2R38. The method could be readily used for other GPCRs for which experimental information is currently lacking.

  13. Molecular Modeling of the Three-Dimensional Structure of Human Sphingomyelin Synthase%Molecular Modeling of the Three-Dimensional Structure of Human Sphingomyelin Synthase

    Institute of Scientific and Technical Information of China (English)

    张亚; 林赋; 邓晓东; 王任小; 叶德泳

    2011-01-01

    Sphingomyelin synthase (SMS) produces sphingomyelin and diacylglycerol from ceramide and phosphatidyl- choline. It plays an important role in cell survival and apoptosis, inflammation, and lipid homeostasis, and therefore has been noticed in recent years as a novel potential drug target. In this study, we combined homology modeling, molecular docking, molecular dynamics simulation, and normal mode analysis to derive a three-dimensional struc- ture of human sphingomyelin synthase (hSMS 1) in complex with sphingomyelin. Our model provides a reasonable explanation on the catalytic mechanism of hSMS 1. It can also explain the high selectivity of hSMS 1 towards phos- phocholine and sphingomyelin as well as some other known experimental results about hSMS1. Moreover, we also derived a complex model of D609, the only known small-molecule inhibitor of hSMS 1 so far. Our hSMS 1 model may serve as a reasonable structural basis for the discovery of more effective small-molecule inhibitors of hSMS 1.

  14. A nitrogen-vacancy spin based molecular structure microscope using multiplexed projection reconstruction

    Science.gov (United States)

    Lazariev, Andrii; Balasubramanian, Gopalakrishnan

    2015-01-01

    Methods and techniques to measure and image beyond the state-of-the-art have always been influential in propelling basic science and technology. Because current technologies are venturing into nanoscopic and molecular-scale fabrication, atomic-scale measurement techniques are inevitable. One such emerging sensing method uses the spins associated with nitrogen-vacancy (NV) defects in diamond. The uniqueness of this NV sensor is its atomic size and ability to perform precision sensing under ambient conditions conveniently using light and microwaves (MW). These advantages have unique applications in nanoscale sensing and imaging of magnetic fields from nuclear spins in single biomolecules. During the last few years, several encouraging results have emerged towards the realization of an NV spin-based molecular structure microscope. Here, we present a projection-reconstruction method that retrieves the three-dimensional structure of a single molecule from the nuclear spin noise signatures. We validate this method using numerical simulations and reconstruct the structure of a molecular phantom β-cyclodextrin, revealing the characteristic toroidal shape. PMID:26370514

  15. A nitrogen-vacancy spin based molecular structure microscope using multiplexed projection reconstruction

    Science.gov (United States)

    Lazariev, Andrii; Balasubramanian, Gopalakrishnan

    2015-09-01

    Methods and techniques to measure and image beyond the state-of-the-art have always been influential in propelling basic science and technology. Because current technologies are venturing into nanoscopic and molecular-scale fabrication, atomic-scale measurement techniques are inevitable. One such emerging sensing method uses the spins associated with nitrogen-vacancy (NV) defects in diamond. The uniqueness of this NV sensor is its atomic size and ability to perform precision sensing under ambient conditions conveniently using light and microwaves (MW). These advantages have unique applications in nanoscale sensing and imaging of magnetic fields from nuclear spins in single biomolecules. During the last few years, several encouraging results have emerged towards the realization of an NV spin-based molecular structure microscope. Here, we present a projection-reconstruction method that retrieves the three-dimensional structure of a single molecule from the nuclear spin noise signatures. We validate this method using numerical simulations and reconstruct the structure of a molecular phantom β-cyclodextrin, revealing the characteristic toroidal shape.

  16. Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

    Directory of Open Access Journals (Sweden)

    Derek Mendez

    2016-11-01

    Full Text Available During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS, which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL is an excellent tool for CXS experiments. A protocol is outlined for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA. From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. It is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules.

  17. Effects of molecular structure on microscopic heat transport in chain polymer liquids

    Energy Technology Data Exchange (ETDEWEB)

    Matsubara, Hiroki, E-mail: matsubara@microheat.ifs.tohoku.ac.jp; Kikugawa, Gota; Ohara, Taku [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Bessho, Takeshi; Yamashita, Seiji [Higashifuji Technical Center, Toyota Motor Corporation, 1200 Mishuku, Susono, Shizuoka 410-1193 (Japan)

    2015-04-28

    In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T{sub c}) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

  18. The molecular clock of neutral evolution can be accelerated or slowed by asymmetric spatial structure.

    Science.gov (United States)

    Allen, Benjamin; Sample, Christine; Dementieva, Yulia; Medeiros, Ruben C; Paoletti, Christopher; Nowak, Martin A

    2015-02-01

    Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a "molecular clock" to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution.

  19. The molecular clock of neutral evolution can be accelerated or slowed by asymmetric spatial structure.

    Directory of Open Access Journals (Sweden)

    Benjamin Allen

    2015-02-01

    Full Text Available Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a "molecular clock" to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution.

  20. Capture ready study

    Energy Technology Data Exchange (ETDEWEB)

    Minchener, A.

    2007-07-15

    There are a large number of ways in which the capture of carbon as carbon dioxide (CO{sub 2}) can be integrated into fossil fuel power stations, most being applicable for both gas and coal feedstocks. To add to the choice of technology is the question of whether an existing plant should be retrofitted for capture, or whether it is more attractive to build totally new. This miscellany of choices adds considerably to the commercial risk of investing in a large power station. An intermediate stage between the non-capture and full capture state would be advantageous in helping to determine the best way forward and hence reduce those risks. In recent years the term 'carbon capture ready' or 'capture ready' has been coined to describe such an intermediate stage plant and is now widely used. However a detailed and all-encompassing definition of this term has never been published. All fossil fuel consuming plant produce a carbon dioxide gas byproduct. There is a possibility of scrubbing it with an appropriate CO{sub 2} solvent. Hence it could be said that all fossil fuel plant is in a condition for removal of its CO{sub 2} effluent and therefore already in a 'capture ready' state. Evidently, the practical reality of solvent scrubbing could cost more than the rewards offered by such as the ETS (European Trading Scheme). In which case, it can be said that although the possibility exists of capturing CO{sub 2}, it is not a commercially viable option and therefore the plant could not be described as ready for CO{sub 2} capture. The boundary between a capture ready and a non-capture ready condition using this definition cannot be determined in an objective and therefore universally acceptable way and criteria must be found which are less onerous and less potentially contentious to assess. 16 refs., 2 annexes.

  1. A molecular dynamics study on the structural and electronic properties of two-dimensional icosahedral B12 cluster based structures

    Science.gov (United States)

    Kah, Cherno Baba; Yu, M.; Jayanthi, C. S.; Wu, S. Y.

    2014-03-01

    Our previous study on one-dimensional icosahedral B12 cluster (α-B12) based chain [Bulletin of APS Annual Meeting, p265 (2013)] and ring structures has prompted us to study the two-dimensional (2D) α-B12 based structures. Recently, we have carried out a systematic molecular dynamics study on the structural stabilities and electronic properties of the 2D α-B12 based structures using the SCED-LCAO method [PRB 74, 15540 (2006)]. We have considered several types of symmetry for these 2D structures such as δ3, δ4, δ6 (flat triangular), and α' types. We have found that the optimized structures are energetically in the order of δ6 < α' < δ3 < δ4 which is different from the energy order of α'< δ6 < δ4 < δ3 found in the 2D boron monolayer sheets [ACS Nano 6, 7443 (2012)]. A detailed discussion of this study will be presented. The first author acknowledges the McSweeny Fellowship for supporting his research in this work.

  2. On the vibration of double-walled carbon nanotubes using molecular structural and cylindrical shell models

    Science.gov (United States)

    Ansari, R.; Rouhi, S.; Aryayi, M.

    2016-01-01

    The vibrational behavior of double-walled carbon nanotubes is studied by the use of the molecular structural and cylindrical shell models. The spring elements are employed to model the van der Waals interaction. The effects of different parameters such as geometry, chirality, atomic structure and end constraint on the vibration of nanotubes are investigated. Besides, the results of two aforementioned approaches are compared. It is indicated that by increasing the nanotube side length and radius, the computationally efficient cylindrical shell model gives rational results.

  3. Two-dimensional dynamics of a free molecular chain with a secondary structure

    DEFF Research Database (Denmark)

    Zolotaryuk, Alexander; Christiansen, Peter Leth; Savin, A.V.

    1996-01-01

    A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model...... of an anharmonic chain in order to include transverse degrees of freedom of the chain molecules. Both the structures are provided by the first- and second-neighbor intermolecular bonds, respectively, resulting in a regular zig-zag (''20 helix'') chain on a plane. The set of two coupled nonlinear field equations...

  4. Strain and structure in nano Ag films deposited on Au: Molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zientarski, Tomasz, E-mail: martom@dyzio.umcs.lublin.pl [Department for the Modelling of Physico-Chemical Processes, Maria Curie-Skłodowska University, ul. Gliniana 33, 20-614 Lublin (Poland); Chocyk, Dariusz [Department of Applied Physics, Lublin University of Technology, ul. Nadbystrzycka 38, 20-618 Lublin (Poland)

    2014-07-01

    Molecular dynamics simulations are applied to analyze the stress and structure of nano Ag thin films deposited on the Au substrate. The interactions in the system are described by the embedded atom method. The kinematical theory of scattering is employed to identify the structure obtained from simulations data. Results shows that the silver layers are adjusted to the crystalline lattice of the gold buffer layers, and during the deposition process only compressive stress is observed. In all the cases the distribution of stress does not depend on temperature.

  5. Molecular dynamics simulations of microscopic structure of ultra strong shock waves in dense helium

    Science.gov (United States)

    Liu, Hao; Kang, Wei; Zhang, Qi; Zhang, Yin; Duan, Huilin; He, X. T.

    2016-12-01

    Hydrodynamic properties and structure of strong shock waves in classical dense helium are simulated using non-equilibrium molecular dynamics methods. The shock speed in the simulation reaches 100 km/s and the Mach number is over 250, which are close to the parameters of shock waves in the implosion process of inertial confinement fusion. The simulations show that the high-Mach-number shock waves in dense media have notable differences from weak shock waves or those in dilute gases. These results will provide useful information on the implosion process, especially the structure of strong shock wave front, which remains an open question in hydrodynamic simulations.

  6. Molecular dynamics simulations of the structure evolutions of Cu-Zr metallic glasses under irradiation

    Science.gov (United States)

    Lang, Lin; Tian, Zean; Xiao, Shifang; Deng, Huiqiu; Ao, Bingyun; Chen, Piheng; Hu, Wangyu

    2017-02-01

    Molecular dynamics simulations have been performed to investigate the structural evolution of Cu64.5Zr35.5 metallic glasses under irradiation. The largest standard cluster analysis (LSCA) method was used to quantify the microstructure within the collision cascade regions. It is found that the majority of clusters within the collision cascade regions are full and defective icosahedrons. Not only the smaller structures (common neighbor subcluster) but also primary clusters greatly changed during the collision cascades; while most of these radiation damages self-recover quickly in the following quench states. These findings indicate the Cu-Zr metallic glasses have excellent irradiation-resistance properties.

  7. A new plug-in software architecture applied for a portable molecular structure browser.

    Science.gov (United States)

    Ueno, Y; Asai, K

    1997-01-01

    A new software configuration method using plug-in style components was established for the tool with the incremental development of software used in protein structural study. Our memory database provides the interface of data and functions among plug-in modules and its host program. A molecular structure browser program was developed together with several plug-in modules on our programming library that maintains graphics portability and user interfaces. This plug-in software architecture is generally useful for large-scale software development and for prototyping parts of the system.

  8. Molecular structure, function, and dynamics of clathrin-mediated membrane traffic.

    Science.gov (United States)

    Kirchhausen, Tom; Owen, David; Harrison, Stephen C

    2014-05-01

    Clathrin is a molecular scaffold for vesicular uptake of cargo at the plasma membrane, where its assembly into cage-like lattices underlies the clathrin-coated pits of classical endocytosis. This review describes the structures of clathrin, major cargo adaptors, and other proteins that participate in forming a clathrin-coated pit, loading its contents, pinching off the membrane as a lattice-enclosed vesicle, and recycling the components. It integrates as much of the structural information as possible at the time of writing into a sketch of the principal steps in coated-pit and coated-vesicle formation.

  9. Quantum chemistry the development of ab initio methods in molecular electronic structure theory

    CERN Document Server

    Schaefer III, Henry F

    2004-01-01

    This guide is guaranteed to prove of keen interest to the broad spectrum of experimental chemists who use electronic structure theory to assist in the interpretation of their laboratory findings. A list of 150 landmark papers in ab initio molecular electronic structure methods, it features the first page of each paper (which usually encompasses the abstract and introduction). Its primary focus is methodology, rather than the examination of particular chemical problems, and the selected papers either present new and important methods or illustrate the effectiveness of existing methods in predi

  10. The structural molecular biology network of the State of São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    João A.R.G. Barbosa

    2006-06-01

    Full Text Available This article describes the achievements of the Structural Molecular Biology Network (SMolBNet, a collaborative program of structural molecular biology, centered in the State of São Paulo, Brazil, and supported by São Paulo State Funding Agency (FAPESP. It gathers twenty scientific groups and is coordinated by the scientific staff of the Center of Structural Molecular Biology, at the National Laboratory of Synchrotron Light (LNLS, in Campinas. The SMolBNet program has been aimed at 1 solving the structure of proteins of interest related to the research projects of the groups. In some cases, the choice has been to select proteins of unknown function or of possible novel structure obtained from the sequenced genomes of the FAPESP genomic program; 2 providing the groups with training in all the steps of the protein structure determination: gene cloning, protein expression, protein purification, protein crystallization and structure determination. Having begun in 2001, the program has been successful in both aims. Here, four groups reveal their participation in the program and describe the structural aspects of the proteins they have selected to study.Esse artigo descreve realizações do Programa SMolBNet (Rede de Biologia Molecular Estrutural do Estado de São Paulo, apoiado pela FAPESP (Fundação de Apoio à Pesquisa do Estado de São Paulo. Ele reúne vinte grupos de pesquisa e é coordenado pelos pesquisadores do Laboratório Nacional de Luz Síncrotron (LNLS, em Campinas. O Programa SMolBNet tem como metas: Elucidar a estrutura tridimensional de proteínas de interesse aos grupos de pesquisa componentes do Programa; Prover os grupos com treinamento em todas as etapas de determinação de estrutura: clonagem gênica, expressão de proteínas, purificação de proteínas, cristalização de proteínas e elucidação de suas estruturas. Tendo começado em 2001, o Programa alcançou sucesso em ambas as metas. Neste artigo, quatro dos grupos

  11. Structures of pattern recognition receptors reveal molecular mechanisms of autoinhibition, ligand recognition and oligomerization.

    Science.gov (United States)

    Chuenchor, Watchalee; Jin, Tengchuan; Ravilious, Geoffrey; Xiao, T Sam

    2014-02-01

    Pattern recognition receptors (PRRs) are essential sentinels for pathogens or tissue damage and integral components of the innate immune system. Recent structural studies have provided unprecedented insights into the molecular mechanisms of ligand recognition and signal transduction by several PRR families at distinct subcellular compartments. Here we highlight some of the recent discoveries and summarize the common themes that are emerging from these exciting studies. Better mechanistic understanding of the structure and function of the PRRs will improve future prospects of therapeutic targeting of these important innate immune receptors.

  12. The impact of ligands on the structure and flexibility of sulfotransferases: a molecular dynamics simulation study.

    Science.gov (United States)

    Zhao, Li; Zhang, Pupu; Long, Shiyang; Wang, Linlin; Tian, Pu

    2015-08-01

    Sulfotransferases catalyze transfer of the sulfuryl-group (-SO3) from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to a large number of substrates. They play an important role in phase II metabolic process. The impact of the cofactor (PAPS) on the structure and flexibility of the enzyme has been studied extensively, and the response of the active-cap region to cofactor binding was proposed as the molecular basis for substrate selectivity. In this study, individual and cooperative effects of the cofactor and substrate on the structure and flexibility of the enzyme were investigated. Molecular dynamics simulations were performed for four systems, including free enzyme, binary complexes (cofactor or substrate bound enzyme) and ternary complex (both cofactor and substrate bound enzyme). The influence of ligands (the cofactor and the substrate) on the structure and flexibility of the enzyme, especially that of the active-site cap region, was analyzed. Moreover, mutual structural impact of the ligands was examined as well. The results show that the impact of both the cofactor and the substrate was significant. Our study indicated that the substrate, such as lithocholic acid (LCA), participated in regulating the structure and flexibility of the enzyme actively rather than merely being selected passively. Additionally, the observed synergistic effects of the cofactor and the substrate demonstrated the importance of examining both ligands in understanding enzymes.

  13. Structure and functional features of olive pollen pectin methylesterase using homology modeling and molecular docking methods.

    Science.gov (United States)

    Jimenez-Lopez, Jose C; Kotchoni, Simeon O; Rodríguez-García, María I; Alché, Juan D

    2012-12-01

    Pectin methylesterases (PMEs), a multigene family of proteins with multiple differentially regulated isoforms, are key enzymes implicated in the carbohydrates (pectin) metabolism of cell walls. Olive pollen PME has been identified as a new allergen (Ole e 11) of potential relevance in allergy amelioration, since it exhibits high prevalence among atopic patients. In this work, the structural and functional characterization of two olive pollen PME isoforms and their comparison with other PME plants was performed by using different approaches: (1) the physicochemical properties and functional-regulatory motifs characterization, (2) primary sequence analysis, 2D and 3D comparative structural features study, (3) conservation and evolutionary analysis, (4) catalytic activity and regulation based on molecular docking analysis of a homologue PME inhibitor, and (5) B-cell epitopes prediction by sequence and structural based methods and protein-protein interaction tools, while T-cell epitopes by inhibitory concentration and binding score methods. Our results indicate that the structural differences and low conservation of residues, together with differences in physicochemical and posttranslational motifs might be a mechanism for PME isovariants generation, regulation, and differential surface epitopes generation. Olive PMEs perform a processive catalytic mechanism, and a differential molecular interaction with specific PME inhibitor, opening new possibilities for PME activity regulation. Despite the common function of PMEs, differential features found in this study will lead to a better understanding of the structural and functional characterization of plant PMEs and help to improve the component-resolving diagnosis and immunotherapy of olive pollen allergy by epitopes identification.

  14. Advanced Structural Determination of Diterpene Esters Using Molecular Modeling and NMR Spectroscopy.

    Science.gov (United States)

    Nothias-Scaglia, Louis-Félix; Gallard, Jean-François; Dumontet, Vincent; Roussi, Fanny; Costa, Jean; Iorga, Bogdan I; Paolini, Julien; Litaudon, Marc

    2015-10-23

    Three new jatrophane esters (1-3) were isolated from Euphorbia amygdaloides ssp. semiperfoliata, including an unprecedented macrocyclic jatrophane ester bearing a hemiketal substructure, named jatrohemiketal (3). The chemical structures of compounds 1-3 and their relative configurations were determined by spectroscopic analysis. The absolute configuration of compound 3 was determined unambiguously through an original strategy combining NMR spectroscopy and molecular modeling. Conformational search calculations were performed for the four possible diastereomers 3a-3d differing in their C-6 and C-9 stereocenters, and the lowest energy conformer was used as input structure for geometry optimization. The prediction of NMR parameters ((1)H and (13)C chemical shifts and (1)H-(1)H coupling constants) by density functional theory (DFT) calculations allowed identifying the most plausible diastereomer. Finally, the stereostructure of 3 was solved by comparison of the structural features obtained by molecular modeling for 3a-3d with NMR-derived data (the values of dihedral angles deduced from the vicinal proton-proton coupling constants ((3)JHH) and interproton distances determined by ROESY). The methodology described herein provides an efficient way to solve or confirm structural elucidation of new macrocyclic diterpene esters, in particular when no crystal structure is available.

  15. Molecular basis of classic galactosemia from the structure of human galactose 1-phosphate uridylyltransferase

    Science.gov (United States)

    McCorvie, Thomas J.; Kopec, Jolanta; Pey, Angel L.; Fitzpatrick, Fiona; Patel, Dipali; Chalk, Rod; Shrestha, Leela; Yue, Wyatt W.

    2016-01-01

    Classic galactosemia is a potentially lethal disease caused by the dysfunction of galactose 1-phosphate uridylyltransferase (GALT). Over 300 disease-associated GALT mutations have been reported, with the majority being missense changes, although a better understanding of their underlying molecular effects has been hindered by the lack of structural information for the human enzyme. Here, we present the 1.9 Å resolution crystal structure of human GALT (hGALT) ternary complex, revealing a homodimer arrangement that contains a covalent uridylylated intermediate and glucose-1-phosphate in the active site, as well as a structural zinc-binding site, per monomer. hGALT reveals significant structural differences from bacterial GALT homologues in metal ligation and dimer interactions, and therefore is a zbetter model for understanding the molecular consequences of disease mutations. Both uridylylation and zinc binding influence the stability and aggregation tendency of hGALT. This has implications for disease-associated variants where p.Gln188Arg, the most commonly detected, increases the rate of aggregation in the absence of zinc likely due to its reduced ability to form the uridylylated intermediate. As such our structure serves as a template in the future design of pharmacological chaperone therapies and opens new concepts about the roles of metal binding and activity in protein misfolding by disease-associated mutants. PMID:27005423

  16. Molecular basis of classic galactosemia from the structure of human galactose 1-phosphate uridylyltransferase.

    Science.gov (United States)

    McCorvie, Thomas J; Kopec, Jolanta; Pey, Angel L; Fitzpatrick, Fiona; Patel, Dipali; Chalk, Rod; Shrestha, Leela; Yue, Wyatt W

    2016-06-01

    Classic galactosemia is a potentially lethal disease caused by the dysfunction of galactose 1-phosphate uridylyltransferase (GALT). Over 300 disease-associated GALT mutations have been reported, with the majority being missense changes, although a better understanding of their underlying molecular effects has been hindered by the lack of structural information for the human enzyme. Here, we present the 1.9 Å resolution crystal structure of human GALT (hGALT) ternary complex, revealing a homodimer arrangement that contains a covalent uridylylated intermediate and glucose-1-phosphate in the active site, as well as a structural zinc-binding site, per monomer. hGALT reveals significant structural differences from bacterial GALT homologues in metal ligation and dimer interactions, and therefore is a zbetter model for understanding the molecular consequences of disease mutations. Both uridylylation and zinc binding influence the stability and aggregation tendency of hGALT. This has implications for disease-associated variants where p.Gln188Arg, the most commonly detected, increases the rate of aggregation in the absence of zinc likely due to its reduced ability to form the uridylylated intermediate. As such our structure serves as a template in the future design of pharmacological chaperone therapies and opens new concepts about the roles of metal binding and activity in protein misfolding by disease-associated mutants.

  17. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

    Science.gov (United States)

    Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

    2016-05-01

    Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.

  18. Coexisting Honeycomb and Kagome Characteristics in the Electronic Band Structure of Molecular Graphene.

    Science.gov (United States)

    Paavilainen, Sami; Ropo, Matti; Nieminen, Jouko; Akola, Jaakko; Räsänen, Esa

    2016-06-08

    We uncover the electronic structure of molecular graphene produced by adsorbed CO molecules on a copper (111) surface by means of first-principles calculations. Our results show that the band structure is fundamentally different from that of conventional graphene, and the unique features of the electronic states arise from coexisting honeycomb and Kagome symmetries. Furthermore, the Dirac cone does not appear at the K-point but at the Γ-point in the reciprocal space and is accompanied by a third, almost flat band. Calculations of the surface structure with Kekulé distortion show a gap opening at the Dirac point in agreement with experiments. Simple tight-binding models are used to support the first-principles results and to explain the physical characteristics behind the electronic band structures.

  19. Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations.

    Science.gov (United States)

    Yang, Kecheng; Różycki, Bartosz; Cui, Fengchao; Shi, Ce; Chen, Wenduo; Li, Yunqi

    2016-01-01

    Sampling enrichment toward a target state, an analogue of the improvement of sampling efficiency (SE), is critical in both the refinement of protein structures and the generation of near-native structure ensembles for the exploration of structure-function relationships. We developed a hybrid molecular dynamics (MD)-Monte Carlo (MC) approach to enrich the sampling toward the target structures. In this approach, the higher SE is achieved by perturbing the conventional MD simulations with a MC structure-acceptance judgment, which is based on the coincidence degree of small angle x-ray scattering (SAXS) intensity profiles between the simulation structures and the target structure. We found that the hybrid simulations could significantly improve SE by making the top-ranked models much closer to the target structures both in the secondary and tertiary structures. Specifically, for the 20 mono-residue peptides, when the initial structures had the root-mean-squared deviation (RMSD) from the target structure smaller than 7 Å, the hybrid MD-MC simulations afforded, on average, 0.83 Å and 1.73 Å in RMSD closer to the target than the parallel MD simulations at 310K and 370K, respectively. Meanwhile, the average SE values are also increased by 13.2% and 15.7%. The enrichment of sampling becomes more significant when the target states are gradually detectable in the MD-MC simulations in comparison with the parallel MD simulations, and provide >200% improvement in SE. We also performed a test of the hybrid MD-MC approach in the real protein system, the results showed that the SE for 3 out of 5 real proteins are improved. Overall, this work presents an efficient way of utilizing solution SAXS to improve protein structure prediction and refinement, as well as the generation of near native structures for function annotation.

  20. CAPTURED India Country Evaluation

    NARCIS (Netherlands)

    O'Donoghue, R.; Brouwers, J.H.A.M.

    2012-01-01

    This report provides the findings of the India Country Evaluation and is produced as part of the overall CAPTURED End Evaluation. After five years of support by the CAPTURED project the End Evaluation has assessed that results are commendable. I-AIM was able to design an approach in which health fol