WorldWideScience

Sample records for biomolecular structural determinations

  1. Biomolecular Structure Determination with Divide and Concur

    Science.gov (United States)

    Kallus, Yoav; Elser, Veit

    2009-03-01

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

  2. Models for solvated biomolecular structures

    OpenAIRE

    Cerutti, David

    2007-01-01

    Methods for estimating the structure and energetics of water around biomolecules are presented with the objective of improving the treatment of the biomolecular simulation environment as well as facilitating the use of complex, rigorous water models in the context of structure prediction problems that demand cheap solutions. Salt solutions around biomolecules are studied using an implicit solvent model with explicitly represented ions, revealing that the structure of the ion atmosphere is muc...

  3. Structural determination of biomolecular interfaces by nuclear magnetic resonance of proteins with reduced proton density

    International Nuclear Information System (INIS)

    Protein interactions are important for understanding many molecular mechanisms underlying cellular processes. So far, interfaces between interacting proteins have been characterized by NMR spectroscopy mostly by using chemical shift perturbations and cross-saturation via intermolecular cross-relaxation. Although powerful, these techniques cannot provide unambiguous estimates of intermolecular distances between interacting proteins. Here, we present an alternative approach, called REDSPRINT (REDduced/Standard PRoton density INTerface identification), to map protein interfaces with greater accuracy by using multiple NMR probes. Our approach is based on monitoring the cross-relaxation from a source protein (or from an arbitrary ligand that need not be a protein) with high proton density to a target protein (or other biomolecule) with low proton density by using isotope-filtered nuclear Overhauser spectroscopy (NOESY). This methodology uses different isotropic labeling for the source and target proteins to identify the source-target interface and also determine the proton density of the source protein at the interface for protein-protein or protein-ligand docking. Simulation indicates significant gains in sensitivity because of the resultant relaxation properties, and the utility of this technique, including a method for direct determination of the protein interface, is demonstrated for two different protein-protein complexes.

  4. Biomolecular structure refinement using the GROMOS simulation software

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-11-15

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

  5. Synthesis and biosynthesis of {sup 13}C-, {sup 15}N-labeled deoxynucleosides useful for biomolecular structural determinations

    Energy Technology Data Exchange (ETDEWEB)

    Ashburn, D.A.; Garcia, K.; Hanners, J.L.; Silks, L.A. III; Unkefer, C.J. [Los Alamos National Laboratory, NM (United States)

    1994-12-01

    Currently, there is a great emphasis on elucidating the structure, function, and dynamics of DNA. Much of the research involved in this study uses nuclear magnetic resonance (NMR) spectroscopy. Effective use of NMR spectroscopy for DNA molecules with mw > 10,000 requires stable isotope enrichment. We present strategies for site-specific isotopic labeling of the purine bases adenosine and guanosine and the biosynthesis of (U-{sup 13}C, {sup 15}N) DNA from methylotropic bacteria. With commercially available 6-chloropurine, an effective two-step route leads to 2{prime}-deoxy-(amino-{sup 15}N)adenosine (dA). The resulting d(amino-{sup 15}N)A is used in a series of reactions to synthesize 2{prime}-deoxy-(2-{sup 13}C,1,amino-{sup 15}N{sub 2})guanosine or any combination thereof. An improved biosynthesis of labeled DNA has been accomplished using Methylobacterium extorquens AS1. Each liter of growth medium contains 4 g of methanol to yield 1 g of lyophilized cells. As much as 200 mg of RNA per liter of culture has been obtained. We are currently developing large-scale isolation protocols. General synthetic pathways to oligomeric DNA will be presented.

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

    NARCIS (Netherlands)

    Fontaine-Vive-Curtaz, F.

    2007-01-01

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

  7. Computational and theoretical aspects of biomolecular structure and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, A.E.; Berendzen, J.; Catasti, P., Chen, X. [and others

    1996-09-01

    This is the final report for a project that sought to evaluate and develop theoretical, and computational bases for designing, performing, and analyzing experimental studies in structural biology. Simulations of large biomolecular systems in solution, hydrophobic interactions, and quantum chemical calculations for large systems have been performed. We have developed a code that implements the Fast Multipole Algorithm (FMA) that scales linearly in the number of particles simulated in a large system. New methods have been developed for the analysis of multidimensional NMR data in order to obtain high resolution atomic structures. These methods have been applied to the study of DNA sequences in the human centromere, sequences linked to genetic diseases, and the dynamics and structure of myoglobin.

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

    Science.gov (United States)

    Bordbar, Aarash; Nagarajan, Harish; Lewis, Nathan E; Latif, Haythem; Ebrahim, Ali; Federowicz, Stephen; Schellenberger, Jan; Palsson, Bernhard O

    2014-01-01

    Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still predicated on human-defined pathways. Here, we introduce an unbiased, pathway structure for genome-scale metabolic networks defined based on principles of parsimony that do not mimic canonical human-defined textbook pathways. Instead, these minimal pathways better describe multiple independent pathway-associated biomolecular interaction datasets suggesting a functional organization for metabolism based on parsimonious use of cellular components. We use the inherent predictive capability of these pathways to experimentally discover novel transcriptional regulatory interactions in Escherichia coli metabolism for three transcription factors, effectively doubling the known regulatory roles for Nac and MntR. This study suggests an underlying and fundamental principle in the evolutionary selection of pathway structures; namely, that pathways may be minimal, independent, and segregated. PMID:24987116

  9. Amplified vibrational circular dichroism as a probe of local biomolecular structure.

    Science.gov (United States)

    Domingos, Sérgio R; Huerta-Viga, Adriana; Baij, Lambert; Amirjalayer, Saeed; Dunnebier, Dorien A E; Walters, Annemarie J C; Finger, Markus; Nafie, Laurence A; de Bruin, Bas; Buma, Wybren Jan; Woutersen, Sander

    2014-03-01

    We show that the VCD signal intensities of amino acids and oligopeptides can be enhanced by up to 2 orders of magnitude by coupling them to a paramagnetic metal ion. If the redox state of the metal ion is changed from paramagnetic to diamagnetic the VCD amplification vanishes completely. From this observation and from complementary quantum-chemical calculations we conclude that the observed VCD amplification finds its origin in vibronic coupling with low-lying electronic states. We find that the enhancement factor is strongly mode dependent and that it is determined by the distance between the oscillator and the paramagnetic metal ion. This localized character of the VCD amplification provides a unique tool to specifically probe the local structure surrounding a paramagnetic ion and to zoom in on such local structure within larger biomolecular systems. PMID:24506134

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

    Science.gov (United States)

    Likic, Vladimir A.

    2006-01-01

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

  11. Nanopatterned structures for biomolecular analysis toward genomic and proteomic applications

    Science.gov (United States)

    Chou, Chia-Fu; Gu, Jian; Wei, Qihuo; Liu, Yingjie; Gupta, Ravi; Nishio, Takeyoshi; Zenhausern, Frederic

    2005-01-01

    We report our fabrication of nanoscale devices using electron beam and nanoimprint lithography (NIL). We focus our study in the emerging fields of NIL, nanophotonics and nanobiotechnology and give a few examples as to how these nanodevices may be applied toward genomic and proteomic applications for molecular analysis. The examples include reverse NIL-fabricated nanofluidic channels for DNA stretching, nanoscale molecular traps constructed from dielectric constrictions for DNA or protein focusing by dielectrophoresis, multi-layer nanoburger and nanoburger multiplets for optimized surface-plasma enhanced Raman scattering for protein detection, and biomolecular motor-based nanosystems. The development of advanced nanopatterning techniques promises reliable and high-throughput manufacturing of nanodevices which could impact significantly on the areas of genomics, proteomics, drug discovery and molecular clinical diagnostics.

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

    Science.gov (United States)

    Vashist, Sandeep Kumar

    2012-02-01

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

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

    OpenAIRE

    Bordbar, Aarash; Nagarajan, Harish; Lewis, Nathan E.; Latif, Haythem; Ebrahim, Ali; Federowicz, Stephen; Schellenberger, Jan; Palsson, Bernhard

    2014-01-01

    Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still predicated on human-defined pathways. Here, we introduce an unbiased, pathway structure for genome-scale metabolic networks defined based on principles of parsimony that do not mimic canonical human-defined textbook pathways. Instead, these minimal pa...

  14. X3DBio2: A visual analysis tool for biomolecular structure comparison

    Science.gov (United States)

    Yi, Hong; Thakur, Sidharth; Sethaphong, Latsavongsakda; Yingling, Yaroslava G.

    2013-01-01

    A major problem in structural biology is the recognition of differences and similarities between related three dimensional (3D) biomolecular structures. Investigating these structure relationships is important not only for understanding of functional properties of biologically significant molecules, but also for development of new and improved materials based on naturally-occurring molecules. We developed a new visual analysis tool, X3DBio2, for 3D biomolecular structure comparison and analysis. The tool is designed for elucidation of structural effects of mutations in proteins and nucleic acids and for assessment of time dependent trajectories from molecular dynamics simulations. X3DBio2 is a freely downloadable open source software and provides tightly integrated features to perform many standard analysis and visual exploration tasks. We expect this tool can be applied to solve a variety of biological problems and illustrate the use of the tool on the example study of the differences and similarities between two proteins of the glycosyltransferase family 2 that synthesize polysaccharides oligomers. The size and conformational distances and retained core structural similarity of proteins SpsA to K4CP represent significant epochs in the evolution of inverting glycosyltransferases.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-01

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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-10-01

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

  18. A computational study of the interaction of graphene structures with biomolecular units.

    Science.gov (United States)

    Carballeira, Diego López; Ramos-Berdullas, Nicolás; Pérez-Juste, Ignacio; Fajín, José Luis Cagide; Cordeiro, M Natália D S; Mandado, Marcos

    2016-06-01

    Due to the great interest that biochemical sensors constructed from graphene nanostructures have raised recently, in this work we analyse in detail the electronic factors responsible for the large affinity of biomolecular units for graphene surfaces using ab initio quantum chemical tools based on density functional theory. Both finite and periodic graphene structures have been employed in our study. Whereas the former allows the analysis of the different energy components contributing to the interaction energy separately, the periodic structure provides a more realistic calculation of the total adsorption energy in an extended graphene surface and serves to validate the results obtained using the finite model. In addition, qualitative relations between interaction energy and electron polarization upon adsorption have been established using the finite model. In this work, we have analysed thermodynamically stable adsorption complexes formed by glycine, melamine, pyronin cation, porphine, tetrabenzoporphine and phthalocyanine with a 2D structure of ninety six carbons and periodic structures formed by cells of fifty and seventy two carbons. Differences in the electrostatic, Pauli repulsion, induction and dispersion energies among aromatic and non-aromatic molecules, charged and non-charged molecules and H-π and stacking interactions have been thoroughly analysed in this work. PMID:27210053

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

    Science.gov (United States)

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

    2015-12-15

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

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

    OpenAIRE

    Gysemans, Maarten

    2009-01-01

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

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

    CERN Document Server

    2014-01-01

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

  2. Integrative NMR for biomolecular research.

    Science.gov (United States)

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

    2016-04-01

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download_packages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html ). PMID:27023095

  3. Biomolecular EPR spectroscopy

    CERN Document Server

    Hagen, Wilfred Raymond

    2008-01-01

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

  4. REACH coarse-grained biomolecular simulation: transferability between different protein structural classes.

    Science.gov (United States)

    Moritsugu, Kei; Smith, Jeremy C

    2008-08-01

    Coarse graining of protein interactions provides a means of simulating large biological systems. The REACH (Realistic Extension Algorithm via Covariance Hessian) coarse-graining method, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation, involves direct mapping between scales without the need for iterative optimization. Here, the transferability of the REACH force field is examined between protein molecules of different structural classes. As test cases, myoglobin (all alpha), plastocyanin (all beta), and dihydrofolate reductase (alpha/beta) are taken. The force constants derived are found to be closely similar in all three proteins. An MD version of REACH is presented, and low-temperature coarse-grained (CG) REACH MD simulations of the three proteins are compared with atomistic MD results. The mean-square fluctuations of the atomistic MD are well reproduced by the CGMD. Model functions for the CG interactions, derived by averaging over the three proteins, are also shown to produce fluctuations in good agreement with the atomistic MD. The results indicate that, similarly to the use of atomistic force fields, it is now possible to use a single, generic REACH force field for all protein studies, without having first to derive parameters from atomistic MD simulation for each individual system studied. The REACH method is thus likely to be a reliable way of determining spatiotemporal motion of a variety of proteins without the need for expensive computation of long atomistic MD simulations. PMID:18469078

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

    Science.gov (United States)

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

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

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

    Science.gov (United States)

    Lu, Jixue; Wang, Shizhen; Fang, Baishan

    2015-07-01

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

  7. Biomolecular Science (Fact Sheet)

    Energy Technology Data Exchange (ETDEWEB)

    2012-04-01

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

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

    CERN Document Server

    Fernández, Ariel

    2016-01-01

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

  9. Advances in integrative modeling of biomolecular complexes

    NARCIS (Netherlands)

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

    2013-01-01

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

  10. Programming in Biomolecular Computation:

    DEFF Research Database (Denmark)

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

    2011-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2011-01-01

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

  12. Programming in Biomolecular Computation

    DEFF Research Database (Denmark)

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

    2010-01-01

    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We introduce a model of computation that is evidently programmable......, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only...... in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient. A prototype model has been implemented (for now in silico on a conventional computer). This work opens new perspectives on just how computation may be specified at the biological level....

  13. Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling

    OpenAIRE

    2009-01-01

    Background Identification of functionally important sites in biomolecular sequences has broad applications ranging from rational drug design to the analysis of metabolic and signal transduction networks. Experimental determination of such sites lags far behind the number of known biomolecular sequences. Hence, there is a need to develop reliable computational methods for identifying functionally important sites from biomolecular sequences. Results We present a mixture of experts approach to b...

  14. Coassembly of aromatic dipeptides into biomolecular necklaces.

    Science.gov (United States)

    Yuran, Sivan; Razvag, Yair; Reches, Meital

    2012-11-27

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

  15. Nanoarchitectonics of biomolecular assemblies for functional applications

    Science.gov (United States)

    Avinash, M. B.; Govindaraju, T.

    2014-10-01

    The stringent processes of natural selection and evolution have enabled extraordinary structure-function properties of biomolecules. Specifically, the archetypal designs of biomolecules, such as amino acids, nucleobases, carbohydrates and lipids amongst others, encode unparalleled information, selectivity and specificity. The integration of biomolecules either with functional molecules or with an embodied functionality ensures an eclectic approach for novel and advanced nanotechnological applications ranging from electronics to biomedicine, besides bright prospects in systems chemistry and synthetic biology. Given this intriguing scenario, our feature article intends to shed light on the emerging field of functional biomolecular engineering.

  16. The biomolecular corona of nanoparticles in circulating biological media

    Science.gov (United States)

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

    2015-08-01

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

  17. Ensemble based convergence assessment of biomolecular trajectories

    CERN Document Server

    Lyman, E; Lyman, Edward; Zuckerman, Daniel M.

    2006-01-01

    Assessing the convergence of a biomolecular simulation is an essential part of any computational investigation. This is because many important quantities (e.g., free energy differences) depend on the relative populations of different conformers; insufficient convergence translates into systematic errors. Here we present a simple method to self-consistently assess the convergence of a simulation. Standard clustering methods first generate a set of reference structures to any desired precision. The trajectory is then classified by proximity to the reference structures, yielding a one-dimensional histogram of structurally distinct populations. Comparing ensembles of different trajectories (or different parts of the same trajectory) built with the same reference structures provides a sensitive, quantitative measure of convergence. Please note: this is a preliminary manuscript, and should be read as such. Comments are most welcome, especially regarding pertinent prior work.

  18. Paramagnetic relaxation enhancements in structure determination of proteins by NMR spectroscopy

    International Nuclear Information System (INIS)

    Solution NMR spectroscopy is a versatile tool to study a variety of a biomolecular parameters such as its structural assembly, its dynamics and its interaction with other molecules. We used the methodological expansion of paramagnetic relaxation enhancements (PREs) to gain additional insights into spatial proximities and surface accessibility of a variety of proteins.The structure of Fst, a toxic, hydrophobic peptide was solved within a membrane mimicking environment. Using PREs, it was possible to show a transmembrane binding mode.Further, the structure of Cla h 8 was solved which is a eukaryotic homologue to prokaryotic cold shock proteins. We were using PREs to determine the high resolution structure and its mode of binding to DNA.Additionally, we solved the structure of Phl p 5a, a major grass pollen allergen. The determination of PREs displayed the dynamic behavior of different parts of the molecule. (author)

  19. Storing and analysing biomolecular contacts

    OpenAIRE

    Walter, Peter

    2011-01-01

    Biomolecular contacts play a crucial role in all areas of life. In particular, protein-protein (PP) interactions are essential for most processes in biological cells. Antigen-antibody recognition, enzyme substrate binding, hormone receptor binding, RNA splicing, DNA replication and signal transduction are just some examples for the rich variety of PP interactions. In the last years modern proteomic methods have helped to get a better understanding of the complexity within living cell and orga...

  20. Abstractions for biomolecular computations

    CERN Document Server

    Okunoye, Babatunde O

    2008-01-01

    Deoxyribonucleic acid is increasingly being understood to be an informational molecule, capable of information processing.It has found application in the determination of non-deterministic algorithms and in the design of molecular computing devices. This is a theoretical analysis of the mathematical properties and relations of the molecules which constituting DNA, which explains in part why DNA is a successful computing molecule.

  1. Organic & Biomolecular Chemistry

    OpenAIRE

    Zhang, Wenyu; Bryson, David I.; Crumpton, Jason B.; Wynn, Jessica; Santos, Webster L.

    2013-01-01

    On-bead high-throughput screening of a medium-sized (1000_2000 Da) branched peptideboronic acid (BPBA) library consisting of 46 656 unique sequences against HIV-1 RRE RNA generated peptides with binding affinities in the low micromolar range. In particular, BPBA1 had a Kd of 1.4 _M with RRE IIB, preference for RNA over DNA (27 fold), and selectivity of up to >75 fold against a panel of RRE IIB variants. Structure_activity studies suggest that the boronic acid moiety and ͐branching in peptide...

  2. Determination of Uranium Oxides Structure

    International Nuclear Information System (INIS)

    Determination of uranium oxides structure have been worked using XRD (X-Ray Diffractometer). Where the diffraction patterns were analyzed by Rietan method. The samples that analysis were UO2,07; UO2,06; UO2,15; UO2,27 and U3O8 compound. Rietan refinement of the diffraction patterns showed cubic structures for UO2,07 and UO2,06, with a = 5,4663 A and 5,4638 A, respectively. UO2,15 compound was found to be a mixture of cubic, a = 5,4637 A and tetragonal structures, a = 5,454 A and c = 5,409 A. The structures of UO2,27 and U3O8 were found to be tetragonal and orthorhombic, respectively with a 5,4717 A and c = 5,407 A for the tetragonal structure, while a 6,7147 A, b = 11, 9506 A and c = 4,1448 A for the orthorhombic one. It was concluded from this investigation that large amounts of x oxygen atoms in UO2+x, transforms the cubic structure gradually to tetragonal and finely to orthorhombic structure. Sample of PPNY's UO2 had cubic structure, so that the structure specification as which expected. (author)

  3. Ultrasonic determination of steel structures

    International Nuclear Information System (INIS)

    In the research project 'Determination of steel structures by means of ultrasound' methods are developed for the non-destructive structure characterization with scattered ultrasound. Measurements were made at about 200 steel samples with frequencies between 5 and 20 Mc/sec. In the range of 0,05 <= d/lambda <= 0,5 (d=mean grain size, lambda = wavelength of the ultrasound pulse) known theories can be applied for the quantitative grain size determination and with an accuracy of +-15% the results agree with the metallographically measured values. The best method for this is the combination of two measurements with two different frequencies. Advantages are given by the measurement of the multiple scattering which is leading to the scattering coefficient and to the grain size with one measurement only and without assumptions concerning other parameters of ultrasound propagation. A structure characterization concerning the homogeneity inside the material is possible, too, because of the time (i.e. sound path-)-dependent scattering measurement. It is able to control the structure of monophasic steels with grain sizes between ASTM 1 and ASTM 11. Today problems unsolved are the martensitic steels, the multiphasic structures

  4. RECENT PROGRESS IN BIOMOLECULAR NMR

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    @@ Structural genomics and proteomics were born from the understanding that functions of a protein are dictated by its 3D structure and dynamics. To understand protein functions on a genomic scale, we must know protein structures on a genomic scale. High resolution NMR can be used for this purpose. Traditional multidimensional NMR structure determination protocols become ineffective for structural genomics since to obtain a structure of a small protein of 15kD requires many months of painstaking spectral analysis and modeling. Recent advances in magnet and probe technology and in experimental methods have expanded the range of proteins amenable to structure determination and make the large scale structure determination possible. These advances are (1) effective expression systems for protein production, (2) introduction of cryoprobe, (3) structure determination with the use of the minimal amount of structural restraints obtained from the chemical shifts, residual dipolar couplings, NOEs, and computer modeling. In this talk,Iwill briefly outline these developments and related works done in our NMR lab.

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

    Directory of Open Access Journals (Sweden)

    Hayward Steven

    2009-10-01

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

  6. Crystal structure determination of Efavirenz

    Energy Technology Data Exchange (ETDEWEB)

    Popeneciu, Horea, E-mail: horea.popeneciu@itim-cj.ro; Dumitru, Ristoiu [College of Environmental Science on Engineering Babes Bolyai University, 30 Fantanele, 400294 Cluj Napoca (Romania); Tripon, Carmen, E-mail: horea.popeneciu@itim-cj.ro; Borodi, Gheorghe, E-mail: horea.popeneciu@itim-cj.ro; Pop, Mihaela Maria, E-mail: mihaelapop@teracrystal.com

    2015-12-23

    Needle-shaped single crystals of the title compound, C{sub 14}H{sub 9}ClF{sub 3}NO{sub 2}, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.

  7. Structure factor determination by electron diffraction

    International Nuclear Information System (INIS)

    A selection of methods for structure factor determination by electron diffraction is presented. Results obtained by the different methods are compared with regard to accuracies in structure determination

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

    OpenAIRE

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

    2011-01-01

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

  9. Structure determination of enterovirus 71

    Energy Technology Data Exchange (ETDEWEB)

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G. (Purdue); (Sentinext)

    2013-02-20

    Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.

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

    Science.gov (United States)

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

    2011-01-01

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

  11. Microwave spectroscopy of biomolecular building blocks.

    Science.gov (United States)

    Alonso, José L; López, Juan C

    2015-01-01

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

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

    Science.gov (United States)

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

    2009-12-01

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

  13. Structural stability versus conformational sampling in biomolecular systems: Why is the charge transfer efficiency in G4-DNA better than in double-stranded DNA?

    OpenAIRE

    Woiczikowski, P. Benjamin; Kubař, Tomáš; Gutiérrez, Rafael; Cuniberti, Gianaurelio; Elstner, Marcus

    2010-01-01

    The electrical conduction properties of G4-DNA are investigated using a hybrid approach, which combines electronic structure calculations, molecular dynamics (MD) simulations, and the formulation of an effective tight-binding model Hamiltonian. Charge transport is studied by computing transmission functions along the MD trajectories. Though G4-DNA is structurally more stable than double-stranded DNA (dsDNA), our results strongly suggest that the potential improvement of the electrical transpo...

  14. Conducting polymer based biomolecular electronic devices

    Indian Academy of Sciences (India)

    B D Malhotra; Rahul Singhal

    2003-08-01

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

  15. Development and application of all-atom structure-based models for studying the role of geometry in biomolecular folding and function

    OpenAIRE

    Noel, Jeffrey Kenneth

    2012-01-01

    Protein dynamics takes place on a rugged funnel-like energy landscape that is biased towards the native state. In naturally occurring proteins, this ruggedness caused by non-native interactions is sufficiently smooth (minimally frustrated) that the landscape is dominated by the native interactions. This provides the theoretical foundation for a class of minimalist protein models called structure- based models (SBMs). In the first half of the thesis we develop and characterize an all-atom SBM ...

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

    Science.gov (United States)

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

    2015-01-01

    Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that are biologically significant. Molecular simulations have become a standard tool for toxicology and pharmacology research, but organizing and sharing data - both within the same organization and among different ones - remains a substantial challenge. In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data. Our efforts include the design of data models and dictionary tools that allow the standardization of the metadata used to describe the biomedical simulations, the development of a thesaurus and ontology for computational reasoning when searching for biomolecular simulations in distributed environments, and the development of systems based on these models to manage and share the data at a large scale (iBIOMES), and within smaller groups of researchers at laboratory scale (iBIOMES Lite), that take advantage of the standardization of the meta data used to describe biomolecular simulations. PMID:26387907

  17. Flourescence from Gas-Phase Biomolecular Ions

    DEFF Research Database (Denmark)

    Nielsen, Steen Brøndsted

    2013-01-01

    This chapter deals with measurements of fluorescence from electronically excited biomolecular ions where there are no interactions with an external environment. Biomolecules with no natural fluorophores are labelled with a dye for such experiments. First, some of the advantages, but also difficul...

  18. Biomolecular Modification of Inorganic Crystal Growth

    Energy Technology Data Exchange (ETDEWEB)

    De Yoreo, J J

    2007-04-27

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

  19. Determinants of Glycosaminoglycan (GAG) Structure.

    Science.gov (United States)

    Prydz, Kristian

    2015-01-01

    Proteoglycans (PGs) are glycosylated proteins of biological importance at cell surfaces, in the extracellular matrix, and in the circulation. PGs are produced and modified by glycosaminoglycan (GAG) chains in the secretory pathway of animal cells. The most common GAG attachment site is a serine residue followed by a glycine (-ser-gly-), from which a linker tetrasaccharide extends and may continue as a heparan sulfate, a heparin, a chondroitin sulfate, or a dermatan sulfate GAG chain. Which type of GAG chain becomes attached to the linker tetrasaccharide is influenced by the structure of the protein core, modifications occurring to the linker tetrasaccharide itself, and the biochemical environment of the Golgi apparatus, where GAG polymerization and modification by sulfation and epimerization take place. The same cell type may produce different GAG chains that vary, depending on the extent of epimerization and sulfation. However, it is not known to what extent these differences are caused by compartmental segregation of protein cores en route through the secretory pathway or by differential recruitment of modifying enzymes during synthesis of different PGs. The topic of this review is how different aspects of protein structure, cellular biochemistry, and compartmentalization may influence GAG synthesis. PMID:26308067

  20. Determinants of Glycosaminoglycan (GAG Structure

    Directory of Open Access Journals (Sweden)

    Kristian Prydz

    2015-08-01

    Full Text Available Proteoglycans (PGs are glycosylated proteins of biological importance at cell surfaces, in the extracellular matrix, and in the circulation. PGs are produced and modified by glycosaminoglycan (GAG chains in the secretory pathway of animal cells. The most common GAG attachment site is a serine residue followed by a glycine (-ser-gly-, from which a linker tetrasaccharide extends and may continue as a heparan sulfate, a heparin, a chondroitin sulfate, or a dermatan sulfate GAG chain. Which type of GAG chain becomes attached to the linker tetrasaccharide is influenced by the structure of the protein core, modifications occurring to the linker tetrasaccharide itself, and the biochemical environment of the Golgi apparatus, where GAG polymerization and modification by sulfation and epimerization take place. The same cell type may produce different GAG chains that vary, depending on the extent of epimerization and sulfation. However, it is not known to what extent these differences are caused by compartmental segregation of protein cores en route through the secretory pathway or by differential recruitment of modifying enzymes during synthesis of different PGs. The topic of this review is how different aspects of protein structure, cellular biochemistry, and compartmentalization may influence GAG synthesis.

  1. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes che...... residues. For Rhodopsin (225 residues) a structure is found at 2.5 Å CA-RMSD from the experimental X-ray structure, and a structure is determined for the Savinase protein (269 residues) with 2.9 Å CA-RMSD from the experimental X-ray structure....

  2. Membrane-based biomolecular smart materials

    International Nuclear Information System (INIS)

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

  3. Improvements in continuum modeling for biomolecular systems

    CERN Document Server

    Qiao, Yu

    2015-01-01

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

  4. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

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

  5. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.;

    2005-01-01

    We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information at...

  6. Determinants of Capital Structure in Family Firms

    OpenAIRE

    Akbarali, Ahmed; Foma, Awambeng

    2015-01-01

    Most firms are using optimal combination of equity and debt so as to maximize firms value and the wealth of the shareholders. To achieve all these, firms should be aware of the factors that influence the capital structure decisions. Previous empirical studies attempted to explain what determines the choice of capital structure in firms. The focus was on firms in general without categorizing family firms and non-family firms. The primary objective of this study is to examine what determines th...

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

    Science.gov (United States)

    McGuigan, Kevin G.

    2008-03-01

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

  8. Distributed structure determination at the JCSG

    International Nuclear Information System (INIS)

    The software suite Xsolve semi-exhaustively explores key parameters of the X-ray structure-determination process to compute multiple three-dimensional protein structures independently and in parallel from a set of diffraction images. An optimal consensus model for subsequent manual refinement is computed from these structures. The Joint Center for Structural Genomics (JCSG), one of four large-scale structure-determination centers funded by the US Protein Structure Initiative (PSI) through the National Institute for General Medical Sciences, has been operating an automated distributed structure-solution pipeline, Xsolve, for well over half a decade. During PSI-2, Xsolve solved, traced and partially refined 90% of the JCSG’s nearly 770 MAD/SAD structures at an average resolution of about 2 Å without human intervention. Xsolve executes many well established publicly available crystallography software programs in parallel on a commodity Linux cluster, resulting in multiple traces for any given target. Additional software programs have been developed and integrated into Xsolve to further minimize human effort in structure refinement. ConsensusModeler exploits complementarities in traces from Xsolve to compute a single optimal model for manual refinement. Xpleo is a powerful robotics-inspired algorithm to build missing fragments and qFit automatically identifies and fits alternate conformations

  9. Capital Structure Determinants and Governance Structure Variety in Franchising

    NARCIS (Netherlands)

    T. Jiang (Tao)

    2009-01-01

    textabstractThis thesis investigates two questions: the determinants of capital structure in franchising and its subsequent impact on the franchise financing decisions; and the efficient governance structure choice in franchising. We posit that firms franchise in order to benefit from the reduced fr

  10. Membrane protein structure determination in membrana.

    Science.gov (United States)

    Ding, Yi; Yao, Yong; Marassi, Francesca M

    2013-09-17

    The two principal components of biological membranes, the lipid bilayer and the proteins integrated within it, have coevolved for specific functions that mediate the interactions of cells with their environment. Molecular structures can provide very significant insights about protein function. In the case of membrane proteins, the physical and chemical properties of lipids and proteins are highly interdependent; therefore structure determination should include the membrane environment. Considering the membrane alongside the protein eliminates the possibility that crystal contacts or detergent molecules could distort protein structure, dynamics, and function and enables ligand binding studies to be performed in a natural setting. Solid-state NMR spectroscopy is compatible with three-dimensional structure determination of membrane proteins in phospholipid bilayer membranes under physiological conditions and has played an important role in elucidating the physical and chemical properties of biological membranes, providing key information about the structure and dynamics of the phospholipid components. Recently, developments in the recombinant expression of membrane proteins, sample preparation, pulse sequences for high-resolution spectroscopy, radio frequency probes, high-field magnets, and computational methods have enabled a number of membrane protein structures to be determined in lipid bilayer membranes. In this Account, we illustrate solid-state NMR methods with examples from two bacterial outer membrane proteins (OmpX and Ail) that form integral membrane β-barrels. The ability to measure orientation-dependent frequencies in the solid-state NMR spectra of membrane-embedded proteins provides the foundation for a powerful approach to structure determination based primarily on orientation restraints. Orientation restraints are particularly useful for NMR structural studies of membrane proteins because they provide information about both three-dimensional structure

  11. A structural determinant required for RNA editing

    Science.gov (United States)

    Tian, Nan; Yang, Yun; Sachsenmaier, Nora; Muggenhumer, Dominik; Bi, Jingpei; Waldsich, Christina; Jantsch, Michael F.; Jin, Yongfeng

    2011-01-01

    RNA editing by adenosine deaminases acting on RNAs (ADARs) can be both specific and non-specific, depending on the substrate. Specific editing of particular adenosines may depend on the overall sequence and structural context. However, the detailed mechanisms underlying these preferences are not fully understood. Here, we show that duplex structures mimicking an editing site in the Gabra3 pre-mRNA unexpectedly fail to support RNA editing at the Gabra3 I/M site, although phylogenetic analysis suggest an evolutionarily conserved duplex structure essential for efficient RNA editing. These unusual results led us to revisit the structural requirement for this editing by mutagenesis analysis. In vivo nuclear injection experiments of mutated editing substrates demonstrate that a non-conserved structure is a determinant for editing. This structure contains bulges either on the same or the strand opposing the edited adenosine. The position of these bulges and the distance to the edited base regulate editing. Moreover, elevated folding temperature can lead to a switch in RNA editing suggesting an RNA structural change. Our results indicate the importance of RNA tertiary structure in determining RNA editing. PMID:21427087

  12. Determinants of capital structure: UK panel data

    OpenAIRE

    Ahi, Seyed Mohammad Ali Hamze

    2013-01-01

    ABSTRACT: The paper investigates capital structure determinants of 5 important non-financial firms listed in FTSE100. The firms are chosen from oil and gas and mining industry. The period chosen for the study is 22 years from 1990 to 2012. Firms are chosen according to capitalization in market. Theories in capital structure such as the trade-off theory, pecking order theory and agency theory are described in order to find the best possible formulation to predict the choice of capital...

  13. DETERMINANTS OF BANK BOARD STRUCTURE IN GHANA

    OpenAIRE

    Michael Adusei

    2012-01-01

    The paper investigates the determinants of bank board structure in Ghana and finds that the Scope of Operations Hypothesis could explain the variation in board size but not board independence. On the other hand, the Board Monitoring Hypothesis could only explain the variation in board independence but not board size. The study also finds that cost-income ratio, foreign majority ownership structure and Ghana Stock Exchange listing status are positively and significantly associated with large b...

  14. Analyzing biomolecular interactions by variable angle ellipsometry

    Science.gov (United States)

    Wu, Jiun-Yan; Lee, Chih-Kung; Lee, J. H.; Shiue, Shuen-Chen; Lee, Shu-Sheng; Lin, Shiming

    2001-10-01

    In this paper, an innovative ellipsometer is developed and applied to metrology of the biomolecular interaction on a protein biochip. Both the theory, optical and opto-mechanical configurations of this newly developed ellipsometer and methodologies adopted in system design to improve the system performance are presented. It will be shown that by measuring the ellipsometric parameters, the corresponding concentration variation in biochemical reaction can be calculated according to stoichiometry analysis. By applying the variable angle ellipsometry to analysis of a multi-layered sample, the thickness and concentration are resolved. It is believed that the newly developed ellipsometer biosensor is able to undertake an accurate measurement on biomedical interaction.

  15. Nanotube-Based Chemical and Biomolecular Sensors

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

  16. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

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

  17. Micro and Nanotechnologies Enhanced Biomolecular Sensing

    Directory of Open Access Journals (Sweden)

    Tza-Huei Wang

    2013-07-01

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

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

    OpenAIRE

    Hayward Steven; Stocks Matthew B; Laycock Stephen D

    2009-01-01

    Abstract Background From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with mo...

  19. Determinants of Capital Structure of UK Firms

    OpenAIRE

    Wu, Meiying

    2010-01-01

    This paper aims to investigate the determinants of capital structure of UK firms and identify which existing theory of capital structure is most relevant and applicable to UK firms. The sample of this study involves 239 listed firms from 9 industries on the FTSE 350 Index in the UK from 2000 to 2009. ANOVA and panel data regression are run to analyze what factors have impact on firm’s decision of capital structure. Each test is run on long-term and short-term leverage as dependent variables. ...

  20. Determination of the neutron spin structure function

    International Nuclear Information System (INIS)

    New measurements of the neutron spin structure function, g1(x), made at SLAC are reported, using longitudinally polarized electrons on a polarized 3He target. The spin structure function of the neutron has been determined from x=0.03 to x=0.6 at an average Q2 of 2 (GeV/c)2, by measuring the asymmetry in deep inelastic scattering of polarized electrons from polarized 3He at energies from 19 to 26 GeV. The integral over the spin structure function has been calculated. (author) 16 refs., 3 figs., 1 tab

  1. Representing Personal Determinants in Causal Structures.

    Science.gov (United States)

    Bandura, Albert

    1984-01-01

    Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

  2. Energy dissipation in biomolecular machines

    Energy Technology Data Exchange (ETDEWEB)

    Lervik, Anders

    2012-07-01

    The operation of a molecular pump, the calcium pump of sarcoplasmic reticulum is studied using mesoscopic non-equilibrium thermodynamics and molecular dynamics. The mesoscopic non-equilibrium thermodynamic description of the pump is compared to the description obtained in the framework of Hill for kinetic enzyme cycles. By comparing these two descriptions at isothermal conditions, they are found to be equivalent. This supports the validity of the mesoscopic approach. An extension of the mesoscopic non-equilibrium framework to also include a heat flux and the corresponding temperature difference is proposed. This can be used to model phenomena such as non-shivering thermogenesis, a process which lack a theoretical description in the kinetic cycle picture. Further, the heat transfer in the calcium pump is studied using molecular dynamics. This is done in order to obtain phenomenological parameters that can be used for the modeling of thermogenesis. A non-stationary non-equilibrium molecular dynamics approach is developed, which may be used to study heat transfer between a small object and the surrounding solvent. This methodology is applied to the calcium pump solvated in water. It is found that the thermal conductivity of the protein is low (0.2 W K-1 m-1) compared to water (0.6 WK-1 m-1). This means that the protein may sustain a large temperature gradient across its structure. The simulations also show that the protein-water surface is important for the heat transfer. The time scale for vibrational energy relaxation is found to be of order 10/100 ps which strengthens the local equilibrium assumption of mesoscopic non-equilibrium thermodynamics. Mesoscopic non-equilibrium thermodynamics is also applied to calculate the thermodynamic efficiency of the calcium pump embedded in lipid bilayers of varying length and from different tissues. This is done in order to show the applicability of mesoscopic non-equilibrium thermodynamics to interpret experimental data. The

  3. Improvements in continuum modeling for biomolecular systems

    Science.gov (United States)

    Yu, Qiao; Ben-Zhuo, Lu

    2016-01-01

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

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

    International Nuclear Information System (INIS)

    Highlights: → Enzyme-based AND/OR logic gates are integrated with a capacitive field-effect sensor. → The AND/OR logic gates compose of multi-enzyme system immobilised on sensor surface. → Logic gates were activated by different combinations of chemical inputs (analytes). → The logic output (pH change) produced by the enzymes was read out by the sensor. - Abstract: The integration of biomolecular logic gates with field-effect devices - the basic element of conventional electronic logic gates and computing - is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO2-Ta2O5 structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta2O5) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

  5. Determinants of Capital Structure of UK Companies

    OpenAIRE

    Huang, Xu

    2013-01-01

    This paper aims to examine the determinants of capital structure of the UK companies and to provide some up-to-date empirical evidence for previous literatures. The sample of this study involves all non-financial companies listed on the FTSE350 Index during the time period from 2003 to 2012. The analysis of variance and panel data regression models are performed to test what factors may affect the UK companies’ financing decisions. In each model, three different measures of financial leverage...

  6. Structural determinants of sigma receptor affinity

    International Nuclear Information System (INIS)

    The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-[3H]3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent

  7. Structural determinants of sigma receptor affinity

    Energy Technology Data Exchange (ETDEWEB)

    Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.

    1987-12-01

    The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.

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

    OpenAIRE

    Chennubhotla, Chakra; Bahar, Ivet

    2006-01-01

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

  9. The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function

    OpenAIRE

    Jeffrey K Noel; Whitford, Paul C.; Onuchic, José N.

    2012-01-01

    Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general de...

  10. Determinate structures for wing camber control

    International Nuclear Information System (INIS)

    An investigation of truss structures for the purpose of creating a continuously variable camber trailing edge device for an aircraft wing is presented. By creating structures that are both statically and kinematically determinate and then substituting truss elements for actuators, it is possible to impose structural deflection without inducing member stress. A limited number of actuators with limited strain capabilities are located within the structure in order to achieve a target deflected shape starting from an initially symmetric profile. Two objective functions are used to achieve this: a geometric objective for which the target displacement is fixed and a shape objective for which the target displacement is dependent on the surface shape of the targeted aerofoil. The proposed shape objective function is able to offer improvements over the geometric objective by removing some of the constraints applied to the targeted structure joint locations. Four methods for selecting the location of a set of actuators are compared, namely exhaustive search, a genetic algorithm, stepwise forward selection (SFS) and incremental forward selection (IFS). Both SFS and IFS are variations of regression methods for subset selection; in each case an approach has been created to allow the imposing of upper and lower bounds on the search space. It is shown that the genetic algorithm is well suited to addressing the problem of optimally locating a set of actuators; however, regression methods, particularly IFS, can provide a rapid tool suitable for addressing large selection problems

  11. Micro- and nanodevices integrated with biomolecular probes.

    Science.gov (United States)

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

    2015-12-01

    Understanding how biomolecules, proteins and cells interact with their surroundings and other biological entities has become the fundamental design criterion for most biomedical micro- and nanodevices. Advances in biology, medicine, and nanofabrication technologies complement each other and allow us to engineer new tools based on biomolecules utilized as probes. Engineered micro/nanosystems and biomolecules in nature have remarkably robust compatibility in terms of function, size, and physical properties. This article presents the state of the art in micro- and nanoscale devices designed and fabricated with biomolecular probes as their vital constituents. General design and fabrication concepts are presented and three major platform technologies are highlighted: microcantilevers, micro/nanopillars, and microfluidics. Overview of each technology, typical fabrication details, and application areas are presented by emphasizing significant achievements, current challenges, and future opportunities. PMID:26363089

  12. Micro- and nanodevices integrated with biomolecular probes

    Science.gov (United States)

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

    2016-01-01

    Understanding how biomolecules, proteins and cells interact with their surroundings and other biological entities has become the fundamental design criterion for most biomedical micro- and nanodevices. Advances in biology, medicine, and nanofabrication technologies complement each other and allow us to engineer new tools based on biomolecules utilized as probes. Engineered micro/nanosystems and biomolecules in nature have remarkably robust compatibility in terms of function, size, and physical properties. This article presents the state of the art in micro- and nanoscale devices designed and fabricated with biomolecular probes as their vital constituents. General design and fabrication concepts are presented and three major platform technologies are highlighted: microcantilevers, micro/nanopillars, and microfluidics. Overview of each technology, typical fabrication details, and application areas are presented by emphasizing significant achievements, current challenges, and future opportunities. PMID:26363089

  13. Biomolecular Markers in Cancer of the Tongue

    Directory of Open Access Journals (Sweden)

    Daris Ferrari

    2009-01-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

  15. Determinants of Capital Structure in Nigeria

    Directory of Open Access Journals (Sweden)

    Oladele John AKINYOMI

    2013-08-01

    Full Text Available Capital structure represents one of the most discussed concepts in financial management. Capital structure refers to how a company finances its operations whether through shareholders equity-fund or debt or a combination of both. Various internal and external factors contribute to the choice of these sources of fund. The external factors include factors such as tax policy, capital market conditions and tax policy, among others. Meanwhile, the internal factors are those that relate to individual firm characteristics. This study examines the determinants of capital structure in Nigeria using the descriptive research design. The population comprised of the eighty-six manufacturing firms that are listed in the Nigerian Stock Exchange. The sample firms were selected using the simple random sampling method. Secondary data obtained from the annual accounts of 24 randomly selected manufacturing firms for 10 years period culminating in 240 firm-year observations. The results of the regression analysis revealed that leverage (a measure of capital structure has a negative relationship with firm size and tax on one hand and a positive relationship with tangibility of assets, profitability and growth on the other hand. However, only with tangibility of assets and firm size that significant relationship is established. It is recommended for future researchers to carry out similar studies in multiple sectors.

  16. Extracting Biomolecular Interactions Using Semantic Parsing of Biomedical Text

    OpenAIRE

    Garg, Sahil; Galstyan, Aram; Hermjakob, Ulf; Marcu, Daniel

    2015-01-01

    We advance the state of the art in biomolecular interaction extraction with three contributions: (i) We show that deep, Abstract Meaning Representations (AMR) significantly improve the accuracy of a biomolecular interaction extraction system when compared to a baseline that relies solely on surface- and syntax-based features; (ii) In contrast with previous approaches that infer relations on a sentence-by-sentence basis, we expand our framework to enable consistent predictions over sets of sen...

  17. Exploiting Microbeams for Membrane Protein Structure Determination.

    Science.gov (United States)

    Warren, Anna J; Axford, Danny; Paterson, Neil G; Owen, Robin L

    2016-01-01

    A reproducible, and sample independent means of predictably obtaining large, well-ordered crystals has proven elusive in macromolecular crystallography. In the structure determination pipeline, crystallisation often proves to be a rate-limiting step, and the process of obtaining even small or badly ordered crystals can prove time-consuming and laborious. This is particularly true in the field of membrane protein crystallography and this is reflected in the limited number of unique membrane protein structures deposited in the protein data bank (less than 650 by June 2016 - http://blanco.biomol.uci.edu/mpstruc ). Over recent years the requirement for, and time and cost associated with obtaining, large crystals has been partially alleviated through the development of beamline instrumentation allowing data collection, and structure solution, from ever-smaller crystals. Advances in several areas have led to a step change in what might be considered achievable during a synchrotron trip over the last decade. This chapter will briefly review the current status of the field, the tools available to ease data collection and processing, and give some examples of exploitation of these for membrane protein microfocus macromolecular crystallography. PMID:27553238

  18. Structural Determinants of Misfolding in Multidomain Proteins.

    Science.gov (United States)

    Tian, Pengfei; Best, Robert B

    2016-05-01

    Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins. PMID:27163669

  19. Structural Determinants of Misfolding in Multidomain Proteins

    Science.gov (United States)

    Tian, Pengfei; Best, Robert B.

    2016-01-01

    Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins. PMID:27163669

  20. Biomolecular surface construction by PDE transform.

    Science.gov (United States)

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

    2012-03-01

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

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

    Science.gov (United States)

    Bülbül, Gonca; Hayat, Akhtar; Andreescu, Silvana

    2016-04-01

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

  2. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C

    1977-01-01

    Crystallography may be described as the science of the structure of materi­ als, using this word in its widest sense, and its ramifications are apparent over a broad front of current scientific endeavor. It is not surprising, therefore, to find that most universities offer some aspects of crystallography in their undergraduate courses in the physical sciences. It is the principal aim of this book to present an introduction to structure determination by X-ray crystal­ lography that is appropriate mainly to both final-year undergraduate studies in crystallography, chemistry, and chemical physics, and introductory post­ graduate work in this area of crystallography. We believe that the book will be of interest in other disciplines, such as physics, metallurgy, biochemistry, and geology, where crystallography has an important part to play. In the space of one book, it is not possible either to cover all aspects of crystallography or to treat all the subject matter completely rigorously. In particular, certain ...

  3. Crystal structure determination of Jatrorrhizine chloride

    Institute of Scientific and Technical Information of China (English)

    LEI XianRong; YANG JianHua; LIN Xiang; DAI Qin; CHENG Qiang; GUO LingHong; LI Hui

    2009-01-01

    Optimum resolution data of powder X-ray diffraction (PXRD) for Jatrorrhizine (Jat) were collected by an X' Pert Pro MPD diffractometer with an X'celerator detector under the stepwise scanning condition as 8.255 ms and 0.00836°per step,2θrange of 50°-80° and total scanning period of 8-10 min. Indexing of the crystal system and a search of the space group from the powder X-ray diffraction data were conducted by the computational crystallography method. The pilot crystal models of Jat were globally optimized with Monte Carlo method and then refined with the Rietveld method. In parallel with PXRD test,single crystals of Jat were cultured in an aqueous solution by a slow-decreasing temperature method,then its crystal structure was determined by single crystal X-ray diffraction (SCXRD). Both crystal structures from PXRD and SCXRD are identical. The results show that the crystal structure of Jat belongs to a monoclinic system and the space group P21/c. The parameters of cell dimensions from PXRD are a=7.69(A),b= 12.55(A),c=20.89(A),β=106.53°,Z=4,and V=1933.4(A)3,meanwhile the parameters from SCXRD are a=7.72(A),b=12.61(A),c=20.99(A),β=106.38°,Z=4,and V=1961.3(A)3.

  4. Integrated Spintronic Platforms for Biomolecular Recognition Detection

    Science.gov (United States)

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

    2008-06-01

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

  5. A multiscale modeling approach for biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-15

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

  6. Determination of Protein Backbone Structures from Residual Dipolar Couplings

    OpenAIRE

    Prestegard, J H; Mayer, K. L.; Valafar, H.; Benison, G. C.

    2005-01-01

    There are a number of circumstances where a focus on determination of the backbone structure of a protein, as opposed to a complete all-atom structure, may be appropriate. This is particularly the case for structures determined as a part of a structural genomics initiative where computational modeling of many sequentially related structures from the backbone of a single family representative is anti...

  7. Utilizing plasma physics to create biomolecular movies

    Energy Technology Data Exchange (ETDEWEB)

    Hau-Riege, S [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-07-24

    In spring of 2000, the LCLS Scientific Advisory Committee selected the top scientific experiments for LCLS. One of the proposed flagship experiments is atomic-resolution three-dimensional structure determination of isolated biolgical macromolecules and particles, with the ultimate goal of obtaining molecular (snapshot) movies. The key enabling insight was that radiation damage may be overcome by using x-ray pulses that are shorter than the time it takes for damage to manifest itself.

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

    Science.gov (United States)

    Urry, Dan W.

    2000-03-01

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

  9. SWISS-PROT: connecting biomolecular knowledge via a protein database.

    Science.gov (United States)

    Gasteiger, E; Jung, E; Bairoch, A

    2001-07-01

    With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. It is important to provide the users of biomolecular databases with a degree of integration between these databases as by nature all of these databases are connected in a scientific sense and each one of them is an important piece to biological complexity. In this review we will highlight our effort in connecting biological information as demonstrated in the SWISS-PROT protein database. PMID:11488411

  10. Determining structure and function in nanomaterial biocomposites

    Science.gov (United States)

    Griffin, David M.

    Polymeric biomaterials represent the leading technologies available today for the repair of tissue damage and for targeted drug delivery. Perhaps the most valuable aspect of polymer-based systems is the extent to which their physical properties (e.g. elasticity, porosity, etc.) can be controlled and tuned by regulating experimental parameters during their synthesis. Biomaterial performance can be improved further still by including supplementary components resulting in a composite material. Synergetic interactions between the constituents of composite materials often results in bulk physical properties that are substantially more than the sum of individual parts. Through understanding and exploiting these sympathetic relationships, novel biocomposites can be developed which exhibit improved efficacy and biocompatibility. Here we report on the synthesis strategies and characterization of novel biocomposites from our laboratory. We look specifically at hydrogel composites containing a physically-associated network of PluronicRTM block copolymer along with a calcium-phosphate mineral component. Rheological results show that composites containing an in situ deposited mineral exhibit a significantly higher elastic modulus than composites of similar composition formed by conventional means. Moreover, analysis of the calcium-phosphate phase of in situ composites revealed that system parameters such as acidity play an integral role in determining the size and stability of the resultant mineral and subsequently the materials' expected in vivo performance. Changes to the structure in PluronicRTM/calcium-phosphate composite hydrogels during dehydration was investigated to provide a look into the mechanisms involved in composite formation. Small angle X-ray scattering analysis of these systems shows that hydrogen bonding interactions between phosphate ions and the polyethylene oxide (PEO) polymer block significantly impact the nanoscale structure and long-range order contained

  11. Deterministic characterization of phase noise in biomolecular oscillators

    International Nuclear Information System (INIS)

    On top of the many external perturbations, cellular oscillators also face intrinsic perturbations due the randomness of chemical kinetics. Biomolecular oscillators, distinct in their parameter sets or distinct in their architecture, show different resilience with respect to such intrinsic perturbations. Assessing this resilience can be done by ensemble stochastic simulations. These are computationally costly and do not permit further insights into the mechanistic cause of the observed resilience. For reaction systems operating at a steady state, the linear noise approximation (LNA) can be used to determine the effect of molecular noise. Here we show that methods based on LNA fail for oscillatory systems and we propose an alternative ansatz. It yields an asymptotic expression for the phase diffusion coefficient of stochastic oscillators. Moreover, it allows us to single out the noise contribution of every reaction in an oscillatory system. We test the approach on the one-loop model of the Drosophila circadian clock. Our results are consistent with those obtained through stochastic simulations with a gain in computational efficiency of about three orders of magnitude

  12. Combining vibrational biomolecular spectroscopy with chemometric techniques for the study of response and sensitivity of molecular structures/functional groups mainly related to lipid biopolymer to various processing applications.

    Science.gov (United States)

    Yu, Gloria Qingyu; Yu, Peiqiang

    2015-09-01

    The objectives of this project were to (1) combine vibrational spectroscopy with chemometric multivariate techniques to determine the effect of processing applications on molecular structural changes of lipid biopolymer that mainly related to functional groups in green- and yellow-type Crop Development Centre (CDC) pea varieties [CDC strike (green-type) vs. CDC meadow (yellow-type)] that occurred during various processing applications; (2) relatively quantify the effect of processing applications on the antisymmetric CH3 ("CH3as") and CH2 ("CH2as") (ca. 2960 and 2923 cm(-1), respectively), symmetric CH3 ("CH3s") and CH2 ("CH2s") (ca. 2873 and 2954 cm(-1), respectively) functional groups and carbonyl C=O ester (ca. 1745 cm(-1)) spectral intensities as well as their ratios of antisymmetric CH3 to antisymmetric CH2 (ratio of CH3as to CH2as), ratios of symmetric CH3 to symmetric CH2 (ratio of CH3s to CH2s), and ratios of carbonyl C=O ester peak area to total CH peak area (ratio of C=O ester to CH); and (3) illustrate non-invasive techniques to detect the sensitivity of individual molecular functional group to the various processing applications in the recently developed different types of pea varieties. The hypothesis of this research was that processing applications modified the molecular structure profiles in the processed products as opposed to original unprocessed pea seeds. The results showed that the different processing methods had different impacts on lipid molecular functional groups. Different lipid functional groups had different sensitivity to various heat processing applications. These changes were detected by advanced molecular spectroscopy with chemometric techniques which may be highly related to lipid utilization and availability. The multivariate molecular spectral analyses, cluster analysis, and principal component analysis of original spectra (without spectral parameterization) are unable to fully distinguish the structural differences in the

  13. A mechanical Turing machine: blueprint for a biomolecular computer.

    Science.gov (United States)

    Shapiro, Ehud

    2012-08-01

    We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and control by molecular recognition unleashing allosteric conformational changes. Logically, the device is not more complicated than biomolecular machines of the living cell, and all its operations are part of the standard repertoire of these machines; hence, a biomolecular embodiment of the device is not infeasible. If implemented, such a biomolecular device may operate in vivo, interacting with its biochemical environment in a program-controlled manner. In particular, it may 'compute' synthetic biopolymers and release them into its environment in response to input from the environment, a capability that may have broad pharmaceutical and biological applications. PMID:22649583

  14. Structural Determinants of Juvenile Offenses in School.

    Science.gov (United States)

    Kowalski, Gregory S.; And Others

    1983-01-01

    Using multiple regression techniques, evaluates the relative contributions of community structure, school structure, and crime prevention efforts to delinquency in public schools. Finds that distance from central business district, school size, and region are of predictive value, when crimes against persons, property, and perceived crime are…

  15. WAY TO DETERMINE STIFFNESS FUNCTION OF STRUCTURE

    Institute of Scientific and Technical Information of China (English)

    WANG De-ming; GAI Bing-zheng

    2005-01-01

    For calculating the stiffness function of a structure, the differential equation of the vibration of the structure was divided into the differential equation on the original stiffness function that was known, and Fredholm integral equation of the first kind on the undetermined stiffness function that was unknown. And the stable solutions of the integral equation, when the smooth factor was equal to zero, was solved by the extrapolation with p smooth factors. So the stiffness function of the structure is obtained. Applied examples show that the method is feasible and effective.

  16. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C

    1995-01-01

    X-ray crystallography provides us with the most accurate picture we can get of atomic and molecular structures in crystals. It provides a hard bedrock of structural results in chemistry and in mineralogy. In biology, where the structures are not fully crystalline, it can still provide valuable results and, indeed, the impact here has been revolutionary. It is still an immense field for young workers, and no doubt will provide yet more striking develop­ ments of a major character. It does, however, require a wide range of intellectual application, and a considerable ability in many fields. This book will provide much help. It is a very straightforward and thorough guide to every aspect of the subject. The authors are experienced both as research workers themselves and as teachers of standing, and this is shown in their clarity of exposition. There are plenty of iliustrations and worked examples to aid the student to obtain a real grasp of the subject.

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

    Science.gov (United States)

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

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

  18. Determining the structure of Carbon-60

    International Nuclear Information System (INIS)

    Carbon-60 is the most stable and best known of the carbon cage structures known collectively as the fullerenes. It is a remarkable molecule that forms a fascinating solid. Although the molecular shape of C sub 6 sub 0 is familiar - it is simply the shape of a soccer ball with 12 pentagons and 20 hexagons - the manner in which it forms a crystal structure is by no means obvious. This talk will focus on the insights which neutron scattering at ISIS has brought to our understanding of solid C sub6 sub 0. At room temperature, the structure may be regarded as forming as essentially ideal cubic-close packed molecular bubble-raft: each molecule is reorienting so rapidly that a time-averaged picture, over as little as a nanosecond, reveals a closely spherical shell of atomic density. At 260 K, a rather unusual structural transition occurs. The molecules order but still retain cubic symmetry. Although this may not appear to be a rather dramatic change, detailed considerations show that a profound transition has occurred that bears close similarities to a solid-liquid phase transition but in two dimensions. Below 260 K, reorientation still occurs but at a dramatically reduced rate as the temperature is lowered. Indeed at around 90 K, The reorientation is so slow that thermodynamic equilibrium cannot be achieved in a reasonable timescale an orientational glass transition occurs. Although the behaviour of solid C sub 6 sub 0 undergoes dramatic changes as a function of temperature, a coherent description has evolved in which neutron scattering plays a central role. Close analogies are to be found in the study of systems as diverse as solid H sub 2 and human-rhinovirus structures. These analogies and the central role played by neutron scattering at ISIS will be emphasised in this paper. 5 figs., 10 refs. (author)

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

    Science.gov (United States)

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

    2016-02-22

    The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2. PMID:26410586

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

    Science.gov (United States)

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

    2015-10-01

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

  1. Some structural determinants of melody recall.

    Science.gov (United States)

    Boltz, M

    1991-05-01

    Sophisticated musicians were asked to recall, using musical notation, a set of unfamiliar folk tunes that varied in rhythmic structure and referents of tonality. The results showed that memory was facilitated by tonic triad members marking phrase endings, but only when their presence was highlighted by a corresponding pattern of temporal accents. Conversely, recall significantly declined when tonal information was either absent or obscured by rhythmic structure. Error analyses further revealed that the retention of overall pitch contour and information at phrase ending points varied as a function of these manipulations. The results are discussed in terms of a framework that links the acts of perceiving and remembering to a common attentional scheme. PMID:1861610

  2. What Determines the Likelihood of Structural Reforms?

    OpenAIRE

    Agnello, Luca; Castro, Vitor; Jalles, João Tovar; Sousa, Ricardo M.

    2014-01-01

    We use data for a panel of 60 countries over the period 1980-2005 to investigate the main drivers of the likelihood of structural reforms. We find that: (i) external debt crises are the main trigger of financial and banking reforms; (ii) inflation and banking crises are the key drivers of external capital account reforms; (iii) banking crises also hasten financial reforms; and (iv) economic recessions play an important role in promoting the necessary consensus for financial, capital, banking ...

  3. RNA Structure Determination Using SAXS Data

    OpenAIRE

    Yang, Sichun; Parisien, Marc; Major, François; Roux, Benoît

    2010-01-01

    Exploiting the experimental information from small-angle x-ray solution scattering (SAXS) in conjunction with structure prediction algorithms can be advantageous in the case of ribonucleic acids (RNA), where global restraints on the 3D fold are often lacking. Traditional usage of SAXS data often starts by attempting to reconstruct the molecular shape ab initio, which is subsequently used to assess the quality of model Here, an alternative strategy is explored whereby the models from a very la...

  4. Structure and determinants of consumer expenditures

    OpenAIRE

    Stejskal, Ladislav; Stávková, Jana

    2011-01-01

    The local and worldwide present economic situation is often judged and discussed on the basis of the consumer expenditures development. Consumer expenditures or a buying behaviour outcome of each individual market subject is in marketing defined as a product and service seeking, from that consumers expect satisfying of their needs. On the basis of the introduced determination authors conducted a marketing research. Results in combination with a marketing insight into consumer expenditures rea...

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

    Science.gov (United States)

    Falkner, Joshua Charles

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

  6. Near-infrared fluorophores as biomolecular probes

    Science.gov (United States)

    Patonay, Gabor; Beckford, Garfield; Strekowski, Lucjan; Henary, Maged; Merid, Yonathan

    2010-02-01

    Near-Infrared (NIR) fluorescence has been valuable in analytical and bioanalytical chemistry. NIR probes and labels have been used for several applications, including hydrophobicity of protein binding sites, DNA sequencing, immunoassays, CE separations, etc. The NIR region (700-1100 nm) has advantages for the spectroscopist due to the inherently lower background interference from the biological matrix and the high molar absorptivities of NIR chromophores. During the studies we report here several NIR dyes were prepared to determine the role of the hydrophobicity of NIR dyes and their charge in binding to amino acids and proteins, e.g., serum albumins. We synthesized NIR dye homologs containing the same chromophore but substituents of varying hydrophobicity. Hydrophobic moieties were represented by alkyl and aryl groups. These NIR dyes of varying hydrophobicity exhibited varying degrees of H-aggregation in aqueous solution indicating that the degree of H-aggregation could be used as an indicator to predict binding characteristics to serum albumins. In order to understand what factors may be important in the binding process, spectral behavior of these varying hydrophobicity dyes were examined in the presence of amino acids. Typical dye structures that exhibit large binding constants to biomolecules were compared in order to optimize applications utilizing non-covalent interactions.

  7. Photoelectron holography applied to surface structural determination

    Energy Technology Data Exchange (ETDEWEB)

    Petersen, B.L.

    1995-05-01

    Photoemitted electron waves are used as coherent source waves for angstrom-scale holographic imaging of local atomic geometry at surfaces. Electron angular distribution patterns are collected above a sample surface and serve as a record of the interference between source wave and waves scattered from surrounding ion cores. Using a mathematical imaging integral transformation, the three-dimensional structural information is obtained directly from these collected patterns. Patterns measured with different electron kinetic energies are phase-summed for image improvement. Pt (111) surface is used as a model system. A pattern 9.6{angstrom}{sup {minus}1} (351 eV) is used to generate a full 3-D image of atom locations around an emitter with nearest neighbors within 0.l{angstrom} of the expected bulk positions. Atoms several layers beyond the nearest neighbors are also apparent. Twin-image reduction and artifact suppression is obtained by phase-summing eight patterns measured from 8.8 to 10.2{angstrom}{sup {minus}1} (295 to 396 eV). 32 were measured in 0.2{angstrom}{sup {minus}1} steps from 6.0 to 12.2{angstrom}{sup {minus}1} (137 to 567 eV) are presented here. Simple models of two-slit interference are compared with electron scattering to illuminate understanding of holographic recording of the structural information. This also shows why it sometimes fails due to destructive interferences. Simple theoretical models of electron scattering are compared to experiment to show the origin of the structural information and the differences that result from atomic scattering and from the source wave. Experimental parameters and their relation to imaging is discussed. Comparison is made to the Pt pattern measured at 351 eV using the simple theoretical model. The remaining data set is also modeled, and the eight appropriate theoretical patterns are used to regenerate the multiple-wavenumber experimental result. A clean Cu (001) surface is also measured and imaged.

  8. How structure determines correlations in neuronal networks.

    Directory of Open Access Journals (Sweden)

    Volker Pernice

    2011-05-01

    Full Text Available Networks are becoming a ubiquitous metaphor for the understanding of complex biological systems, spanning the range between molecular signalling pathways, neural networks in the brain, and interacting species in a food web. In many models, we face an intricate interplay between the topology of the network and the dynamics of the system, which is generally very hard to disentangle. A dynamical feature that has been subject of intense research in various fields are correlations between the noisy activity of nodes in a network. We consider a class of systems, where discrete signals are sent along the links of the network. Such systems are of particular relevance in neuroscience, because they provide models for networks of neurons that use action potentials for communication. We study correlations in dynamic networks with arbitrary topology, assuming linear pulse coupling. With our novel approach, we are able to understand in detail how specific structural motifs affect pairwise correlations. Based on a power series decomposition of the covariance matrix, we describe the conditions under which very indirect interactions will have a pronounced effect on correlations and population dynamics. In random networks, we find that indirect interactions may lead to a broad distribution of activation levels with low average but highly variable correlations. This phenomenon is even more pronounced in networks with distance dependent connectivity. In contrast, networks with highly connected hubs or patchy connections often exhibit strong average correlations. Our results are particularly relevant in view of new experimental techniques that enable the parallel recording of spiking activity from a large number of neurons, an appropriate interpretation of which is hampered by the currently limited understanding of structure-dynamics relations in complex networks.

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

    Directory of Open Access Journals (Sweden)

    Michael-Rock Goldsmith

    2014-01-01

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

  10. Structural and institutional determinants of investment activity in Africa

    OpenAIRE

    Chuku, Chuku; Onye, Kenneth; Ajah, Hycent

    2015-01-01

    This paper considers the structural and institutional determinants of investment activity in selected African countries within a neoclassical framework. Generalized method of moments and a family of panel data estimation techniques are utilized in addition to nonparametric kernel regression techniques to uncover the relationship. Three main findings emerge; (i) financial openness and institutional quality are reasonably robust structural and institutional determinants of investment activity...

  11. Determination of atomic cluster structure with cluster fusion algorithm

    DEFF Research Database (Denmark)

    Obolensky, Oleg I.; Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters.......We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters....

  12. Structural Determinants of Sleeping Beauty Transposase Activity.

    Science.gov (United States)

    Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán

    2016-08-01

    Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold. PMID:27401040

  13. Determination of Ice Characteristics for Marine Hydroengineering Structures

    Energy Technology Data Exchange (ETDEWEB)

    Kantarzhi, I. G., E-mail: kantardgi@yandex.ru [Moscow State University of Civil Engineering (MSGU) (Russian Federation); Maderich, V. S., E-mail: vladmad@gmail.com; Koshebutskii, V. I., E-mail: koshik1@gmail.com [Ukrainian Center of Environmental and Water Projects (UTsÉVP) (Ukraine)

    2016-01-15

    Problems and potential approaches to determining ice characteristics for sea hydroengineering structures design are considered. A system for numerical modeling of ice dynamics is presented. The system may be used to define ice characteristics on approaches to structures with due regard for local hydrometeorological conditions and ice loads on structures. System application examples are presented for determining computational scenarios for ice loads at structures of the Pevek floating nuclear power plant (FNPP), as well as for the breakwater pier under reconstruction in Vanino. A scenario approach is used to determined ice loads.

  14. Audit Fee Determinants in different Ownership Structures : The Swedish Setting

    OpenAIRE

    Ask, Joakim; LJ Holm, Mattias

    2013-01-01

    The aim of this study is to test the audit fee determinants for companies listed on Nasdaq OMX Stockholm Stock Exchange and to examine whether the audit fee determinants diverge for ownership structures. By testing the audit fee determinants in a Swedish setting the study contributes to the research body in two ways; by testing a previously sparsely researched setting and examining the monitoring need for different ownership structures. The results indicate that audit fees are explained to a ...

  15. Determinants of Capital Structure: Empirical Evidence From UK

    OpenAIRE

    XU, WENJING

    2010-01-01

    This paper investigates the determinants of capital structure for the companies in the United Kingdom. The aim of this study is to determine which capital structure is more appropriate to UK listed companies. Results obtained will be compared against previous empirical and theoretical predictions. Panel data set containing 342 UK public quoted companies across 8 industries during the period from 2000-2009 is employed. A Pooled OLS regression is constructed to discuss what the determinants...

  16. The methodology of determining the corrosion of steel structures

    OpenAIRE

    S.D. Fedotov; A.V. Ulybin; N.N. Shabrov

    2013-01-01

    The problems of determining the corrosive wear of steel structures are considered. The results of applying ultrasonic method to determine the remaining profile of the structure are described. The main advantages and disadvantages of ultrasonic thickness meters comparing to mechanical devices are given. Low reliability of the method based on evaluating the thickness of the corrosion oxides is substantiated. The problems of determining the original section of the elements are outlined. The alg...

  17. Ab initio structure determination via powder X-ray diffraction

    Indian Academy of Sciences (India)

    Digamber G Porob; T N Guru Row

    2001-10-01

    Structure determination by powder X-ray diffraction data has gone through a recent surge since it has become important to get to the structural information of materials which do not yield good quality single crystals. Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination of -NaBi3V2O10.

  18. Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability

    Energy Technology Data Exchange (ETDEWEB)

    Sigala, Paul A.; Ruben, Eliza A.; Liu, Corey W.; Piccoli, Paula M. B.; Hohenstein, Edward G.; Martinez, Todd J.; Schultz, Arthur J.; Herschiag, Daniel

    2015-05-06

    Hydrogen bonds profoundly influence the architecture and activity of biological macromolecules. Deep appreciation of hydrogen bond contributions to biomolecular function thus requires a detailed understanding of hydrogen bond structure and energetics and the relationship between these properties. Hydrogen bond formation energies (Delta G(f)) are enormously more favorable in aprotic solvents than in water, and two classes of contributing factors have been proposed to explain this energetic difference, focusing respectively on the isolated and hydrogen-bonded species: (I) water stabilizes the dissociated donor and acceptor groups much better than aprotic solvents, thereby reducing the driving force for hydrogen bond formation; and (II) water lengthens hydrogen bonds compared to aprotic environments, thereby decreasing the potential energy within the hydrogen bond. Each model has been proposed to provide a dominant contribution to Delta G(f), but incisive tests that distinguish the importance of these contributions are lacking. Here we directly test the structural basis of model II. Neutron crystallography, NMR spectroscopy, and quantum mechanical calculations demonstrate that O-H center dot center dot center dot O hydrogen bonds in crystals, chloroform, acetone, and water have nearly identical lengths and very similar potential energy surfaces despite Delta G(f) differences >8 kcal/mol across these solvents. These results rule out a substantial contribution from solvent-dependent differences in hydrogen bond structure and potential energy after association (model II) and thus support the conclusion that differences in hydrogen bond Delta G(f) are predominantly determined by solvent interactions with the dissociated groups (model I). These findings advance our understanding of universal hydrogen-bonding interactions and have important implications for biology and engineering.

  19. MOTOR: model assisted software for NMR structure determination.

    Science.gov (United States)

    Schieborr, Ulrich; Sreeramulu, Sridhar; Elshorst, Bettina; Maurer, Marcus; Saxena, Krishna; Stehle, Tanja; Kudlinzki, Denis; Gande, Santosh Lakshmi; Schwalbe, Harald

    2013-11-01

    Eukaryotic proteins with important biological function can be partially unstructured, conformational flexible, or heterogenic. Crystallization trials often fail for such proteins. In NMR spectroscopy, parts of the polypeptide chain undergoing dynamics in unfavorable time regimes cannot be observed. De novo NMR structure determination is seriously hampered when missing signals lead to an incomplete chemical shift assignment resulting in an information content of the NOE data insufficient to determine the structure ab initio. We developed a new protein structure determination strategy for such cases based on a novel NOE assignment strategy utilizing a number of model structures but no explicit reference structure as it is used for bootstrapping like algorithms. The software distinguishes in detail between consistent and mutually exclusive pairs of possible NOE assignments on the basis of different precision levels of measured chemical shifts searching for a set of maximum number of consistent NOE assignments in agreement with 3D space. Validation of the method using the structure of the low molecular-weight-protein tyrosine phosphatase A (MptpA) showed robust results utilizing protein structures with 30-45% sequence identity and 70% of the chemical shift assignments. About 60% of the resonance assignments are sufficient to identify those structural models with highest conformational similarity to the real structure. The software was benchmarked by de novo solution structures of fibroblast growth factor 21 (FGF21) and the extracellular fibroblast growth factor receptor domain FGFR4 D2, which both failed in crystallization trials and in classical NMR structure determination. PMID:23852655

  20. Spatially encoded strategies in the execution of biomolecular-oriented 3D NMR experiments

    International Nuclear Information System (INIS)

    Three-dimensional nuclear magnetic resonance (3D NMR) provides one of the foremost analytical tools available for the elucidation of biomolecular structure, function and dynamics. Executing a 3D NMR experiment generally involves scanning a series of time-domain signals S(t3), as a function of two time variables (t1, t2) which need to undergo parametric incrementations throughout independent experiments. Recent years have witnessed extensive efforts towards the acceleration of this kind of experiments. Among the different approaches that have been proposed counts an 'ultrafast' scheme, which distinguishes itself from other propositions by enabling-at least in principle-the acquisition of the complete multidimensional NMR data set within a single transient. 2D protein NMR implementations of this single-scan method have been demonstrated, yet its potential for 3D acquisitions has only been exemplified on model organic compounds. This publication discusses a number of strategies that could make these spatial encoding protocols compatible with 3D biomolecular NMR applications. These include a merging of 2D ultrafast NMR principles with temporal 2D encoding schemes, which can yield 3D HNCO spectra from peptides and proteins within ∼100 s timescales. New processing issues that facilitate the collection of 3D NMR spectra by relying fully on spatial encoding principles are also assessed, and shown capable of delivering HNCO spectra within 1 s timescales. Limitations and prospects of these various schemes are briefly addressed

  1. Group transfer theory of single molecule imaging experiments in the F-ATPase biomolecular motor

    Science.gov (United States)

    Volkan-Kacso, Sandor; Marcus, Rudolph

    I describe a chemo-mechanical theory to treat single molecule imaging and ``stalling'' experiments on the F-ATPase enzyme. This enzyme is an effective stepping biomolecular rotary motor with a rotor shaft and a stator ring. Using group transfer theoretical approach the proposed structure-based theory couples the binding transition of nucleotides in the stator subunits and the physics of torsional elasticity in the rotor. The twisting of the elastic rotor domain acts as a perturbation upon the driving potential, the Gibbs free energy. In the theory, without the use of adjustastable parameters, we predict the rate and equilibrium constant dependence of steps such as ATP binding and phosphate release as a function of manipulated rotor angle. Then we compare these predictions to available data from stalling experiments. Besides treating experiments, the theory can provide guides for atomistic simulations, which could calculate the reorganization parameter and the torsional spring constant. The framework is generic and I discuss its application to other single molecule experiments, such as controlled rotation and other biomolecular motors, including motor-DNA complexes and linear motors.[PNAS, Early Edition, Oct. 19, 2015, doi: 10.1073/pnas.1518489112

  2. Automating the determination of 3D protein structure

    Energy Technology Data Exchange (ETDEWEB)

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  3. The Determinants of Capital Structure: An Empirical Evidence from Germany

    OpenAIRE

    Pornsuwankul, Juthamart/Miss

    2012-01-01

    Abstract This paper develops a preliminary study to explore the determinants of capital structure of listed and unlisted companies in Germany using panel data methodology. The findings suggest that the capital structure of listed and unlisted firms is significantly different. Also, some insights from the modern finance theory of capital structure are portable to Germany in that firm-specific factors that are identified to be significant in explaining capital structure in empirical studies...

  4. Quantifying Modularity in the Evolution of Biomolecular Systems

    OpenAIRE

    2004-01-01

    Functional modules are considered the primary building blocks of biomolecular systems. Here we study to what extent functional modules behave cohesively across genomes:That is, are functional modules also evolutionary modules? We probe this question by analyzing for a large collection of functional modules the phyletic patterns of their genes across 110 genomes. The majority of functional modules display limited evolutionary modularity. This result confirms certain comparative genome analyses...

  5. The biomolecular and ultrastructural basis of epidermolysis bullosa:

    OpenAIRE

    Ciolan, Maria; Olariu, Liviu; Solovan, Caius

    2005-01-01

    Transmission electron microscopy, immunoelectron microscopy, immunofluorescence and antigenic mapping have improved our understanding of the dermo-epidermal junction. We have reviewed some ultrastructural and biomolecular aspects related to the dermo-epidermal junction. In part, they are implicated in the pathogenesis of a group of hereditary disorders characterized by skin fragility, collectively known as epidermolysis bullosa (EB). These disorders could benefit in the near future from a gen...

  6. A mechanical Turing machine: blueprint for a biomolecular computer

    OpenAIRE

    Shapiro, Ehud

    2012-01-01

    We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and control by molecular recognition unleashing allosteric conformational changes. Logically, the device is not more complicated than biomolecular machines of the living cell, and a...

  7. Dynamic Presentation of Immobilized Ligands Regulated through Biomolecular Recognition

    OpenAIRE

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

    2010-01-01

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

  8. 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...

  9. CONCIDERING OF FUNDATION SLOPE TO DETERMINE THE ENGENEERING STRUCTURE HEIGHT

    OpenAIRE

    Zubko, Z.

    2005-01-01

    The article considers some aspects of determining of engineering structure height. It proposes the technique for terrain slope consideration in the course of base adjustment under difficult conditions of geodetic surveying.

  10. Structure Determination of Membrane Proteins in Five Easy Pieces

    OpenAIRE

    Marassi, Francesca M.; Das, Bibhuti B.; Lu, George J.; Nothnagel, Henry J.; Park, Sang Ho; Son, Woo Sung; Tian, Ye; Opella, Stanley J.

    2011-01-01

    A general method for determining the structures of membrane proteins in phospholipid bilayers under physiological conditions is described. Membrane proteins are high priority targets for structure determination, and are challenging for the existing experimental methods. Because membrane proteins reside in a liquid crystalline phospholipid bilayer membranes it is important to study them in this type of environment. The approach we have developed can be summarized in five steps, and incorporate...

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

    Institute of Scientific and Technical Information of China (English)

    CHEN MinXin; LU BenZhuo

    2013-01-01

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

  12. Biomolecular transport and separation in nanotubular networks.

    Energy Technology Data Exchange (ETDEWEB)

    Stachowiak, Jeanne C.; Stevens, Mark Jackson (Sandia National Laboratories, Albuquerque, NM); Robinson, David B.; Branda, Steven S.; Zendejas, Frank; Meagher, Robert J.; Sasaki, Darryl Yoshio; Bachand, George David (Sandia National Laboratories, Albuquerque, NM); Hayden, Carl C.; Sinha, Anupama; Abate, Elisa; Wang, Julia; Carroll-Portillo, Amanda (Sandia National Laboratories, Albuquerque, NM); Liu, Haiqing (Sandia National Laboratories, Albuquerque, NM)

    2010-09-01

    Cell membranes are dynamic substrates that achieve a diverse array of functions through multi-scale reconfigurations. We explore the morphological changes that occur upon protein interaction to model membrane systems that induce deformation of their planar structure to yield nanotube assemblies. In the two examples shown in this report we will describe the use of membrane adhesion and particle trajectory to form lipid nanotubes via mechanical stretching, and protein adsorption onto domains and the induction of membrane curvature through steric pressure. Through this work the relationship between membrane bending rigidity, protein affinity, and line tension of phase separated structures were examined and their relationship in biological membranes explored.

  13. NMRFAM-SDF: a protein structure determination framework

    International Nuclear Information System (INIS)

    The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR—from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website ( http://nmrfam.wisc.edu/software.htm http://nmrfam.wisc.edu/software.htm )

  14. NMRFAM-SDF: a protein structure determination framework.

    Science.gov (United States)

    Dashti, Hesam; Lee, Woonghee; Tonelli, Marco; Cornilescu, Claudia C; Cornilescu, Gabriel; Assadi-Porter, Fariba M; Westler, William M; Eghbalnia, Hamid R; Markley, John L

    2015-08-01

    The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR--from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm). PMID:25900069

  15. NMRFAM-SDF: a protein structure determination framework

    Energy Technology Data Exchange (ETDEWEB)

    Dashti, Hesam; Lee, Woonghee; Tonelli, Marco; Cornilescu, Claudia C.; Cornilescu, Gabriel; Assadi-Porter, Fariba M.; Westler, William M.; Eghbalnia, Hamid R.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)

    2015-08-15

    The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR—from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website ( http://nmrfam.wisc.edu/software.htm http://nmrfam.wisc.edu/software.htm )

  16. Determination of absolute structure using Bayesian statistics on Bijvoet differences

    NARCIS (Netherlands)

    Hooft, R.W.W.; Straver, L.H.; Spek, A.L.

    2008-01-01

    A new probabilistic approach is introduced for the determination of the absolute structure of a compound which is known to be enantiopure based on Bijvoet-pair intensity differences. The new method provides relative probabilities for different models of the chiral composition of the structure. The o

  17. Condutância molecular e biomolecular

    Directory of Open Access Journals (Sweden)

    Gama A. Arnóbio S. da

    2000-01-01

    Full Text Available The concept of molecular conductance is discussed in terms of the propagation of an electronic interaction, between electron donor and acceptor groups, through the bonds of a molecular structure where these groups are embedded. The electronic interaction propagation is described by a Green's function matrix element, in a donor-bridge-acceptor molecular system reduced to a two-level representation.

  18. Generative probabilistic models extend the scope of inferential structure determination

    DEFF Research Database (Denmark)

    Olsson, Simon; Boomsma, Wouter; Frellsen, Jes;

    2011-01-01

    Conventional methods for protein structure determination from NMR data rely on the ad hoc combination of physical forcefields and experimental data, along with heuristic determination of free parameters such as weight of experimental data relative to a physical forcefield. Recently, a theoretical...

  19. Labor Market Structure and Salary Determination among Professional Basketball Players.

    Science.gov (United States)

    Wallace, Michael

    1988-01-01

    The author investigates the labor market structure and determinants of salaries for professional basketball players. An expanded version of the resource perspective is used. A three-tiered model of labor market segmentation is revealed for professional basketball players, but other variables also are important in salary determination. (Author/CH)

  20. Determinants of euro term structure of credit spreads

    OpenAIRE

    Astrid Van Landschoot

    2004-01-01

    In this paper, we investigate the determinants of the Euro term structure of credit spreads. More specifically, we analyze whether the sensitivity of credit spread changes to financial and macroeconomic variables depends on bond characteristics such as rating and maturity. According to the structural models and empirical evidence on credit spreads, we find that changes in the level and the slope of the default-free term structure, the market return, implied volatility, and liquidity risk sign...

  1. Determinants of Capital Structure: A Cross-Country Comparison

    OpenAIRE

    Martin, James

    2013-01-01

    This paper is a cross-country comparison of capital structure; specifically its firm level determinants and how these fluctuate between both Japan and the United States to test the efficacy of competing capital structure theories within contrasting institutional traditions. The purpose of the study is to bring to light the possible effect of such institutional differences on the capital structure decision for financial managers. I utilize a pre-crisis sample of 292 firms, 147 from Japan and 1...

  2. Determinants of Capital Structure: An Empirical Analysis of UK Organisations.

    OpenAIRE

    Gundroo, Shadaab/ SG

    2009-01-01

    In modern day finance, capital structure remains one of those issues under much controversy despite extensive research from academics and practitioners alike. There is a number of existing theories and empirical work on capital structure but as of yet no universal model has been found. The aim of this paper is to analyze the determinants of the capital structure of 73 UK companies over a 5 year period (2004-2008). This study adds to the relatively limited empirical literature on factors infl...

  3. Structural determination of wild-type lactose permease

    OpenAIRE

    Guan, Lan; Mirza, Osman; Verner, Gillian; Iwata, So; Kaback, H. Ronald

    2007-01-01

    Here we describe an x-ray structure of wild-type lactose permease (LacY) from Escherichia coli determined by manipulating phospholipid content during crystallization. The structure exhibits the same global fold as the previous x-ray structures of a mutant that binds sugar but cannot catalyze translocation across the membrane. LacY is organized into two six-helix bundles with twofold pseudosymmetry separated by a large interior hydrophilic cavity open only to the cytoplasmic side and containin...

  4. STRUCTURAL UNEMPLOYMENT AND ITS DETERMINANTS IN SOUTHEAST EUROPE

    OpenAIRE

    Botrić, Valerija

    2011-01-01

    This paper provides comparative analysis of the structural unemployment for a group of transition countries in Southeast Europe, based on relatively simple measure, NAWRU. The paper also investigates and discusses the determinants of relatively high structural unemployment in the region. The results of the empirical estimates point to the remittances and overall changes in business climate as being the significant variables that explain relatively high structural unemployment in analyzed coun...

  5. The determinants of capital structure: Some evidence from banks

    OpenAIRE

    Heider, Florian; Gropp, Reint

    2008-01-01

    This paper documents that standard cross-sectional determinants of firm leverage also apply to the capital structure of large banks in the United States and Europe. We find a remarkable consistency in sign, significance and economic magnitude. Like non-financial firms, banks appear to have stable capital structures at levels that are specific to each individual bank. The results suggest that capital requirements may only be of second-order importance for banks’ capital structures and confirm ...

  6. Ten Simple Rules for Creating Biomolecular Graphics

    OpenAIRE

    Mura, Cameron

    2014-01-01

    One need only compare the number of three-dimensional molecular illustrations in the first (1990) and third (2004) editions of Voet & Voet's "Biochemistry" in order to appreciate this field's profound communicative value in modern biological sciences -- ranging from medicine, physiology, and cell biology, to pharmaceutical chemistry and drug design, to structural and computational biology. The clich\\'e about a picture being worth a thousand words is quite poignant here: The information 'conte...

  7. Integral membrane protein structure determination using pseudocontact shifts

    International Nuclear Information System (INIS)

    Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general

  8. Integral membrane protein structure determination using pseudocontact shifts

    Energy Technology Data Exchange (ETDEWEB)

    Crick, Duncan J.; Wang, Jue X. [University of Cambridge, Department of Biochemistry (United Kingdom); Graham, Bim; Swarbrick, James D. [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Mott, Helen R.; Nietlispach, Daniel, E-mail: dn206@cam.ac.uk [University of Cambridge, Department of Biochemistry (United Kingdom)

    2015-04-15

    Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

  9. Structural determination of intact proteins using mass spectrometry

    Science.gov (United States)

    Kruppa, Gary; Schoeniger, Joseph S.; Young, Malin M.

    2008-05-06

    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  10. Energy group structure determination using particle swarm optimization

    International Nuclear Information System (INIS)

    Highlights: ► Particle swarm optimization is applied to determine broad group structure. ► A graph representation of the broad group structure problem is introduced. ► The approach is tested on a fuel-pin model. - Abstract: Multi-group theory is widely applied for the energy domain discretization when solving the Linear Boltzmann Equation. To reduce the computational cost, fine group cross libraries are often down-sampled into broad group cross section libraries. Cross section data collapsing generally involves two steps: Firstly, the broad group structure has to be determined; secondly, a weighting scheme is used to evaluate the broad cross section library based on the fine group cross section data and the broad group structure. A common scheme is to average the fine group cross section weighted by the fine group flux. Cross section collapsing techniques have been intensively researched. However, most studies use a pre-determined group structure, open based on experience, to divide the neutron energy spectrum into thermal, epi-thermal, fast, etc. energy range. In this paper, a swarm intelligence algorithm, particle swarm optimization (PSO), is applied to optimize the broad group structure. A graph representation of the broad group structure determination problem is introduced. And the swarm intelligence algorithm is used to solve the graph model. The effectiveness of the approach is demonstrated using a fuel-pin model

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still predicated on human-defined pathways. Here, we intr...

  12. Protein hydrogels with engineered biomolecular recognition

    Science.gov (United States)

    Mi, Lixin

    Extracellular matrices (ECMs) are the hydrated macromolecular gels in which cells migrate and proliferate and organize into tissues in vivo . The development of artificial ECM with the required mechanical, physico-chemical, and biological properties has long been a challenge in the biomaterial research field. In this dissertation, a novel set of bioactive protein hydrogels has been synthesized and characterized at both molecular and materials levels. The self-recognized and self-assembled protein copolymers have the ability to provide engineered biofunctionality through the controlled arrangement of bioactive domains on the nanoscale. Genetic engineering methods have been employed to synthesize these protein copolymers. Plasmid DNA carrying genes to express both di- and tri-block proteins have been constructed using molecular cloning techniques. These genes were expressed in bacterial E. coli to ensure homogeneous protein length and anticipated structure. Three diblock protein sequences having a leucine zipper construct on one end and polyelectrolyte (AGAGAGPEG)10 on the other, have been studied by circular dichroism, size-exclusion chromatography, analytical ultracentrifugation, and static light scattering to characterize their secondary structure, structural stability, and oligomeric state. The results show that ABC diblock mixtures form very stable heterotrimer aggregates via self-recognition and self-assembly of the coiled coil end domains. Tri-block proteins with two leucine zipper motif ends flanking the polyelectrolyte random coil in the middle have been investigated by circular dichroism and fluorescence spectroscopy, and the hydrogels formed by self-assembly of these tri-blocks have been studied using transmission electronic microscopy and diffusing wave spectroscopy. The reversible gelation behavior is the result of heterotrimeric aggregation of helices to form the physical crosslinks in the gel, with the polyelectrolyte region center block retaining

  13. Scanning probe and optical tweezer investigations of biomolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Rigby-Singleton, Shellie

    2002-07-01

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Zhou, Pei; Wagner, Gerhard

    2010-01-01

    Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR.We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs. PMID:19731047

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

    Science.gov (United States)

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

    2015-12-01

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

  17. Contribution to structural determination of triterpenes by computer aid

    International Nuclear Information System (INIS)

    The development of nuclear magnetic resonance has made possible the structural knowledge of several substances. In this work, 13C NMR were used to identify the molecular structure of triterpenes. A system composed by several routines written in FOXBASIC was developed to be used as a help to structural determination of triterpenes. A database of 1,000 triterpenes belonging to different backbones was built. The fields contain the chemical shift of each carbon in the molecule and a 10 digit hexadecimal code that characterizes the carbon environment. The code with the general formula: C. α1 α2 α3 α4. A1 A1E. β1 β2, where C designates the nature of the carbon responsible for the chemical shift and the other symbols represent its chemical environment. This system showed to be useful in structure determination of known and unknown triterpenes. (author)

  18. Determinants of capital structure: Evidence from Istanbul stock exchange

    OpenAIRE

    Samery, Mohammad

    2013-01-01

    ABSTRACT: This thesis aims to explain determinants of capital structure evidence from istanbul stock exchange from three companies (Turkcell ,Vodafone and Deutesche Telekom).The two main theories used are for trade-off theory and pecking order theory. The essential of the pecking order is the manager's of capital structure decision are influenced by the market perception of manager's superior information. The trade-off theory provides support for manager's trade-off between benefits and costs...

  19. Determinants of Capital Structure on UK Quoted Companies

    OpenAIRE

    Vo, Hai Tuan

    2012-01-01

    The dissertation aims to examine the determinants influencing the capital structure decisions on UK listed firms and identify which theory is the most relevant one toward UK companies. A panel data set of 234 firms from 9 different industries on FTSE 350 was recorded from 2002-2012 to analyze the factors affecting capital structure. The one-way ANOVA is employed to validate whether the industry effects importantly seize any influence in explaining firms’ debt ratios. Moreover, statistical tes...

  20. Structural Determinants of the Natural Rate of Unemployment in Canada

    OpenAIRE

    Coe, David T

    1990-01-01

    This paper presents empirical estimates of the policy and structural determinants of the natural rate of unemployment in Canada. The paper begins with a discussion of structural features of the economy which impinge on the adjustment of real wages to their equilibrium level. Estimates are presented showing how the generosity of the unemployment insurance system is related to past levels of unemployment. The empirical results indicate that government policies have been largely responsible for ...

  1. Membrane Protein Structure Determination: Back to the Membrane

    OpenAIRE

    Yao, Yong; Ding, Yi; Tian, Ye; Opella, Stanley J.; Marassi, Francesca M.

    2013-01-01

    NMR spectroscopy enables the structures of membrane proteins to be determined in the native-like environment of the phospholipid bilayer membrane. This chapter outlines the methods for membrane protein structural studies using solid-state NMR spectroscopy with samples of membrane proteins incorporated in proteoliposomes or planar lipid bilayers. The methods for protein expression and purification, sample preparation, and NMR experiments are described and illustrated with examples from OmpX an...

  2. Determinants of Capital Structure in Listed Norwegian Firms

    OpenAIRE

    Nilssen, Cathrine Marie

    2014-01-01

    The main goal for most firms is to maximise firm value and the wealth of shareholders. In order to achieve this goal, firms should use an optimal combination of equity and debt that will result in a low weighted average cost of capital for the firm. It is therefore necessary for firms to be aware of the factors that influence their capital structure decision. Several empirical studies have attempted to explain what determines the choice of capital structure in firms. Howev...

  3. Determinants of Market Structure and the Airline Industry

    Science.gov (United States)

    Raduchel, W.

    1972-01-01

    The general economic determinants of market structure are outlined with special reference to the airline industry. Included are the following facets: absolute size of firms; distributions of firms by size; concentration; entry barriers; product and service differentiation; diversification; degrees of competition; vertical integration; market boundaries; and economies of scale. Also examined are the static and dynamic properties of market structure in terms of mergers, government policies, and economic growth conditions.

  4. Structure determination of drug target proteins by neutron crystallography

    International Nuclear Information System (INIS)

    High resolution X-ray crystallography provides information for most of the atoms comprising the proteins, with the exception of hydrogen atoms. Whereas, neutron crystallography, which is a powerful technique for locating hydrogen atoms, enables us to obtain accurate atomic positions within proteins. Neutron diffraction data can provide information of the location of hydrogen atoms to the structural information determined by X-ray crystallography. Here, we show the recent results of the structural determination of drug-target proteins, porcine pancreatic elastase and human immuno-deficiency virus type-1 protease by both X-ray and neutron diffraction. The structure of porcine pancreatic elastase with its potent inhibitor was determined to 0.094 nm resolution by X-ray diffraction and 0.165 nm resolution by neutron diffraction. The structure of HIV-PR with its potent inhibitor was also determined to 0.093 nm resolution by X-ray diffraction and 0.19 nm resolution by neutron diffraction. The ionization state and the location of hydrogen atoms of the catalytic residue in these enzymes were determined by neutron diffraction. Furthermore, collaborative use of both X-ray and neutron crystallography to identify the location of ambiguous hydrogen atoms will be shown. (author)

  5. Determinants of Capital Structure: Panel Data Evidence from UK Firms

    OpenAIRE

    Li, Rui

    2008-01-01

    This dissertation intends to analyse and examine the determinants of the capital structure with an unbalanced panel of 1504 listed UK companies from 2000 to 2007. A range of classical capital theories including Modigliani-Miller (M-M)irrelevance theory, the trade-off, pecking-order and agency theories, are deployed to explore and predict the signs and significance of each determinant pointed out by Titman and Wessels (1988) and Harris and Raviv (1991). In the investigation, we first employ th...

  6. Slavnov determinants, Yang-Mills structure constants, and discrete KP

    OpenAIRE

    Foda, O.; Wheeler, M.

    2012-01-01

    Using Slavnov's scalar product of a Bethe eigenstate and a generic state in closed XXZ spin-1/2 chains, with possibly twisted boundary conditions, we obtain determinant expressions for tree-level structure constants in 1-loop conformally-invariant sectors in various planar (super) Yang-Mills theories. When certain rapidity variables are allowed to be free rather than satisfy Bethe equations, these determinants become discrete KP tau-functions.

  7. Symmetry determination following structure solution in P1

    OpenAIRE

    Palatinus, Lukas; Lee, Arie van der

    2008-01-01

    A new method for space-group determination is described. It is based on a symmetry analysis of the structure-factor phases resulting from a structure solution in space group P1. The output of the symmetry analysis is a list of all symmetry operations compatible with the lattice. Each symmetry operation is assigned a symmetry agreement factor that is used to select the symmetry operations that are the elements of the space group of the structure. On the basis of the list of the selected operat...

  8. Capital Structure of Agricultural Businesses and its Determinants

    Directory of Open Access Journals (Sweden)

    R. Aulová

    2013-06-01

    Full Text Available The article deals with the analysis of the capital structure of agricultural businesses of legal entities and its determinants. It discusses the effect of selected determinants on the capital structure of businesses, expressed by way of three categories of indebtedness. The analysis of the determinants of capital structure is conducted by way of multiple linear regression. Also being verified is the hypothesis of whether the effect of individual determinants of capital structure is in accordance with the theoretical assumptions of conditional theories of capital structure and empirical studies.The panel data for the article were acquired from the Albertina database, provided by the company Soliditet, s.r.o. Specifically, the data used were those from accounting statements for the years 2004 – 2010 for the agricultural businesses of legal entities. In total, the object of examination was 16075 businesses, which were divided up according to legal forms (joint stock company, cooperative, and limited liability company and subsequently the relevant size group. In total, 18 groups of businesses were created, whereby the average balance and profit and loss account were drawn up for each group, on the basis of which the relevant calculations were conducted. The article is a part of the grant project IGA 20121069 “Identification of the main determinants of the result of economic activity of agricultural businesses of legal entities and the determination of their specifics” and of the institutional research intentions MSM 6046070906 „Economics sources of Czech agriculture and their efficient use in the context of multifunctional agri-food systems“.

  9. Role of biomolecular logic systems in biosensors and bioactuators

    Science.gov (United States)

    Mailloux, Shay; Katz, Evgeny

    2014-09-01

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

  10. Biomolecular logic systems: applications to biosensors and bioactuators

    Science.gov (United States)

    Katz, Evgeny

    2014-05-01

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

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

    Directory of Open Access Journals (Sweden)

    J.G. Simonsen

    2011-01-01

    Full Text Available Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem conspicuously absent from the literature on biomolecular computing; to partially redress this absence, we introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm; it is also uniform: new ``hardware'' is not needed to solve new problems; and (last but not least it is Turing complete in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient.

  12. Perspective: Coarse-grained models for biomolecular systems

    Science.gov (United States)

    Noid, W. G.

    2013-09-01

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

  13. Biomolecular interaction analysis for carbon nanotubes and for biocompatibility prediction.

    Science.gov (United States)

    Chen, Xiaoping; Fang, Jinzhang; Cheng, Yun; Zheng, Jianhui; Zhang, Jingjing; Chen, Tao; Ruan, Benfang Helen

    2016-07-15

    The interactions between carbon nanotubes (CNTs) and biologics have been commonly studied by various microscopy and spectroscopy methods. We tried biomolecular interaction analysis to measure the kinetic interactions between proteins and CNTs. The analysis demonstrated that wheat germ agglutinin (WGA) and other proteins have high affinity toward carboxylated CNT (f-MWCNT) but essentially no binding to normal CNT (p-MWCNT). The binding of f-MWCNT-protein showed dose dependence, and the observed kinetic constants were in the range of 10(-9) to 10(-11) M with very small off-rates (10(-3) to 10(-7) s(-1)), indicating a relatively tight and stable f-MWCNT-protein complex formation. Interestingly in hemolysis assay, p-MWCNT showed good biocompatibility, f-MWCNT caused 30% hemolysis, but WGA-coated f-MWCNT did not show hemolysis. Furthermore, the f-MWCNT-WGA complex demonstrated enhanced cytotoxicity toward cancer cells, perhaps through the glycoproteins expressed on the cells' surface. Taken together, biomolecular interaction analysis is a precise method that might be useful in evaluating the binding affinity of biologics to CNTs and in predicting biological actions. PMID:27108187

  14. Determination of f_0(980) Structure by Fragmentation Functions

    CERN Document Server

    Hirai, M; Oka, M; Sudoh, K

    2008-01-01

    We discuss internal structure of an exotic hadron by using fragmentation functions. The fragmentation functions for the f_0(980) meson are obtained by a global analysis of e^++e^- \\to f_0+X data. Quark configuration of the f_0(980) could be determined by peak positions and second moments of the obtained fragmentation functions.

  15. Macromolecular structure determination in the post-genome era

    International Nuclear Information System (INIS)

    Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system for the structure determination steps of this process, starting with the initial characterization of the frozen sample, followed by data collection, data reduction, phase determination, and model building. This paper focuses on the data collection elements of this high-throughput system

  16. The Determination of Molecular Structure from Rotational Spectra

    Science.gov (United States)

    Laurie, V. W.; Herschbach, D. R.

    1962-07-01

    An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

  17. Synthesis and structure determination of novel hexasubstituted cyclohexadienes

    Institute of Scientific and Technical Information of China (English)

    Hong Mei Qu; Xin Hui Niu; Juan Li; Jun Liu; Li Li Jiang; Jian Ke Tang; Li Shan Zhou

    2012-01-01

    The linear trienes were obtained in high yields by copper-mediated cycloaddition of 2,5-bis(trimethylsilyl)zirconacyclopentadienes with dimethyl acetylenedicarboxylate (DMAD) which can be quantitatively converted to novel asymmetric hexasubstituted cyclohexadienes with high (E)-stereoselectivity.The structure of cyclohexadienes was determined via X-ray analysis.

  18. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

    Science.gov (United States)

    Mariana, Neni

    2010-01-01

    Few researches have been concerned about relation between children's spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was…

  19. From bacterial to human dihydrouridine synthase: automated structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Whelan, Fiona, E-mail: fiona.whelan@york.ac.uk; Jenkins, Huw T., E-mail: fiona.whelan@york.ac.uk [The University of York, Heslington, York YO10 5DD (United Kingdom); Griffiths, Samuel C. [University of Oxford, Headington, Oxford OX3 7BN (United Kingdom); Byrne, Robert T. [Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377 Munich (Germany); Dodson, Eleanor J.; Antson, Alfred A., E-mail: fiona.whelan@york.ac.uk [The University of York, Heslington, York YO10 5DD (United Kingdom)

    2015-06-30

    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

  20. Structure determination of membrane proteins in five easy pieces.

    Science.gov (United States)

    Marassi, Francesca M; Das, Bibhuti B; Lu, George J; Nothnagel, Henry J; Park, Sang Ho; Son, Woo Sung; Tian, Ye; Opella, Stanley J

    2011-12-01

    Rotational Alignment (RA) solid-state NMR provides the basis for a general method for determining the structures of membrane proteins in phospholipid bilayers under physiological conditions. Membrane proteins are high priority targets for structure determination, and are challenging for existing experimental methods. Because membrane proteins reside in liquid crystalline phospholipid bilayer membranes it is important to study them in this type of environment. The RA solid-state NMR approach we have developed can be summarized in five steps, and incorporates methods of molecular biology, biochemistry, sample preparation, the implementation of NMR experiments, and structure calculations. It relies on solid-state NMR spectroscopy to obtain high-resolution spectra and residue-specific structural restraints for membrane proteins that undergo rotational diffusion around the membrane normal, but whose mobility is otherwise restricted by interactions with the membrane phospholipids. High resolution spectra of membrane proteins alone and in complex with other proteins and ligands set the stage for structure determination and functional studies of these proteins in their native, functional environment. PMID:21964394

  1. From bacterial to human dihydrouridine synthase: automated structure determination

    International Nuclear Information System (INIS)

    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer

  2. Direct experimental determination of the atomic structure at internal interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Browning, N.D. [Oak Ridge National Lab., TN (United States)]|[Illinois Univ., Chicago, IL (United States); Pennycook, S.J. [Oak Ridge National Lab., TN (United States)

    1995-07-01

    A crucial first step in understanding the effect that internal interfaces have on the properties of materials is the ability to determine the atomic structure at the interface. As interfaces can contain atomic disorder, dislocations, segregated impurities and interphases, sensitivity to all of these features is essential for complete experimental characterization. By combining Z-contrast imaging and electron energy loss spectroscopy (EELS) in a dedicated scanning transmission electron microscope (STEM), the ability to probe the structure, bonding and composition at interfaces with the necessary atomic resolution has been obtained. Experimental conditions can be controlled to provide, simultaneously, both incoherent imaging and spectroscopy. This enables interface structures observed in the image to be interpreted intuitively and the bonding in a specified atomic column to be probed directly by EELS. The bonding and structure information can then be correlated using bond-valence sum analysis to produce structural models. This technique is demonstrated for 25{degrees}, 36{degrees} and 67{degrees} symmetric and 45{degrees} and 25{degrees} asymmetric [001] tilt grain boundaries in SrTiO{sub 3} The structures of both types of boundary were found to contain partially occupied columns in the boundary plane. From these experimental results, a series of structural units were identified which could be combined, using continuity of gain boundary structure principles, to construct all [001] tilt boundaries in SrTiO{sub 3}. Using these models, the ability of this technique to address the issues of vacancies and dopant segregation at grain boundaries in electroceramics is discussed.

  3. X-ray structure determination and deuteration of nattokinase

    Energy Technology Data Exchange (ETDEWEB)

    Yanagisawa, Yasuhide [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Chatake, Toshiyuki, E-mail: chatake@rri.kyoto-u.ac.jp [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki [Kurashiki University of Science and the Arts, 2640 Nishinoura, Tsurajima-cho, Kurashiki, Okayama 712-8505 (Japan); Kawaguchi, Akio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Chiba-Kamosida, Kaori [Nippon Advanced Technology Co. Ltd, J-PARC, 2-4 Shirane Shirakata, Tokai, Ibaraki 319-1195 (Japan); Ogawa, Megumi; Adachi, Tatsumi [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Morimoto, Yukio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan)

    2013-11-01

    X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis. Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D{sub 2}O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D{sub 2}O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

  4. Overconfidence, Managerial Optimism, and the Determinants of Capital Structure

    Directory of Open Access Journals (Sweden)

    Alexandre di Miceli da Silveira

    2008-12-01

    Full Text Available This research examines the determinants of the capital structure of firms introducing a behavioral perspective that has received little attention in corporate finance literature. The following central hypothesis emerges from a set of recently developed theories: firms managed by optimistic and/or overconfident people will choose more levered financing structures than others, ceteris paribus. We propose different proxies for optimism/overconfidence, based on the manager’s status as an entrepreneur or non-entrepreneur, an idea that is supported by theories and solid empirical evidence, as well as on the pattern of ownership of the firm’s shares by its manager. The study also includes potential determinants of capital structure used in earlier research. We use a sample of Brazilian firms listed in the Sao Paulo Stock Exchange (Bovespa in the years 1998 to 2003. The empirical analysis suggests that the proxies for the referred cognitive biases are important determinants of capital structure. We also found as relevant explanatory variables: profitability, size, dividend payment and tangibility, as well as some indicators that capture the firms’ corporate governance standards. These results suggest that behavioral approaches based on human psychology research can offer relevant contributions to the understanding of corporate decision making.

  5. X-ray structure determination at low resolution

    International Nuclear Information System (INIS)

    Refinement is meaningful even at 4 Å or lower, but with present methodologies it should start from high-resolution crystal structures whenever possible. As an example of structure determination in the 3.5–4.5 Å resolution range, crystal structures of the ATPase p97/VCP, consisting of an N-terminal domain followed by a tandem pair of ATPase domains (D1 and D2), are discussed. The structures were originally solved by molecular replacement with the high-resolution structure of the N-D1 fragment of p97/VCP, whereas the D2 domain was manually built using its homology to the D1 domain as a guide. The structure of the D2 domain alone was subsequently solved at 3 Å resolution. The refined model of D2 and the high-resolution structure of the N-D1 fragment were then used as starting models for re-refinement against the low-resolution diffraction data for full-length p97. The re-refined full-length models showed significant improvement in both secondary structure and R values. The free R values dropped by as much as 5% compared with the original structure refinements, indicating that refinement is meaningful at low resolution and that there is information in the diffraction data even at ∼4 Å resolution that objectively assesses the quality of the model. It is concluded that de novo model building is problematic at low resolution and refinement should start from high-resolution crystal structures whenever possible

  6. Observation and Structure Determination of an Oxide Quasicrystal Approximant.

    Science.gov (United States)

    Förster, S; Trautmann, M; Roy, S; Adeagbo, W A; Zollner, E M; Hammer, R; Schumann, F O; Meinel, K; Nayak, S K; Mohseni, K; Hergert, W; Meyerheim, H L; Widdra, W

    2016-08-26

    We report on the first observation of an approximant structure to the recently discovered two-dimensional oxide quasicrystal. Using scanning tunneling microscopy, low-energy electron diffraction, and surface x-ray diffraction in combination with ab initio calculations, the atomic structure and the bonding scheme are determined. The oxide approximant follows a 3^{2}.4.3.4 Archimedean tiling. Ti atoms reside at the corners of each tiling element and are threefold coordinated to oxygen atoms. Ba atoms separate the TiO_{3} clusters, leading to a fundamental edge length of the tiling 6.7 Å. PMID:27610863

  7. Numerical and experimental determination of in-structure temperature profiles

    Directory of Open Access Journals (Sweden)

    Zozulák Marek

    2015-06-01

    Full Text Available When building physics simulations are done initial conditions express the actual hygrothermal state of building envelope. For the temperature field simulations initial condition is represented by the initial temperature in the body profile at the start of heat transfer. In-structure temperature varies quickly so temperature initial conditions are often neglected. Nevertheless in specific cases initial conditions have to be taken into an account even when simple temperature field simulations are done. The contribution shows various temperature initial conditions determination for insulated construction of outdoor test cell. Comparison of measured and calculated temperature profiles in structure shows correctness of start-up pre-calculation initial condition consideration

  8. Membrane protein structure determination: back to the membrane.

    Science.gov (United States)

    Yao, Yong; Ding, Yi; Tian, Ye; Opella, Stanley J; Marassi, Francesca M

    2013-01-01

    NMR spectroscopy enables the structures of membrane proteins to be determined in the native-like environment of the phospholipid bilayer membrane. This chapter outlines the methods for membrane protein structural studies using solid-state NMR spectroscopy with samples of membrane proteins incorporated in proteoliposomes or planar lipid bilayers. The methods for protein expression and purification, sample preparation, and NMR experiments are described and illustrated with examples from OmpX and Ail, two bacterial outer membrane proteins that function in bacterial virulence. PMID:23975776

  9. Single-particle structure determination by X-ray free-electron lasers: Possibilities and challenges

    Directory of Open Access Journals (Sweden)

    A. Hosseinizadeh

    2015-07-01

    Full Text Available Single-particle structure recovery without crystals or radiation damage is a revolutionary possibility offered by X-ray free-electron lasers, but it involves formidable experimental and data-analytical challenges. Many of these difficulties were encountered during the development of cryogenic electron microscopy of biological systems. Electron microscopy of biological entities has now reached a spatial resolution of about 0.3 nm, with a rapidly emerging capability to map discrete and continuous conformational changes and the energy landscapes of biomolecular machines. Nonetheless, single-particle imaging by X-ray free-electron lasers remains important for a range of applications, including the study of large “electron-opaque” objects and time-resolved examination of key biological processes at physiological temperatures. After summarizing the state of the art in the study of structure and conformations by cryogenic electron microscopy, we identify the primary opportunities and challenges facing X-ray-based single-particle approaches, and possible means for circumventing them.

  10. Empirical Analysis of the Determinants of Marketing Contract Structures

    OpenAIRE

    Paulson, Nicholas D.; Katchova, Ani L.; Sergio H. Lence

    2008-01-01

    Initial draft replaced by updated/revised version. This is an electronic version of a journal article, please cite as: Paulson, N.D., A.L. Katchova, and S.H. Lence. “An Empirical Analysis of the Determinants of Marketing Contract Structures for Corn and Soybeans.” Journal of Agricultural and Food Industrial Organization 8(2010), 4: 1-23.

  11. Regional Mechanics Determine Collagen Fiber Structure in Healing Myocardial Infarcts

    OpenAIRE

    Fomovsky, Gregory M.; Rouillard, Andrew D.; Holmes, Jeffrey W.

    2012-01-01

    Following myocardial infarction, the mechanical properties of the healing infarct are an important determinant of heart function and the risk of progression to heart failure. In particular, mechanical anisotropy (having different mechanical properties in different directions) in the healing infarct can preserve pump function of the heart. Based on reports of different collagen structures and mechanical properties in various animal models, we hypothesized that differences in infarct size, shap...

  12. The potential for biological structure determination with pulsed neutrons

    International Nuclear Information System (INIS)

    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed

  13. Empirical Study on Capital Structure Determinants in Chinese Listed Companies

    OpenAIRE

    Zhang, Jiye

    2010-01-01

    This paper develops a preliminary study to investigate the determinants of capital structure of Chinese-listed companies using panel data. The analysis of the research is based on the dataset of 200 Chinese listed firms which publicly traded A-shares on both Shanghai and Shenzhen Stock Exchange between 2005 and 2009. The different theories, specifically, the trade-off, pecking order, agency theory, market timing and signalling theories, are deployed to clarify and predict the signs and signif...

  14. The potential for biological structure determination with pulsed neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, C.C. [CLRC Rutherford Appleton Laboratory, Chilton Didcot Oxon (United Kingdom)

    1994-12-31

    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed.

  15. Structural Determination and Daily Variations of Porcine Milk Oligosaccharides

    OpenAIRE

    Tao, Nannan; Ochonicky, Karen L.; German, J Bruce; Donovan, Sharon M.; Lebrilla, Carlito B.

    2010-01-01

    Free milk oligosaccharides (OS) is a major component of mammalian milk. Swine are important agricultural species and biomedical models. Despite their importance, little is known of the OS profile of porcine milk. Herein, the porcine milk glycome was elucidated and monitored over the entire lactation period by liquid chromatography profiling and structural determination with mass spectrometry. Milk was collected from second parity sows (n=3) at farrowing and on days 1, 4, 7 and 24 of lactation...

  16. Determination of the Basin Structure Beneath European Side of Istanbul

    Science.gov (United States)

    Karabulut, Savas; Cengiz Cinku, Mulla; Thomas, Michael; Lamontagne, Maurice

    2016-04-01

    Istanbul (near North Anatolian Fault Zone:NAFZ, Turkey) is located in northern part of Sea of Marmara, an area that has been influenced by possible Marmara Earthquakes. The general geology of Istanbul divided into two stratigraphic unit such as sedimentary (from Oligocene to Quaternary Deposits) and bedrock (Paleozoic and Eocene). The bedrock units consists of sand stone, clay stone to Paleozoic age and limestone to Eocene age and sedimentary unit consist of sand, clay, mil and gravel from Oligocene to Quaternary age. Earthquake disaster mitigation studies divided into two important phases, too. Firstly, earthquake, soil and engineering structure problems identify for investigation area, later on strategic emergency plan can prepare for these problems. Soil amplification play important role the disaster mitigation and the site effect analysis and basin structure is also a key parameter for determining of site effect. Some geophysical, geological and geotechnical measurements are requeired to defined this relationship. Istanbul Megacity has been waiting possible Marmara Earthquake and their related results. In order to defined to possible damage potential related to site effect, gravity measurements carried out for determining to geological structure, basin geometry and faults in Istanbul. Gravity data were collected at 640 sites by using a Scientrex CG-5 Autogravity meter Standard corrections applied to the gravity data include those for instrumental drift, Earth tides and latitude, and the free-air and Bouguer corrections. The corrected gravity data were imported into a Geosoft database to create a grid and map of the Bouguer gravity anomaly (grid cell size of 200 m). As a previously results, we determined some lineminants, faults and basins beneath Istanbul City. Especially, orientation of faults were NW-SE direction and some basin structures determined on between Buyukcekmece and Kucukcekmece Lake.

  17. MOTIVATION INTERNALIZATION AND SIMPLEX STRUCTURE IN SELF-DETERMINATION THEORY.

    Science.gov (United States)

    Ünlü, Ali; Dettweiler, Ulrich

    2015-12-01

    Self-determination theory, as proposed by Deci and Ryan, postulated different types of motivation regulation. As to the introjected and identified regulation of extrinsic motivation, their internalizations were described as "somewhat external" and "somewhat internal" and remained undetermined in the theory. This paper introduces a constrained regression analysis that allows these vaguely expressed motivations to be estimated in an "optimal" manner, in any given empirical context. The approach was even generalized and applied for simplex structure analysis in self-determination theory. The technique was exemplified with an empirical study comparing science teaching in a classical school class versus an expeditionary outdoor program. Based on a sample of 84 German pupils (43 girls, 41 boys, 10 to 12 years old), data were collected using the German version of the Academic Self-Regulation Questionnaire. The science-teaching format was seen to not influence the pupils' internalization of identified regulation. The internalization of introjected regulation differed and shifted more toward the external pole in the outdoor teaching format. The quantification approach supported the simplex structure of self-determination theory, whereas correlations may disconfirm the simplex structure. PMID:26595290

  18. Simulation of Parallel Logical Operations with Biomolecular Computing

    Directory of Open Access Journals (Sweden)

    Mahnaz Kadkhoda

    2008-01-01

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

  19. Ion irradiation and biomolecular radiation damage II. Indirect effect

    CERN Document Server

    Wang, Wei; Su, Wenhui

    2010-01-01

    It has been reported that damage of genome in a living cell by ionizing radiation is about one-third direct and two-thirds indirect. The former which has been introduced in our last paper, concerns direct energy deposition and ionizing reactions in the biomolecules; the latter results from radiation induced reactive species (mainly radicals) in the medium (mainly water) surrounding the biomolecules. In this review, a short description of ion implantation induced radical formation in water is presented. Then we summarize the aqueous radical reaction chemistry of DNA, protein and their components, followed by a brief introduction of biomolecular damage induced by secondary particles (ions and electron). Some downstream biological effects are also discussed.

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

    International Nuclear Information System (INIS)

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

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

    CERN Document Server

    Schwantes, Christian R; Pande, Vijay S

    2014-01-01

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

  2. Determination of the stretch tensor for structural transformations

    Science.gov (United States)

    Chen, Xian; Song, Yintao; Tamura, Nobumichi; James, Richard D.

    2016-08-01

    Structural transformations in crystalline solids are increasingly the basis of the functional behavior of materials. Recently, in diverse alloy systems, both low hysteresis and reversibility of phase transformations have been linked to the satisfaction of the nongeneric conditions of compatibility between phases. According to the Cauchy-Born rule, these conditions are expressed as properties of transformation stretch tensor. The transformation stretch tensor is difficult to measure directly due to the lack of knowledge about the exact transforming pathway during the structural change, and the complicating effects of microstructure. In this paper we give a rigorous algorithmic approach for determining the transformation stretch tensor from X-ray measurements of structure and lattice parameters. For some traditional and emerging phase transformations, the results given by the algorithm suggest unexpected transformation mechanisms.

  3. Local magnetic structure determination using polarized neutron holography

    Energy Technology Data Exchange (ETDEWEB)

    Szakál, Alex, E-mail: szakal.alex@wigner.mta.hu; Markó, Márton, E-mail: marko.marton@wigner.mta.hu; Cser, László, E-mail: cser.laszlo@wigner.mta.hu [Wigner Research Centre for Physics, Konkoly Thege M. út 29-33, H-1121 Budapest (Hungary)

    2015-05-07

    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems.

  4. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L

    2000-01-01

    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  5. Synthesis and Structural Determination of Temocapril Sulfoxide Hydrochlorides

    Energy Technology Data Exchange (ETDEWEB)

    Seong, Seok Bong; Moon, Jong Taik; Kim, Jung Ahn; Choo, Dong Joon; Lee, Jae Yeol [Kyung Hee Univ., Seoul (Korea, Republic of)

    2012-10-15

    Impurity (or related substance) control in pharmaceutical products is a primary goal of drug development. Stringent international regulatory requirements have been in place for several years as outlined in the International Conference on Harmonization (ICH) Guidelines Q3A (R), Q3B (R) and Q3C. According to ICH guidelines, impurities associated with the manufacture of a drug substance, also known as an active pharmaceutical ingredient (API), are classified into the following categories: (1) organic impurities (process and drug-related); (2) inorganic impurities (3) residual solvents. Many potential impurities result from the API manufacturing process including starting materials, isomers, intermediates, reagents, solvents, catalysts and reaction by-products. These potential impurities should be investigated to determine process control mechanisms for their removal and the need for specification controls at appropriate points in the process. The suggested structures of the impurities can be synthesized and will provide the final evidence for their structures, previously determined by spectroscopic methods. Therefore it is essential to know the structure of these impurities in the bulk drug in order to alter the reaction condition and to reduce the quantity of impurity to an acceptable level. Isolation, identification and quantification of impurities help the pharmaceutical company to obtain a pure substance with less toxicity and safety in drug therapy.

  6. Assessment of carotid plaque vulnerability using structural and geometrical determinants

    International Nuclear Information System (INIS)

    Because many acute cerebral ischemic events are caused by rupture of vulnerable carotid atheroma and subsequent thrombosis, the present study used both idealized and patient-specific carotid atheromatous plaque models to evaluate the effect of structural determinants on stress distributions within plaque. Using a finite element method, structural analysis was performed using models derived from in vivo high-resolution magnetic resonance imaging (MRI) of carotid atheroma in 40 non-consecutive patients (20 symptomatic, 20 asymptomatic). Plaque components were modeled as hyper-elastic materials. The effects of varying fibrous cap thickness, lipid core size and lumen curvature on plaque stress distributions were examined. Lumen curvature and fibrous cap thickness were found to be major determinants of plaque stress. The size of the lipid core did not alter plaque stress significantly when the fibrous cap was relatively thick. The correlation between plaque stress and lumen curvature was significant for both symptomatic (p=0.01; correlation coefficient: 0.689) and asymptomatic patients (p=0.01; correlation coefficient: 0.862). Lumen curvature in plaques of symptomatic patients was significantly larger than those of asymptomatic patients (1.50±1.0 mm-1 vs 1.25±0.75 mm-1; p=0.01). Specific plaque morphology (large lumen curvature and thin fibrous cap) is closely related to plaque vulnerability. Structural analysis using high-resolution MRI of carotid atheroma may help in detecting vulnerable atheromatous plaque and aid the risk stratification of patients with carotid disease. (author)

  7. Synthesis and Structural Determination of Temocapril Sulfoxide Hydrochlorides

    International Nuclear Information System (INIS)

    Impurity (or related substance) control in pharmaceutical products is a primary goal of drug development. Stringent international regulatory requirements have been in place for several years as outlined in the International Conference on Harmonization (ICH) Guidelines Q3A (R), Q3B (R) and Q3C. According to ICH guidelines, impurities associated with the manufacture of a drug substance, also known as an active pharmaceutical ingredient (API), are classified into the following categories: (1) organic impurities (process and drug-related); (2) inorganic impurities (3) residual solvents. Many potential impurities result from the API manufacturing process including starting materials, isomers, intermediates, reagents, solvents, catalysts and reaction by-products. These potential impurities should be investigated to determine process control mechanisms for their removal and the need for specification controls at appropriate points in the process. The suggested structures of the impurities can be synthesized and will provide the final evidence for their structures, previously determined by spectroscopic methods. Therefore it is essential to know the structure of these impurities in the bulk drug in order to alter the reaction condition and to reduce the quantity of impurity to an acceptable level. Isolation, identification and quantification of impurities help the pharmaceutical company to obtain a pure substance with less toxicity and safety in drug therapy

  8. Structure Determination of Natural Products by Nuclear Magnetic Resonance Spectroscopy

    Science.gov (United States)

    Li, Du.

    High-field NMR experiments were used to determine the full structures of six new natural products extracted from plants. These are: four saponins (PT-2, P1, P2 and P3) from the plant Alphitonia zizyphoides found in Samoa; one sesquiterpene (DF-4) from Douglas fir and one diterpene derivative (E-2) from a Chinese medicinal herb. By concerted use of various 1D and 2D NMR techniques, the structures of the above compounds were established and complete resonance assignments were achieved. The 2D INADEQUATE technique coupled with a computerized spectral analysis was extensively used. When carried out on concentrations as low as 60 mg of sample, this technique provided absolute confirmation of the assignments for 35 of the possible 53 C-C bonds for PT-2. On 30 mg of sample of E-21, it revealed 22 of 28 possible C-C bonds.

  9. Determination of the structure of UFe2Al10 compound

    International Nuclear Information System (INIS)

    The atomic structure of a new ternary phase UFe2Al10 appearing in the U-Fe-Al system was determined using direct methods applied to X-ray powder diffraction data. High resolution electron microscopy combined with the methods of crystallographic image processing was used for the verification of the structural model. The UFe2Al10 phase is orthorhombic and belongs to Cmcm space group, its unit cell contains 40 Al, eight Fe, and four U atoms. The lattice parameters obtained after Rietveld refinement are: a=8.919 A, b=10.208 A, and c=9.018 A. The reliability factors characterizing the Rietveld refinement procedure are: Rp=5.9%, Rwp=8.1%, and Rb=2.9%

  10. The Phenix Software for Automated Determination of Macromolecular Structures

    Science.gov (United States)

    Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor; Chen, Vincent B.; Echols, Nathaniel; Headd, Jeffrey J.; Hung, Li-Wei; Jain, Swati; Kapral, Gary J.; Grosse Kunstleve, Ralf W.; McCoy, Airlie J.; Moriarty, Nigel W.; Oeffner, Robert D.; Read, Randy J.; Richardson, David C.; Richardson, Jane S.; Terwilliger, Thomas C.; Zwart, Peter H.

    2011-01-01

    X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favour of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. PMID:21821126

  11. The determinants of Capital structure of firms in Japan

    OpenAIRE

    CHEN, ZHANQUAN

    2013-01-01

    This dissertation is going to study the determinants of capital structure of firms in Japan. As previous empirical researches, they all pointed out the factors in different countries. Therefore, it is going to carry out the empirical research in Japanese firms. The sample data used in this dissertation is from a panel data set of 193 non-financial companies in the NIKKIE 225 during the periods from 2003 to 2013. Firstly, it presents MM theory and two mainly modern theories which are the trade...

  12. Methods for empirical formula, molecular structure determination and colloid characterisation

    International Nuclear Information System (INIS)

    Determination of empirical formula and of molecular structures in issues pertinent to the fuel cycle, waste management and remediation, as well as in risk assessment associated with radionuclide release and its migration to the near and far field of a repository present a particular challenge. Speciation techniques in these areas are needed for extraction chemistry of actinides, aquatic reactions of actinide ions (e.g. tetravalent actinide hydrolysis, formation of ternary complexes and redox chemistry), reactions at the water/mineral interface, formation of secondary phases and the formation of and interaction with colloids. The range of concentrations of interest is extreme, from relatively pure substances such as the fuels themselves, to tracer levels in far-field release scenarios. Actinide speciation in extractant solutions used for separation techniques for partitioning technologies involves investigation of solutions with often acidic pH, whereas speciation in cement pore waters, for example, can involve very basic solutions. Finally, the amount of sample available may be limited, e.g. pore water samples can be as small as μL quantities. There exist a variety of techniques for determining empirical formula and molecular structure of radionuclide species. The actual contents and components of the sample at hand in addition to the degree of complexity required dictates the method that is chosen. The speciation of radionuclides is often governed by their association with or formation to colloids. The characterisation of such colloids is imperative and their quantification and characterisation is, therefore, included as a separate treatise. (author)

  13. Determining Subsurface Structure From Microtremors Using a Passive Circular Array

    Science.gov (United States)

    Folger, D. S.; Doser, D. I.; Velasco, A. A.

    2005-12-01

    The amount of damage to a structure during an earthquake is related to the ground motion at that site. Therefore, it is important to study seismic waves that propagate through specific soil types to understand site response. However, active seismic surveys are susceptible to noise interference and are limited due to spatial need while boreholes are costly. We develop a method using a passive array to study Rayleigh waves from microtremors, waves originating from building appliances, cars, pedestrians walking, etc. By using everyday noises as the source, site-specific analysis can be done in urban areas without worrying about noise interference or disturbing the public with explosions or other loud active sources. The array is comprised of short period Texans, self contained geophones, which record continuously for 24 hours. Our technique differs slightly from traditional SPAC (SPatial Auto-Correlation) methods used in passive arrays. We first cross correlate time windows between two receivers then stack the correlations to determine a phase delay. Performing the correlation at different frequencies will create a dispersion curve that can be inverted for shear velocity. This approach is similar to the two-station phase delay method used in regional tomography studies at much longer periods. Stacking removes off-azimuth energy, so we do not need to assume a source direction. Preliminary results from a previous passive array survey conducted near El Paso, Texas show 1-D velocity models can be created by cross-correlating noise at various frequencies. We will conduct another survey in alluvium sands at Rio Bosque Park east of El Paso. We will validate the results with active seismic refraction and surface wave survey results as well as other geophysical techniques to determine if a passive array using microtremors is an accurate method of determining subsurface structure.

  14. A Determination of the Neutron Spin Structure Function

    International Nuclear Information System (INIS)

    The authors report the results of the experiment E142 which measured the spin dependent structure function of the neutron, g1n(x, Q2). The experiment was carried out at the Stanford Linear Accelerator Center by measuring an asymmetry in the deep inelastic scattering of polarized electrons from a polarized 3He target, at electron energies from 19 to 26 GeV. The structure function was determined over the kinematic range 0.03 2 2. An evaluation of the integral ∫01 g1n(x,Q2)dx at fixed Q2 = 2 (GeV/c)2 yields the final result Λ1n = -0.032 ± 0.006 (stat.) ± 0.009 (syst.). This result, when combined with the integral of the proton spin structure function measured in other experiments, confirms the fundamental Bjorken sum rule with O(αs3) corrections to within one standard deviation. This is a major success for perturbative Quantum Chromodynamics. Some ancillary results include the findings that the Ellis-Jaffe sum rule for the neutron is violated at the 2 σ level, and that the total contribution of the quarks to the helicity of the nucleon is 0.36 ± 0.10. The strange sea polarization is estimated to be small and negative, Δs = -0.07 ± 0.04

  15. Simple surface structure determination from Fourier transforms of angle-resolved photoemission extended fine structure

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Y. [Pennsylvania State Univ., University Park, PA (United States)]|[Lawrence Berkeley Lab., CA (United States); Shirley, D.A. [Pennsylvania State Univ., University Park, PA (United States)

    1995-02-01

    The authors show by Fourier analyses of experimental data, with no further treatment, that the positions of all the strong peaks in Fourier transforms of angle-resolved photoemission extended fine structure (ARPEFS) from adsorbed surfaces can be explicitly predicted from a trial structure with an accuracy of about {+-} 0.3 {angstrom} based on a single-scattering cluster model together with the concept of a strong backscattering cone, and without any additional analysis. This characteristic of ARPEFS Fourier transforms can be developed as a simple method for determining the structures of adsorbed surfaces to an accuracy of about {+-} 0.1 {angstrom}.

  16. Self-assembling biomolecular catalysts for hydrogen production

    Science.gov (United States)

    Jordan, Paul C.; Patterson, Dustin P.; Saboda, Kendall N.; Edwards, Ethan J.; Miettinen, Heini M.; Basu, Gautam; Thielges, Megan C.; Douglas, Trevor

    2016-02-01

    The chemistry of highly evolved protein-based compartments has inspired the design of new catalytically active materials that self-assemble from biological components. A frontier of this biodesign is the potential to contribute new catalytic systems for the production of sustainable fuels, such as hydrogen. Here, we show the encapsulation and protection of an active hydrogen-producing and oxygen-tolerant [NiFe]-hydrogenase, sequestered within the capsid of the bacteriophage P22 through directed self-assembly. We co-opted Escherichia coli for biomolecular synthesis and assembly of this nanomaterial by expressing and maturing the EcHyd-1 hydrogenase prior to expression of the P22 coat protein, which subsequently self assembles. By probing the infrared spectroscopic signatures and catalytic activity of the engineered material, we demonstrate that the capsid provides stability and protection to the hydrogenase cargo. These results illustrate how combining biological function with directed supramolecular self-assembly can be used to create new materials for sustainable catalysis.

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

    Science.gov (United States)

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

    2007-07-23

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

  18. Structural Determinants of Clostridium difficile Toxin A Glucosyltransferase Activity

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Rory N.; Chumbler, Nicole M.; Rutherford, Stacey A.; Farrow, Melissa A.; Friedman, David B.; Spiller, Ben; Lacy, D. Borden (Vanderbilt)

    2012-03-28

    The principle virulence factors in Clostridium difficile pathogenesis are TcdA and TcdB, homologous glucosyltransferases capable of inactivating small GTPases within the host cell. We present crystal structures of the TcdA glucosyltransferase domain in the presence and absence of the co-substrate UDP-glucose. Although the enzymatic core is similar to that of TcdB, the proposed GTPase-binding surface differs significantly. We show that TcdA is comparable with TcdB in its modification of Rho family substrates and that, unlike TcdB, TcdA is also capable of modifying Rap family GTPases both in vitro and in cells. The glucosyltransferase activities of both toxins are reduced in the context of the holotoxin but can be restored with autoproteolytic activation and glucosyltransferase domain release. These studies highlight the importance of cellular activation in determining the array of substrates available to the toxins once delivered into the cell.

  19. Structure determination of trans-cinnamaldehyde by broadband microwave spectroscopy.

    Science.gov (United States)

    Zinn, Sabrina; Betz, Thomas; Medcraft, Chris; Schnell, Melanie

    2015-06-28

    The rotational spectrum of trans-cinnamaldehyde ((E)-3-phenyl-2-propenal, C9H8O) was recorded by chirped-pulse Fourier transform microwave spectroscopy in the frequency range of 2-8.5 GHz. The odourant molecule is the essential component of cinnamon oil and causes the characteristic smell. The rotational signatures of two conformers were observed: s-trans-trans- and s-cis-trans-cinnamaldehyde. The rotational spectra of s-trans-trans-cinnamaldehyde and all of its (13)C-monosubstituted species in natural abundance were assigned and the corresponding carbon backbone structure was determined. The second conformer s-cis-trans-cinnamaldehyde is about 9 kJ mol(-1) higher in energy and could also be identified in the spectrum. PMID:26030313

  20. The Structural Determinants behind the Epigenetic Role of Histone Variants.

    Science.gov (United States)

    Cheema, Manjinder S; Ausió, Juan

    2015-01-01

    Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family) haven't often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism. PMID:26213973

  1. The Structural Determinants behind the Epigenetic Role of Histone Variants

    Directory of Open Access Journals (Sweden)

    Manjinder S. Cheema

    2015-07-01

    Full Text Available Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family haven’t often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism.

  2. Unhealthy prisons: exploring structural determinants of prison health.

    Science.gov (United States)

    de Viggiani, Nick

    2007-01-01

    Prisoner health is influenced as much by structural determinants (institutional, environmental, political, economic and social) as it is by physical and mental constitutions of prisoners themselves. Prison health may therefore be better understood with greater insight into how people respond to imprisonment - the psychological pressures of incarceration, the social world of prison, being dislocated from society, and the impact of the institution itself with its regime and architecture. As agencies of disempowerment and deprivation, prisons epitomise the antithesis of a healthy setting. The World Health Organisation's notion of a 'healthy prison' is in this sense an oxymoron, yet the UK government has signalled that it is committed to WHO's core health promotion principles as a route to reducing health inequalities. This paper reports on the findings of an ethnographic study which was conducted in an adult male training prison in England, using participant observation, group interviewing, and one-to-one semi-structured interviews with prisoners and prison officers. The paper explores how different layers of prison life impact on the health of prisoners, arguing that health inequalities are enmeshed within the workings of the prison system itself. PMID:17286709

  3. Structure of HIV-1 protease determined by neutron crystallography

    International Nuclear Information System (INIS)

    HIV-1 protease is an aspartic protease, and plays an essential role in replication of HIV. To develop HIV-1 protease inhibitors through structure-based drug design, it is necessary to understand the catalytic mechanism and inhibitor recognition of HIV-1 protease. We have determined the crystal structure of HIV-1 protease in complex with KNI-272 to 1.9 A resolution by neutron crystallography in combination with 1.4 A resolution X-ray diffraction data. The results show that the carbonyl group of hydroxymethylcarbonyl (HMC) in KNI-272 forms a hydrogen bonding interaction with protonated Asp 25 and the hydrogen atom from the hydroxyl group of HMC forms a hydrogen bonding interaction with the deprotonated Asp125. This is the first neutron report for HIV-1/inhibitor complex and shows directly the locations of key hydrogen atoms in catalysis and in the binding of a transition-state analog. The results confirm key aspect of the presumed catalytic mechanism of HIV-1 protease and will aid in the further development of protease inhibitors. (author)

  4. The Detection of Structural Deformation Errors in Attitude Determination

    Institute of Scientific and Technical Information of China (English)

    M. J. Moore; C. Rizos; J. Wang

    2003-01-01

    In the determination of the attitude parameters from a multi-antenna GPS array, one of the major assumptions is that the body frame is rigid at all times. If this assumption is not true then the derived attitude parameters will be in error. It is well known that in airborne platforms the wings often experience some displacement during flight, especially during periods of initializing maneouvres, such as taking off, landing,and banking. Often it is at these points in time that it is most critical to have the most precise attitude parameters.There are a number of techniques available for the detection of modeling errors.The CUSUM algorithm has successfully been implemented in the past to detect small persistent changes. In this paper the authors investigate different methods of generating the residuals, to be tested by the CUSUM algorithm, in an effort to determine which technique is best suited for the detection of structural deformation of an airborne platform. The methods investigated include monitoring the mean of the residuals generated from the difference between the known body frame coordinates, and those calculated from the derived attitude parameters. The generated residuals are then passed to a CUSUM algorithm to detect any small persistent changes. An alternative method involves transforming the generated residuals into the frequency domain through the use of the Fast Fourier Transform. The CUSUM algorithm is then used to detect any frequency changes. The final technique investigated involves transforming the generated residuals using the Haar wavelet. The wavelet coefficients are then monitored by the CUSUM algorithm in order to detect any significant change to the rigidity of the body frame.Detecting structural deformation, and quantifying the degree of deformation, during flight will ensure that these effects can be removed from the system, thus ensuring the most precise and reliable attitude parameter solutions. This paper, through a series

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-08-15

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

  7. The Effect of Biomolecular Gradients on Mesenchymal Stem Cell Chondrogenesis under Shear Stress

    Directory of Open Access Journals (Sweden)

    Alexander L. Rivera

    2015-03-01

    Full Text Available Tissue engineering is viewed as a promising option for long-term repair of cartilage lesions, but current engineered cartilage constructs fail to match the mechanical properties of native tissue. The extracellular matrix of adult human articular cartilage contains highly organized collagen fibrils that enhance the mechanical properties of the tissue. Unlike articular cartilage, mesenchymal stem cell (MSC based tissue engineered cartilage constructs lack this oriented microstructure and therefore display much lower mechanical strength. The goal of this study was to investigate the effect of biomolecular gradients and shear stress on MSCs undergoing chondrogenesis within a microfluidic device. Via poly(dimethyl siloxane soft-lithography, microfluidic devices containing a gradient generator were created. Human MSCs were seeded within these chambers and exposed to flow-based transforming growth factor β1 (TGF-β1 gradients. When the MSCs were both confluent and exposed to shear stress, the cells aligned along the flow direction. Exposure to TGF-β1 gradients led to chondrogenesis of MSCs, indicated by positive type II collagen staining. These results, together with a previous study that showed that aligned MSCs produce aligned collagen, suggest that oriented cartilage tissue structures with superior mechanical properties can be obtained by aligning MSCs along the flow direction and exposing MSCs to chondrogenic gradients.

  8. A Quick-responsive DNA Nanotechnology Device for Bio-molecular Homeostasis Regulation

    Science.gov (United States)

    Wu, Songlin; Wang, Pei; Xiao, Chen; Li, Zheng; Yang, Bing; Fu, Jieyang; Chen, Jing; Wan, Neng; Ma, Cong; Li, Maoteng; Yang, Xiangliang; Zhan, Yi

    2016-01-01

    Physiological processes such as metabolism, cell apoptosis and immune responses, must be strictly regulated to maintain their homeostasis and achieve their normal physiological functions. The speed with which bio-molecular homeostatic regulation occurs directly determines the ability of an organism to adapt to conditional changes. To produce a quick-responsive regulatory system that can be easily utilized for various types of homeostasis, a device called nano-fingers that facilitates the regulation of physiological processes was constructed using DNA origami nanotechnology. This nano-fingers device functioned in linked open and closed phases using two types of DNA tweezers, which were covalently coupled with aptamers that captured specific molecules when the tweezer arms were sufficiently close. Via this specific interaction mechanism, certain physiological processes could be simultaneously regulated from two directions by capturing one biofactor and releasing the other to enhance the regulatory capacity of the device. To validate the universal application of this device, regulation of the homeostasis of the blood coagulant thrombin was attempted using the nano-fingers device. It was successfully demonstrated that this nano-fingers device achieved coagulation buffering upon the input of fuel DNA. This nano-device could also be utilized to regulate the homeostasis of other types of bio-molecules. PMID:27506964

  9. Automatic Structure Determination of Organic Molecules: Principle and Implementation of the LSD Program

    Institute of Scientific and Technical Information of China (English)

    NUZILLARD,Jean-Marc

    2003-01-01

    The LSD (Logic for Structure Determination) program generates organic molecular structures from 1D and 2D NMR data without resorting to chemical shift databases. Its use in the resolution of natural product structure determination problems has been already reported in the literature. This paper describes how data and structures are internally represented and processed by LSD to build solution structures.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-01

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

  11. Duplication and Divergence Effect on Network Motifs in Undirected Bio-Molecular Networks.

    Science.gov (United States)

    Pei Wang; Jinhu Lu; Xinghuo Yu; Zengrong Liu

    2015-06-01

    Duplication and divergence are two basic evolutionary mechanisms of bio-molecular networks. Real-world bio-molecular networks and their statistical characteristics can be well mimicked by artificial algorithms based on the two mechanisms. Bio-molecular networks consist of network motifs, which act as building blocks of large-scale networks. A fundamental question is how network motifs are evolved from long time evolution and natural selection. By considering the effect of various duplication and divergence strategies, we find that the underlying duplication scheme of the real-world undirected bio-molecular networks would rather follow the anti-preference strategy than the random one. The anti-preference duplication mechanism and the dimerization processes can lead to the formation of various motifs, and robustly conserve proper quantities of motifs in the artificial networks as that in the real-world ones. Furthermore, the anti-preference mechanism and edge deletion divergence can robustly preserve the sparsity of the networks. The investigations reveal the possible evolutionary mechanisms of network motifs in real-world bio-molecular networks, and have potential implications in the design, synthesis and reengineering of biological networks for biomedical purpose. PMID:25203993

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

    Science.gov (United States)

    Chingin, Konstantin; Xu, Ning; Chen, Huanwen

    2014-06-01

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

  13. Determination of the structure function F2 at HERMES

    International Nuclear Information System (INIS)

    In this thesis we present the first measurement of inclusive proton and deuteron deep-inelastic scattering cross sections at the HERMES experiment. The measurement is performed using the 27.6 GeV lepton beam provided by the HERA storage ring in conjunction with hydrogen and deuterium gas targets internal to the beam pipe. The relevant systematic effects such as radiative corrections, detector smearing, acceptance, particle misidentification, misalignment, tracking related effects and trigger efficiencies are taken into account. Based on these results, the structure functions Fp2 and Fd2 are determined using the parameterization R1998 for the longitudinal-to-transverse virtual-photon absorption cross section R. A phenomenological fit of the proton deep-inelastic scattering cross section is performed based on all available data and using photoproduction data in order to pin down the low Q2 region. A second fit is performed to the world data on the deuteron-to-proton cross section ratio in order to study its Q2 evolution, the difference between higher twist contributions in proton and deuteron, and the difference between R as obtained from the two targets. It can be confirmed that R obtained for proton and deuteron is in agreement. The Gottfried integral is evaluated from the fit at different values of Q2. The result at Q2=4 GeV2 agrees with previous measurements by NMC and no indication for a Q2 dependence of the Gottfried integral is found. (orig.)

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2013-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-28

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

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

    International Nuclear Information System (INIS)

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

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology with...... transcriptome data, thereby allowing the identification of key biological features (Reporter Features) around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription...... Factors, Reporter Proteins and Reporter Complexes, and use this to decipher the logic of regulatory circuits playing a key role in yeast glucose repression and human diabetes. Conclusion: Reporter Features offer the opportunity to identify regulatory hot-spots in bio-molecular interaction networks that...

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

    Directory of Open Access Journals (Sweden)

    Amit Majumder

    2012-11-01

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

  20. Decoupling structural and environmental determinants of sap velocity

    Science.gov (United States)

    Caylor, K. K.; Dragoni, D.

    2007-12-01

    Characterization of transpiration based on the water use of individual tress has the advantage of preserving vital information on the plant-environment functional links and flux partitioning between species and landscape areas. Whole-tree transpiration has been estimated by means of sap velocity probes, which offer the dual advantages of practicality and repeatability. However, the assumptions underlying the technique require careful verification in order to determine total sap flow from point-based estimates of sap velocity. Our work presents a novel theoretical framework for the study of individual tree sap flow that incorporates both spatial and temporal variability in sap velocities. The instantaneous sap velocity at any point in the radial profile of xylem tissue is defined as the product of two components: (1) a time-invariant sap velocity distribution linked to the species- specific anatomical and structural properties of the conducting xylem, and (2) a time-varying term linked to the dynamics of the atmospheric water demand and available soil moisture. The separation of structural and temporal variation in sap velocity observations provides a direct mechanism for investigating how sap flow is governed by variation in environmental conditions as well as a means for comparing characteristic rates of plant water use among individuals of varying size. Most critically, this approach allows for a consistent and physically meaningful method for extrapolating point observations of sap velocity across the entire depth of conducting xylem. Experimental evidence supports our theoretical framework in the case of a population of sugar maples in a mixed deciduous forest, where observations were taken from a wide range of tree sizes, under varying soil water availability and atmospheric transpiration demand. We have also applied our approach to a small homogeneous sample of dwarf apple trees in a managed orchard, with favorable results. While these results require further

  1. The structural determinants of insulin-like peptide 3 activity

    Directory of Open Access Journals (Sweden)

    Ross AD Bathgate

    2012-02-01

    Full Text Available INSL3 is a hormone and/or paracrine factor which is a member of the relaxin peptide family. It has key roles as a fertility regulator in both males and females. The receptor for INSL3 is the leucine rich repeat (LRR containing G-protein coupled receptor 8 (LGR8 which is now known as relaxin family peptide receptor 2 (RXFP2. Receptor activation by INSL3 involves binding to the LRRs in the large ectodomain of RXFP2 by residues within the B-chain of INSL3 as well as an interaction with the transmembrane exoloops of the receptor. Although the binding to the LRRs is well characterized the features of the peptide and receptor involved in the exoloop interaction are currently unknown. This study was designed to determine the key INSL3 determinants for RXFP2 activation. A chimeric peptide approach was first utilized to demonstrate that the A-chain is critical for receptor activation. Replacement of the INSL3 A-chain with that from the related peptides INSL5 and INSL6 resulted in complete loss of activity despite only minor changes in binding affinity. Subsequent replacement of specific A-chain residues with those from the INSL5 peptide highlighted that the N-terminus of the A-chain of INSL3 is critical for its activity. Remarkably, replacement of the entire N-terminus with four or five alanine residues resulted in peptides with near native activity suggesting that specific residues are not necessary for activity. Additionally removal of two amino acids at the C-terminus of the A-chain and mutation of Lys-8 in the B-chain also resulted in minor decreases in peptide activity. Therefore we have demonstrated that the activity of the INSL3 peptide is driven predominantly by residues 5-9 in the A-chain, with minor additional contributions from the two C-terminal A-chain residues and Lys-8 in the B-chain. Using this new knowledge, we were able to produce a truncated INSL3 peptide structure which retained native activity, despite having 14 fewer residues than

  2. Discovery and Structure Determination of the Orphan Enzyme Isoxanthopterin Deaminase

    Energy Technology Data Exchange (ETDEWEB)

    Hall, R.S.; Swaminathan, S.; Agarwal, R.; Hitchcock, D.; Sauder, J. M.; Burley, S. K.; Raushel, F. M.

    2010-05-25

    Two previously uncharacterized proteins have been identified that efficiently catalyze the deamination of isoxanthopterin and pterin 6-carboxylate. The genes encoding these two enzymes, NYSGXRC-9339a (gi|44585104) and NYSGXRC-9236b (gi|44611670), were first identified from DNA isolated from the Sargasso Sea as part of the Global Ocean Sampling Project. The genes were synthesized, and the proteins were subsequently expressed and purified. The X-ray structure of Sgx9339a was determined at 2.7 {angstrom} resolution (Protein Data Bank entry 2PAJ). This protein folds as a distorted ({beta}/{alpha}){sub 8} barrel and contains a single zinc ion in the active site. These enzymes are members of the amidohydrolase superfamily and belong to cog0402 within the clusters of orthologous groups (COG). Enzymes in cog0402 have previously been shown to catalyze the deamination of guanine, cytosine, S-adenosylhomocysteine, and 8-oxoguanine. A small compound library of pteridines, purines, and pyrimidines was used to probe catalytic activity. The only substrates identified in this search were isoxanthopterin and pterin 6-carboxylate. The kinetic constants for the deamination of isoxanthopterin with Sgx9339a were determined to be 1.0 s{sup -1}, 8.0 {micro}M, and 1.3 x 10{sup 5} M{sup -1} s{sup -1} (k{sub cat}, K{sub m}, and k{sub cat}/K{sub m}, respectively). The active site of Sgx9339a most closely resembles the active site for 8-oxoguanine deaminase (Protein Data Bank entry 2UZ9). A model for substrate recognition of isoxanthopterin by Sgx9339a was proposed on the basis of the binding of guanine and xanthine in the active site of guanine deaminase. Residues critical for substrate binding appear to be conserved glutamine and tyrosine residues that form hydrogen bonds with the carbonyl oxygen at C4, a conserved threonine residue that forms hydrogen bonds with N5, and another conserved threonine residue that forms hydrogen bonds with the carbonyl group at C7. These conserved active site

  3. From Correlation to Causality: Statistical Approaches to Learning Regulatory Relationships in Large-Scale Biomolecular Investigations.

    Science.gov (United States)

    Ness, Robert O; Sachs, Karen; Vitek, Olga

    2016-03-01

    Causal inference, the task of uncovering regulatory relationships between components of biomolecular pathways and networks, is a primary goal of many high-throughput investigations. Statistical associations between observed protein concentrations can suggest an enticing number of hypotheses regarding the underlying causal interactions, but when do such associations reflect the underlying causal biomolecular mechanisms? The goal of this perspective is to provide suggestions for causal inference in large-scale experiments, which utilize high-throughput technologies such as mass-spectrometry-based proteomics. We describe in nontechnical terms the pitfalls of inference in large data sets and suggest methods to overcome these pitfalls and reliably find regulatory associations. PMID:26731284

  4. Market power versus capital structure determinants: Do they impact leverage?

    Directory of Open Access Journals (Sweden)

    Agha Jahanzeb

    2015-12-01

    Full Text Available The purpose of this study is to investigate the association between market power and capital structure. This study will further provide a logical explanation towards the factors affecting capital structure. This study analysed 176 non-financial Pakistani companies listed on Karachi Stock Exchange over the period of 2003–2012. Capital structure has been tried to investigate with a different perspective by investigating its association with market power. It has been seen that there is a significant and positive relation between market power and capital structure. Size and liquidity remained significantly negative with capital structure, whereas profitability and dividend payout remained significantly positive with capital structure. To the best of authors’ knowledge, this is the first study that investigates the relationship between market power and capital structure in any developing economy by employing the data of non-financial Pakistani firms.

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

    Science.gov (United States)

    Kurzynski, Michal; Torchala, Mieczyslaw; Chelminiak, Przemyslaw

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Bachand, George David; Carroll-Portillo, Amanda

    2006-11-01

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

  7. Local structure analyzers as determinants of preattentive pattern discrimination.

    Science.gov (United States)

    Kröse, B J

    1987-01-01

    Contemporary literature suggests that preattentive texture or pattern discrimination is induced by differences between local structure features or "textons." This paper presents a model for the description of such local structure features based on the computation of local autocorrelations within the image. By means of this structure model a measure of structure dissimilarity is introduced. Experiments have been carried out to test a hypothesized relation between the detectability of a target pattern in a field of background patterns and the value of the structure dissimilarity measure. The experimental results show that it seems justified to relate, in a quantitative way, the detectability of the target pattern to the value of the structure dissimilarity measure. PMID:3828403

  8. Nucleon structure as a background for determination of fundamental parameters

    International Nuclear Information System (INIS)

    We consider deep inelastic, (quasi-) elastic lepton-nucleon scattering and investigate the possibilities of eliminating or suppressing theoretical uncertainties induced by nucleon structure in measuring the Standard Model parameters or in searching for new physics. On the basis of rather general hypothesis about nucleon structure we have obtained new relations between cross sections and neutral current parameters which are independent of the nucleon structure. We also investigate a dependence of the QCD Λ-parameter extracted from the data on unknown large scale nucleon structure and propose a modification of the conventional QCD predictions which are weakly dependent of this uncertainty factor. (author). 9 refs, 1 tab

  9. Novel test structures for temperature budget determination during wafer processing

    OpenAIRE

    Faber, E. J.; Wolters, R.A.M.; Schmitz, J.

    2010-01-01

    Temperature is a crucial parameter in many planar technology processing steps. However, the determination of the actual temperature history at the device side of the substrate is not straightforward. We present a novel method for determining the temperature history of the process side of silicon wafers and chips, which is based on well-known silicide formation reactions of metal-Si systems and is determined via (4 point probe) resistance measurements. In this case we explored the Pd-Si system...

  10. Capital structure of listed portuguese companies: determinants of debt adjustment

    OpenAIRE

    Serrasqueiro, Zélia; Rogão, Márcia

    2009-01-01

    Purpose – This study aims to evaluate the impact of listed Portuguese companies' specific determinants on adjustment of actual debt towards target debt ratio. The specific determinants on adjustment of actual debt towards target debt ratio that we consider are: asset tangibility, size, profitability and market to book ratio. Design/methodology/approach – Dynamic panel estimators are used to determine adjustment of the actual level of debt towards optimal leve...

  11. Environmental filtering determines metacommunity structure in wetland microcrustaceans.

    Science.gov (United States)

    Gascón, Stéphanie; Arranz, Ignasi; Cañedo-Argüelles, Miguel; Nebra, Alfonso; Ruhí, Albert; Rieradevall, Maria; Caiola, Nuno; Sala, Jordi; Ibàñez, Carles; Quintana, Xavier D; Boix, Dani

    2016-05-01

    Metacommunity approaches are becoming popular when analyzing factors driving species distribution at the regional scale. However, until the popularization of the variation partitioning technique it was difficult to assess the main drivers of the observed patterns (spatial or environmental). Here we propose a new framework linking the emergence of different metacommunity structures (e.g., nested, Gleasonian, Clementsian) to spatial and environmental filters. This is a novel approach that provides a more profound analysis of how both drivers could lead to similar metacommunity structures. We tested this framework on 110 sites covering a strong environmental gradient (i.e., microcrustacean assemblages organized along a salinity gradient, from freshwater to brackish water wetlands). First we identified the metacommunity structure that better fitted these microcrustacean assemblages. Then, we used hierarchical variation partitioning to quantify the relative influences of environmental filters and the distance among wetlands on the identified structure. Our results showed that under strong environmental filtering metacommunity structures were non-random. We also noted that even passive dispersers, that are supposed to be poorly spatially filtered, showed spatial signals at a large geographical scale. However, some difficulties arose when inferring biotic interactions at finer-scale spatial signals. Overall, our study shows the potential of elements of metacommunity structure combined with variation partition techniques to detect environmental drivers and broadscale patterns of metacommunity structure, and that some caution is needed when interpreting finer-scale spatial signals. PMID:26781303

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

    DEFF Research Database (Denmark)

    Andersson-Engels, Stefan; Andersen, Peter E.

    2014-01-01

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

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

    OpenAIRE

    Monney, Angèle; Albrecht, Martin

    2013-01-01

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

  14. Crystal Structure of Mitochondrial Respiratory Membrane Protein Complex Ⅱ Determined

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ Scientists at the CAS Institute of Biophysics (IBP) and Tsinghua University have gained new insights into the mechanism of mitochondria, the subcellular structures which generate energy for living cells.

  15. WHAT DETERMINES THE CAPITAL STRUCTURE OF LISTED FIRMS IN ROMANIA

    Directory of Open Access Journals (Sweden)

    Floriniţa Duca

    2012-10-01

    Full Text Available This paper examines the relative importance of four factors in the capital structure decisions of Romanian listed firms. The existing empirical research on capital structure has been largely confined to developed countries. The Romanian Financial Market has been developing at an exponential rate and dedicated research in the field is required. We used 100 firms listed in 2010 at the Bucharest Stock Exchange. The objective of this paper is to build on previous studies model all the important factors affecting capital structure decisions. We find that factors such as tangibility of assets, firm size, liquidity, and profitability have significant influences on the leverage structure chosen by firms.These results are believed to have significant implications for the theory of finance and to be of importance to the corporate treasure in choice of new financing and to the financial analyst.

  16. Structural determinants of reductive terpene cyclization in iridoid biosynthesis

    DEFF Research Database (Denmark)

    Kries, Hajo; Caputi, Lorenzo; Stevenson, Clare E M;

    2016-01-01

    The carbon skeleton of ecologically and pharmacologically important iridoid monoterpenes is formed in a reductive cyclization reaction unrelated to canonical terpene cyclization. Here we report the crystal structure of the recently discovered iridoid cyclase (from Catharanthus roseus) bound to a...

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

    Directory of Open Access Journals (Sweden)

    Alexander V Ratushny

    2011-06-01

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

  18. Determinants of Capital Structure in the Swedish Dairy Farm Industry

    OpenAIRE

    Bergmark, Sten; Dahlberg, Emil

    2015-01-01

    We have examined the capital structure of the Swedish dairy farm industry and the driving forces behind this capital structure. This industry has undergone some major changes during modern time. These changes constitutes mainly of the number of farms and technological development. This, in combination with reported low profitability in the industry, has sparked a high media coverage about the survivability of the agricultural industry due to its important social function. The survivability of...

  19. Determinants of Capital Structure : Evidence from a Major Developing Economy

    OpenAIRE

    2014-01-01

    A major shortcoming of capital structure studies on developing economies is that they generally restrict their analyses to large publicly-traded manufacturing firms. Consequently, we know little about the applicability of various capital structure theories to firms that are private, small, and/or outside the manufacturing industry in these economies. In this paper, we conduct a comparative test of the trade-off and pecking order theories using a comprehensive firm-level dataset that covers ma...

  20. The Determinants of Capital Structure in Energy Sector

    OpenAIRE

    Saeed, Abubakr

    2007-01-01

    This mater thesis is concerns to test that if financial patterns of listed firms in energy sector of Pakistan follow any foremost capital structure theories. The analysis was implemented on a sample of 22 listed firms during the period 2001 to 2005. The results of pooled regression model show that both Static trade-off theory and Pecking order theory are pertinent corporate capital structure theories to the firms in Pakistani energy sector.

  1. Crystal structure solution from experimentally determined atomic pair distribution functions

    OpenAIRE

    Juhas, Pavol; Granlund, Luke; Gujarathi, Saurabh R.; Duxbury, Phillip M.; Billinge, Simon J. L.

    2010-01-01

    The paper describes an extension of the Liga algorithm for structure solution from atomic pair distribution function (PDF), to handle periodic crystal structures with multiple elements in the unit cell. The procedure is performed in 2 separate steps - at first the Liga algorithm is used to find unit cell sites consistent with pair distances extracted from the experimental PDF. In the second step the assignment of atom species over cell sites is solved by minimizing the overlap of their empiri...

  2. WHAT DETERMINES THE CAPITAL STRUCTURE OF LISTED FIRMS IN ROMANIA

    OpenAIRE

    Floriniţa Duca

    2012-01-01

    This paper examines the relative importance of four factors in the capital structure decisions of Romanian listed firms. The existing empirical research on capital structure has been largely confined to developed countries. The Romanian Financial Market has been developing at an exponential rate and dedicated research in the field is required. We used 100 firms listed in 2010 at the Bucharest Stock Exchange. The objective of this paper is to build on previous studies model all the important f...

  3. Environmental and Structural Determinants of Innovation in School Districts.

    Science.gov (United States)

    Burnham, Robert A.

    Conceptualizing organizations as open systems of interrelated variables, this study of 184 Illinois school districts determined the relationships among innovation adoption, selected organizational characteristics, and environmental variability. Organizational characteristics were differentiation (development of specialized organizational…

  4. Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory

    Science.gov (United States)

    Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.

    2012-01-01

    This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

  5. Simulation-free determination of structural grating parameters with GISAXS

    International Nuclear Information System (INIS)

    New technologies such as next-generation semiconductor and lithography techniques rely on complex surface structures with characteristic dimensions in the nanometre range. The functionality of such structures depends greatly on their feature size, thus, dimensional nanometrology is essential for precise control of nanostructured devices. Grazing Incidence Small Angle X-ray Scattering (GISAXS) is a tool for non-destructive length measurement in the nanometre range. Structure parameter retrieval from GISAXS scattering data generally requires simulation of the morphology due to the loss of phase information during image acquisition. Here we present an approach to obtain dimensional parameters of highly ordered surface structures directly from the scattering data without the need of simulation. Line gratings have been investigated with GISAXS and important parameters such as line and groove width, etching depth and period length can be obtained from scattering images by Fourier transformation. The analysis method was applied to different test grating structures as well as to simulated scattering patterns for validation. The experiments were performed at the Four-Crystal Monochromator (FCM) beamline in the PTB laboratory at the electron storage ring BESSY II using the SAXS setup of the Helmholtz-Zentrum Berlin (HZB).

  6. Structural Determinants of Cadherin-23 Function in Hearing and Deafness

    Energy Technology Data Exchange (ETDEWEB)

    Sotomayor, Marcos; Weihofen, Wilhelm A.; Gaudet, Rachelle; Corey, David P. (Harvard-Med); (Harvard)

    2010-06-21

    The hair-cell tip link, a fine filament directly conveying force to mechanosensitive transduction channels, is composed of two proteins, protocadherin-15 and cadherin-23, whose mutation causes deafness. However, their molecular structure, elasticity, and deafness-related structural defects are unknown. We present crystal structures of the first and second extracellular cadherin repeats of cadherin-23. Overall, structures show typical cadherin folds, but reveal an elongated N terminus that precludes classical cadherin interactions and contributes to an N-terminal Ca{sup 2+}-binding site. The deafness mutation D101G, in the linker region between the repeats, causes a slight bend between repeats and decreases Ca{sup 2+} affinity. Molecular dynamics simulations suggest that cadherin-23 repeats are stiff and that either removing Ca{sup 2+} or mutating Ca{sup 2+}-binding residues reduces rigidity and unfolding strength. The structures define an uncharacterized cadherin family and, with simulations, suggest mechanisms underlying inherited deafness and how cadherin-23 may bind with itself and with protocadherin-15 to form the tip link.

  7. Compressed Sensing Electron Tomography for Determining Biological Structure.

    Science.gov (United States)

    Guay, Matthew D; Czaja, Wojciech; Aronova, Maria A; Leapman, Richard D

    2016-01-01

    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets. PMID:27291259

  8. Structural Determinants of Specific Lipid Binding to Potassium Channels

    NARCIS (Netherlands)

    Weingarth, M.H.; Prokofyev, A.; van der Cruijsen, E.A.W.; Nand, D.; Bonvin, A.M.J.J.; Pongs, O.; Baldus, M.

    2013-01-01

    We have investigated specific lipid binding to the pore domain of potassium channels KcsA and chimeric KcsAKv1.3 on the structural and functional level using extensive coarse-grained and atomistic molecular dynamics simulations, solid-state NMR, and single channel measurements. We show that, while K

  9. Compressed Sensing Electron Tomography for Determining Biological Structure

    Science.gov (United States)

    Guay, Matthew D.; Czaja, Wojciech; Aronova, Maria A.; Leapman, Richard D.

    2016-01-01

    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets.

  10. Compressed Sensing Electron Tomography for Determining Biological Structure

    Science.gov (United States)

    Guay, Matthew D.; Czaja, Wojciech; Aronova, Maria A.; Leapman, Richard D.

    2016-06-01

    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets.

  11. Fractal structure and fractal dimension determination at nanometer scale

    Institute of Scientific and Technical Information of China (English)

    张跃; 李启楷; 褚武扬; 王琛; 白春礼

    1999-01-01

    Three-dimensional fractures of different fractal dimensions have been constructed with successive random addition algorithm, the applicability of various dimension determination methods at nanometer scale has been studied. As to the metallic fractures, owing to the limited number of slit islands in a slit plane or limited datum number at nanometer scale, it is difficult to use the area-perimeter method or power spectrum method to determine the fractal dimension. Simulation indicates that box-counting method can be used to determine the fractal dimension at nanometer scale. The dimensions of fractures of valve steel 5Cr21Mn9Ni4N have been determined with STM. Results confirmed that fractal dimension varies with direction at nanometer scale. Our study revealed that, as to theoretical profiles, the dependence of fractal dimension with direction is simply owing to the limited data set number, i.e. the effect of boundaries. However, the dependence of fractal dimension with direction at nanometer scale in rea

  12. A Study of Characteristics and Determinants of Capital Structure in the US Context

    OpenAIRE

    Tian, Musha

    2013-01-01

    This paper aims to explore the characteristics and determinants of capital structure of listed US companies. Mainly three key theories on capital structure (the static trade-off theory, the pecking order theory and the agency cost theory) are discussed specifically. The predicted relevant determinants are analysed and evaluated. Employing the balanced panel data methodology, the capital structure determinants of 266 companies from Standard & Poor’s 500 Index for the time period of 1998-2012 a...

  13. Iron phosphate glasses: Structure determination and radiation tolerance

    Science.gov (United States)

    Jolley, Kenny; Smith, Roger

    2016-05-01

    Iron phosphate glass (IPG) has gained recent interest for use in encapsulating radioactive waste for long term storage. In this work, we investigate 5 different compositions of iron phosphate glass. We consider amorphous structures of 3 known crystalline phases: Fe2+Fe23+ (P2O7)2, Fe43+ (P2O7)3 and Fe3+(PO3)3, and structures of IPG (40 mol% Fe2O3 and 60 mol% P2O5), with 4% and 17% Fe2+ ion concentrations. Using constant volume molecular dynamics (MD), we quench a set of structures for each glass composition, to find the optimal density structure. We found that the lowest energy structures of IPG with 4% and 17% concentration of Fe2+, have a density of 3.25 and 3.28 g/cm3 respectively. This is slightly higher than the experimentally measured values of 2.9 and 2.95 g/cm3 respectively. We also estimate an upper and lower bound on the melting temperatures of each glass, then for each glass, we simulate radiation damage cascades at 4 keV. The cascade structures can be in the form of either a concentrated thermal spike or more diffuse with sub-cascade branching. We found that the glass compositions with a higher Fe/P atomic ratio, contained a greater number of displacements after the cascade. We also found that the IPG with 4% Fe2+, contained slightly fewer displacements than the IPG with 17% Fe2+. This is consistent with our previous work, which showed that the threshold displacement energies are lower for glasses with a lower Fe2+ content. In all the simulations, many PO4 polyhedra are destroyed during the early stages of irradiation, but recover strongly over a time scale of picoseconds, leaving very few over or under co-ordinated P atoms at the end of the ballistic phase. This is in contrast to recent work in apatite. The strong recovery indicates that phosphate glasses with a low Fe2+ content could be good materials for waste encapsulation.

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

    Directory of Open Access Journals (Sweden)

    Garry Laverty

    2014-07-01

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

  15. Structure Determination of Disordered Materials from Diffraction Data

    Science.gov (United States)

    Cliffe, Matthew J.; Dove, Martin T.; Drabold, D. A.; Goodwin, Andrew L.

    2010-03-01

    We show that the information gained in spectroscopic experiments regarding the number and distribution of atomic environments can be used as a valuable constraint in the refinement of the atomic-scale structures of nanostructured or amorphous materials from pair distribution function (PDF) data. We illustrate the effectiveness of this approach for three paradigmatic disordered systems: molecular C60, a-Si, and a-SiO2. Much improved atomistic models are attained in each case without any a priori assumptions regarding coordination number or local geometry. We propose that this approach may form the basis for a generalized methodology for structure “solution” from PDF data applicable to network, nanostructured and molecular systems alike.

  16. Structural Determinants of Oligomerization of the Aquaporin-4 Channel.

    Science.gov (United States)

    Kitchen, Philip; Conner, Matthew T; Bill, Roslyn M; Conner, Alex C

    2016-03-25

    The aquaporin (AQP) family of integral membrane protein channels mediate cellular water and solute flow. Although qualitative and quantitative differences in channel permeability, selectivity, subcellular localization, and trafficking responses have been observed for different members of the AQP family, the signature homotetrameric quaternary structure is conserved. Using a variety of biophysical techniques, we show that mutations to an intracellular loop (loop D) of human AQP4 reduce oligomerization. Non-tetrameric AQP4 mutants are unable to relocalize to the plasma membrane in response to changes in extracellular tonicity, despite equivalent constitutive surface expression levels and water permeability to wild-type AQP4. A network of AQP4 loop D hydrogen bonding interactions, identified using molecular dynamics simulations and based on a comparative mutagenic analysis of AQPs 1, 3, and 4, suggest that loop D interactions may provide a general structural framework for tetrameric assembly within the AQP family. PMID:26786101

  17. Structured boron doped diamond electrodes for determination of dopamine

    Czech Academy of Sciences Publication Activity Database

    Vojs, Marian; Behúl, M.; Michniak, P.; Řeháček, V.; Marton, M.; Veselý, M.; Kromka, Alexander

    Žilina: University of Žilina, 2013 - (Pudiš, D.; Lettrichová, I.; Šušlik, Ĺ.; Kováč jr., J.; Vincze, A.), s. 135-139 ISBN 978-80-554-0689-3. [International Conference on Advances in Electronic and Photonic Technologies. Nový Smokovec (SK), 02.06.2013-05.06.2013] Institutional support: RVO:68378271 Keywords : boron-doped diamond (BDD) * dopamine * nano -structuring Subject RIV: BM - Solid Matter Physics ; Magnetism

  18. FINITE VOLUME METHOD FOR DETERMINING THE NATURAL CHARACTERISTICS OF STRUCTURES

    OpenAIRE

    N. FALLAH

    2013-01-01

    In this paper a finite volume based formulation is developed to calculate the structural natural characteristics including the natural frequencies and the critical buckling loads of slender beam/beam-columns in which the shear effects are taken into account. For natural frequency calculations, both shear effects and rotational inertia effects are considered. In this finite volume based approach, the equilibrium equations of control volumes are expressed and used with the boundary conditions t...

  19. Structural determinants of reductive terpene cyclization in iridoid biosynthesis.

    Science.gov (United States)

    Kries, Hajo; Caputi, Lorenzo; Stevenson, Clare E M; Kamileen, Mohammed O; Sherden, Nathaniel H; Geu-Flores, Fernando; Lawson, David M; O'Connor, Sarah E

    2016-01-01

    The carbon skeleton of ecologically and pharmacologically important iridoid monoterpenes is formed in a reductive cyclization reaction unrelated to canonical terpene cyclization. Here we report the crystal structure of the recently discovered iridoid cyclase (from Catharanthus roseus) bound to a mechanism-inspired inhibitor that illuminates substrate binding and catalytic function of the enzyme. Key features that distinguish iridoid synthase from its close homolog progesterone 5β-reductase are highlighted. PMID:26551396

  20. Determination of the pion and kaon structure functions

    International Nuclear Information System (INIS)

    Quark structure functions have been extracted from low-p/sub T/ inclusive hadron production data for the pion and kaon with use of the recombination model. n/sup π/=1.0 +- 0.1 and n/sup K/=2.5 +- 0.6 is obtained, where n is the leading (1-x) power of the nonstrange--valence-quark distribution. Both the pion and kaon nonstrange--sea-quark functions have napprox. =3.5

  1. The Structural Determinants behind the Epigenetic Role of Histone Variants

    OpenAIRE

    Manjinder S. Cheema; Juan Ausió

    2015-01-01

    Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone v...

  2. Mobile internet services : integration models and structural determinants

    OpenAIRE

    Gressgård, Leif Jarle; Methlie, Leif B.; Stensaker, Inger G.

    2003-01-01

    The overall purpose of this report is to contribute in developing theory related to the supply side of mobile and electronic commerce. We explore how mobile services are organized and which factors explain different choices in terms of supply side organization. Based on a theoretical framework called MAPIT, we particularly focus on how structural conditions affect organization of new services. We apply the framework in a multiple case study of five mobile services. As expected, we found that ...

  3. Neural Network Enhanced Structure Determination of Osteoporosis, Immune System, and Radiation Repair Proteins Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose a dual objective innovation that has valuable NASA applicability and tremendous commercial potential. The first innovation is the structure determination...

  4. Neural Network Enhanced Structure Determination of Osteoporosis, Immune System, and Radiation Repair Proteins Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation will utilize self learning neural network technology to determine the structure of osteoporosis, immune system disease, and excess radiation...

  5. Music structure determines heart rate variability of singers.

    Science.gov (United States)

    Vickhoff, Björn; Malmgren, Helge; Aström, Rickard; Nyberg, Gunnar; Ekström, Seth-Reino; Engwall, Mathias; Snygg, Johan; Nilsson, Michael; Jörnsten, Rebecka

    2013-01-01

    Choir singing is known to promote wellbeing. One reason for this may be that singing demands a slower than normal respiration, which may in turn affect heart activity. Coupling of heart rate variability (HRV) to respiration is called Respiratory sinus arrhythmia (RSA). This coupling has a subjective as well as a biologically soothing effect, and it is beneficial for cardiovascular function. RSA is seen to be more marked during slow-paced breathing and at lower respiration rates (0.1 Hz and below). In this study, we investigate how singing, which is a form of guided breathing, affects HRV and RSA. The study comprises a group of healthy 18 year olds of mixed gender. The subjects are asked to; (1) hum a single tone and breathe whenever they need to; (2) sing a hymn with free, unguided breathing; and (3) sing a slow mantra and breathe solely between phrases. Heart rate (HR) is measured continuously during the study. The study design makes it possible to compare above three levels of song structure. In a separate case study, we examine five individuals performing singing tasks (1-3). We collect data with more advanced equipment, simultaneously recording HR, respiration, skin conductance and finger temperature. We show how song structure, respiration and HR are connected. Unison singing of regular song structures makes the hearts of the singers accelerate and decelerate simultaneously. Implications concerning the effect on wellbeing and health are discussed as well as the question how this inner entrainment may affect perception and behavior. PMID:23847555

  6. Dangerous and endangered youth: social structures and determinants of violence.

    Science.gov (United States)

    Scheper-Hughes, Nancy

    2004-12-01

    Structural violence is violence that is permissible, even encouraged. It refers to the invisible social machinery of inequality that reproduces social relations of exclusion and marginalization via ideologies, stigmas, and dangerous discourses (such as "youth violence" itself) attendant to race, class, sex, and other invidious distinctions. Structural violence "naturalizes" poverty, sickness, hunger, and premature death, erasing their social and political origins so that they are taken for granted and no one is held accountable except the poor themselves. Structural violence also refers to the ease with which humans are capable of reducing the socially vulnerable (even those from their own class and community) into expendable non-persons, thus allowing the licence--even the duty--to kill them. I exemplify this through two ethnographic critical case studies: the operation of a virulent death squad in Northeast Brazil that mobilized the support of ordinary people in an almost genocidal attack against Afro-Brazilian street kids and young "marginals"; and the uneasy truce with, and incomplete integration of "dangerous and endangered" youth still living in squatter camps and shack communities of urban South Africa. PMID:15817729

  7. Quantification of the impact of PSI:Biology according to the annotations of the determined structures

    OpenAIRE

    DePietro, Paul J; Julfayev, Elchin S.; McLaughlin, William A.

    2013-01-01

    Background Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third phase entailed the formation of PSI:Biology Partnerships which are composed of structural genomics centers and biomedical science laboratories. We present a method to examine the impact of protein structures determined under the auspices of PSI:Biology by measuring their rates ...

  8. Investigation of the most appropriate capital structure theory and leverage level determinants

    OpenAIRE

    Lew, Sung Hee

    2012-01-01

    This thesis examines capital structure theories and debt level determinants to develop a better understanding, and to establish the most appropriate theory to explain the behaviour of firms‟ debt and equity choices. It tests three major capital structure theories (e.g. the trade-off, pecking order and market timing theories) using static and dynamic statistical models and 13 capital structure determinants, based on three major capital structure theories. The study uses 4,598 sa...

  9. Structural determination of some uranyl compounds by vibrational spectroscopy

    International Nuclear Information System (INIS)

    The vibrational spectra of different uranyl compounds has been studied and of it spectral information has been used the fundamental asymmetric vibrational frequency, to determine the length and constant bond force U=O by means of the combination of the concept of absorbed energy and the mathematical expression of Badger modified by Jones. It is intended a factor that simplifies the mathematical treatment and the results are compared with the values obtained for other methods. (Author)

  10. Role, Structure, and Determinants of Debt Covenants: Evidence from Japan

    OpenAIRE

    Kochiyama, Takuma; Nakamura, Ryosuke

    2014-01-01

    We examine types of financial covenants and how they are used in Japanese loan markets. Since previous literature on covenants focused on US firms, little is known about financial covenants in the so-called bank-oriented countries. We use a hand-collected dataset to explore the (1) types of financial covenants and (2) determinants of the use and strictness of financial covenants. Our binominal regression analysis shows that financial factors such as profitability, leverage, and interest rates...

  11. A General Chemistry Experiment Incorporating Synthesis and Structural Determination

    Science.gov (United States)

    van Ryswyk, Hal

    1997-07-01

    An experiment for the general chemistry laboratory is described wherein gas chromatography-mass spectroscopy (GC-MS) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) are used to characterize the products of a series of microscale reactions on vanillin. A single sophisticated instrument can be incorporated into the laboratory given sufficient attention to the use of sampling accessories and software macros. Synthetic experiments coupled with modern instrumental techniques can be used in the general chemistry laboratory to illustrate the concepts of synthesis, structure, bonding, and spectroscopy.

  12. The determination of planetary structure in tidally relaxed inclined systems

    OpenAIRE

    Mardling, Rosemary A.

    2010-01-01

    [Abridged] The recent discovery of a transiting planet on a non-circular orbit with a massive highly eccentric companion orbiting HAT-P-13 offers the possibility of probing the structure of the short-period planet. The ability to do this relies on the system being in a quasi-equilibrium state in the sense that the eccentricities are constant on the usual secular timescale, and decay on a timescale which is much longer than the age of the system. Since the equilibrium eccentricity is effective...

  13. Determination of HART I Blade Structural Properties by Laboratory Testing

    Science.gov (United States)

    Jung, Sung N.; Lau, Benton H.

    2012-01-01

    The structural properties of higher harmonic Aeroacoustic Rotor Test (HART I) blades were measured using the original set of blades tested in the German-dutch wind tunnel (DNW) in 1994. the measurements include bending and torsion stiffness, geometric offsets, and mass and inertia properties of the blade. the measured properties were compared to the estimated values obtained initially from the blade manufacturer. The previously estimated blade properties showed consistently higher stiffness, up to 30 percent for the flap bending in the blade inboard root section.

  14. Determinants of the mouse ultrasonic vocal structure and repertoire.

    Science.gov (United States)

    Heckman, Jesse; McGuinness, Brigit; Celikel, Tansu; Englitz, Bernhard

    2016-06-01

    Mouse ultrasonic vocalizations (USV) exhibit a high degree of complexity as demonstrated in recent years. A multitude of factors have been identified to influence USVs on the spectrotemporal as well as structural - e.g. syntactic - level. A synthesis of the various studies that attributes semantics to USV properties or sequences is still lacking. Presently, we address the factors modulating the composition of USVs, specifically age, gender, genetic background (including the targeted FoxP2 mutagenesis), behavioral state and individuality. It emerges that the different factors share a set of common influences, e.g. vocalization rate and frequency range are universally modulated across independent variables described; however, distinct influences exist for sequential structure (different effects for age, behavioral state and genetic background) or vocal repertoire (age). Recently, USV research has seen important advances based on the quantitative maturation of methods on multiple levels of vocalization. Adoption of these methods to address the natural statistics of USV will ultimately benefit several related research areas, e.g. neurolinguistics, neurodevelopmental disorders, multisensory and sensorimotor research. PMID:27060755

  15. Using Dust as Probes to Determine Sheath Extent and Structure

    CERN Document Server

    Douglass, Angela; Qiao, Ke; Matthews, Lorin; Hyde, Truell

    2016-01-01

    Two in-situ experimental methods are presented in which dust particles are used to determine the extent of the sheath and gain information about the time-averaged electric force profile within a RF plasma sheath. These methods are advantageous because they are not only simple and quick to carry out, but they also can be performed using standard dusty plasma experimental equipment. In the first method, dust particles are tracked as they fall through the plasma toward the lower electrode. These trajectories are then used to determine the electric force on the particle as a function of height as well as the extent of the sheath. In the second method, dust particle levitation height is measured across a wide range of RF voltages. Similarities were observed between the two experiments, but in order to understand the underlying physics behind these observations, the same conditions were replicated using a self-consistent fluid model. Through comparison of the fluid model and experimental results, it is shown that t...

  16. Theoretical models for the emergence of biomolecular homochirality

    Science.gov (United States)

    Walker, Sara Imari

    Little is known about the emergence of life from nonliving precursors. A key missing-piece is the origin of homochirality: nearly all life is characterized by exclusively dextrorotary sugars and levorotary amino acids. The research presented in this thesis addresses the challenge of uncovering mechanisms for chiral symmetry breaking in a prebiotic environment and implications for the origin of life on Earth. Expanding on a well-known model for chiral selection through polymerization, and modeling the spatiotemporal dynamics starting from near-racemic initial conditions, it is demonstrated that the net chirality of molecular building blocks grows with the longest polymer in the reaction network (of length N) with critical behavior for the onset of chiral asymmetry determined by the value of N. This surprising result indicates that significant chiral asymmetry occurs only for systems which permit growth of long polymers. Expanding on this work, the effects of environmental disturbances on the evolution of chirality in prebiotic reaction-diffusion networks are studied via the implementation of a stochastic spatiotemporal Langevin equation. The results show that environmental interactions can have significant impact on the evolution of prebiotic chirality: the history of prebiotic chirality is therefore interwoven with the Earths early environmental history in a mechanism we call punctuated chirality. This result establishes that the onset of homochirality is not an isolated phenomenon: chiral selection must occur in tandem with the transition from chemistry to biology, otherwise the prebiotic soup is unstable to environmental events. Addressing the challenge of understanding the role of chirality in the transition from non-life to life, the diffusive slowdown of reaction networks induced, for example, through tidal cycles or evaporating pools, is modeled. The results of this study demonstrate that such diffusive slowdown leads to the stabilization of homochiral

  17. Crystal structure determination of strontium and calcium azide

    Energy Technology Data Exchange (ETDEWEB)

    Krischner, H.; Kelz, G. (Technische Univ., Graz (Austria). Inst. fuer Physikalische und Theoretische Chemie)

    1982-11-01

    Crystal structures of strontium azide and calcium azide have been investigated by means of the X-ray powder method. Both compounds crystallize or orthorhombic in space group Fddd. Strontium and calcium are surrounded by eight terminal nitrogen atoms of different azide groups which form antiprisms. The azide groups are linear in Sr(N/sub 3/)/sub 2/ with distances of 118.2(12) pm but show a small deviation from linearity in Ca(N/sub 3/)/sub 2/ with distances of 116.9(15) pm. The final R-values are 0.080 for Sr(N/sub 3/)/sub 2/ and 0.067 for Ca(N/sub 3/)/sub 2/, respectively.

  18. Crystal structure determination of strontium and calcium azide

    International Nuclear Information System (INIS)

    Crystal structures of strontium azide and calcium azide have been investigated by means of the X-ray powder method. Both compounds crystallize or orthorhombic in space group Fddd. Strontium and calcium are surrounded by eight terminal nitrogen atoms of different azide groups which form antiprisms. The azide groups are linear in Sr(N3)2 with distances of 118.2(12) pm but show a small deviation from linearity in Ca(N3)2 with distances of 116.9(15) pm. The final R-values are 0.080 for Sr(N3)2 and 0.067 for Ca(N3)2, respectively. (author)

  19. Quantitative X-ray determination of CFRP micro structures

    International Nuclear Information System (INIS)

    Beyond imaging the mass distribution of materials by X-ray absorption techniques recent synchrotron and laboratory X-ray refraction techniques provide interface contrast imaging of micro structures. This is of specific relevance to carbon fibre composites (CFRP) which constitute advanced aerospace components. Apart from merely finding isolated flaws like cracks or pores within the natural high interface density only the quantitative measurement of the differences after defined mechanical treatment provides a reliable understanding of the related macroscopic properties. The contribution of the fibre matrix interface of CFRP laminates to the mechanical properties is investigated by relating the mechanical damage to the additional fibre debonding after impact and fatigue. Composites of industrially sized carbon fibres for aerospace applications and of unsized fibres are compared. (orig.)

  20. Epoxide Chemistry: Guided Inquiry Experiment Emphasizing Structure Determination and Mechanism

    Science.gov (United States)

    Krishnamurty, H. G.; Jain, Niveta; Samby, Kiran

    2000-04-01

    This paper presents an operationally simple three-step synthesis of an a-hydroxy acid based on epoxide chemistry. The focus of the experiment is on the preparation of the chalcone epoxide and its reaction with hot alcoholic alkali. The experiment leads to an unpredicted reaction product. Its structure is established as 2-benzyl-2-phenylglycollic acid by chemical and spectroscopic analysis. The hydroxyacid is a good example to bring home an important NMR principle: the nonequivalence of hydrogens adjacent to a stereogenic center. The formation of the alpha-hydroxy acid is a mechanistic puzzle. A stepwise mechanism can be developed applying lecture-based organic chemistry concepts. On the other hand, acid-catalyzed (H2SO4, BF3) reaction of the chalcone epoxide gives benzoylphenylacetaldehyde. The exercise can be used as a multistep organic chemistry experiment. It also gives students a research-type experience.

  1. Electron Crystallography Novel Approaches for Structure Determination of Nanosized Materials

    CERN Document Server

    Weirich, Thomas E; Zou, Xiaodong

    2006-01-01

    During the last decade we have been witness to several exciting achievements in electron crystallography. This includes structural and charge density studies on organic molecules complicated inorganic and metallic materials in the amorphous, nano-, meso- and quasi-crystalline state and also development of new software, tailor-made for the special needs of electron crystallography. Moreover, these developments have been accompanied by a now available new generation of computer controlled electron microscopes equipped with high-coherent field-emission sources, cryo-specimen holders, ultra-fast CCD cameras, imaging plates, energy filters and even correctors for electron optical distortions. Thus, a fast and semi-automatic data acquisition from small sample areas, similar to what we today know from imaging plates diffraction systems in X-ray crystallography, can be envisioned for the very near future. This progress clearly shows that the contribution of electron crystallography is quite unique, as it enables to r...

  2. Structure and partitioning of bacterial DNA: determined by a balance of competion and expansion forces?

    DEFF Research Database (Denmark)

    Woldringh, C. L.; Jensen, Peter Ruhdal; Westerhoff, H. V.

    1995-01-01

    The mechanisms that determine chromosome structure and chromosome partitioning in bacteria are largely unknown. Here we discuss two hypotheses: (i) the structure of the Escherichia coli nucleoid is determined by DNA binding proteins and DNA supercoiling, representing a compaction force on the one...

  3. FINITE VOLUME METHOD FOR DETERMINING THE NATURAL CHARACTERISTICS OF STRUCTURES

    Directory of Open Access Journals (Sweden)

    N. FALLAH

    2013-02-01

    Full Text Available In this paper a finite volume based formulation is developed to calculate the structural natural characteristics including the natural frequencies and the critical buckling loads of slender beam/beam-columns in which the shear effects are taken into account. For natural frequency calculations, both shear effects and rotational inertia effects are considered. In this finite volume based approach, the equilibrium equations of control volumes are expressed and used with the boundary conditions to obtain the eigenvalue equation in the standard format. Then, the natural characteristics of beam/beam-columns are obtained by solving the eigenvalue equations. The formulation is tested on a number of benchmark problems. Accordingly, the proposed formulation has been found to accurately predict the natural frequencies and the critical buckling loads of the test problems. Also, the formulation is tested for the very thin and thick beams. It is found that the formulation is also able to analyze the thin beams in which no shear locks is observed.

  4. Benzofuranyl Esters: Synthesis, Crystal Structure Determination, Antimicrobial and Antioxidant Activities

    Directory of Open Access Journals (Sweden)

    C. S. Chidan Kumar

    2015-09-01

    Full Text Available A series of five new 2‐(1‐benzofuran‐2‐yl‐2‐oxoethyl 4-(un/substitutedbenzoates 4(a–e, with the general formula of C8H5O(C=OCH2O(C=OC6H4X, X = H, Cl, CH3, OCH3 or NO2, was synthesized in high purity and good yield under mild conditions. The synthesized products 4(a–e were characterized by FTIR, 1H-, 13C- and 1H-13C HMQC NMR spectroscopic analysis and their 3D structures were confirmed by single-crystal X-ray diffraction studies. These compounds were screened for their antimicrobial and antioxidant activities. The tested compounds showed antimicrobial ability in the order of 4b < 4a < 4c < 4d < 4e and the highest potency with minimum inhibition concentration (MIC value of 125 µg/mL was observed for 4e. The results of antioxidant activities revealed the highest activity for compound 4e (32.62% ± 1.34% in diphenyl-2-picrylhydrazyl (DPPH radical scavenging, 4d (31.01% ± 4.35% in ferric reducing antioxidant power (FRAP assay and 4a (27.11% ± 1.06% in metal chelating (MC activity.

  5. Mesopore quality determines the lifetime of hierarchically structured zeolite catalysts

    Science.gov (United States)

    Milina, Maria; Mitchell, Sharon; Crivelli, Paolo; Cooke, David; Pérez-Ramírez, Javier

    2014-05-01

    Deactivation due to coking limits the lifetime of zeolite catalysts in the production of chemicals and fuels. Superior performance can be achieved through hierarchically structuring the zeolite porosity, yet no relation has been established between the mesopore architecture and the catalyst lifetime. Here we introduce a top-down demetallation strategy to locate mesopores in different regions of MFI-type crystals with identical bulk porous and acidic properties. In contrast, well-established bottom-up strategies as carbon templating and seed silanization fail to yield materials with matching characteristics. Advanced characterization tools capable of accurately discriminating the mesopore size, distribution and connectivity are applied to corroborate the concept of mesopore quality. Positron annihilation lifetime spectroscopy proves powerful to quantify the global connectivity of the intracrystalline pore network, which, as demonstrated in the conversions of methanol or of propanal to hydrocarbons, is closely linked to the lifetime of zeolite catalysts. The findings emphasize the need to aptly tailor hierarchical materials for maximal catalytic advantage.

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

    CERN Document Server

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

    2007-01-01

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

  7. Micromachining microcarrier-based biomolecular encoding for miniaturized and multiplexed immunoassay.

    Science.gov (United States)

    Zhi, Zheng-liang; Morita, Yasutaka; Hasan, Quamrul; Tamiya, Eiichi

    2003-08-15

    Micromachining techniques, which originated in the microelectronics industry, have been employed to manufacture microparticles bearing an engraved dot-type signature for biomolecular encoding. These metallic microstructures are photolithographically defined and manufactured in a highly reproducible manner. In addition, the code introduced on the particle face is a straightforward visible feature that is easily recognizable with the use of optical microscopy. The number of distinct codes theoretically could be many thousands, depending on the coding element numbers. Such microparticles are, thus, with appropriate surface organic functionalizations, ideal for encoding biomolecular libraries and serving as a platform for developing high-throughput multiplexed bioassay schemes based on suspension array technology. As proof of this statement, we demonstrated that encoded microparticles tagged with antibodies to human immunoglobulin classes are capable, using imaging detection as the interrogating approach, of high sensitivity and high specificity, as well as multiplexed detection of the respective antigens in a microliter-sample volume. PMID:14651038

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

    Science.gov (United States)

    Onoda, Mitsuyoshi; Malhotra, Bansi D.

    2012-04-01

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

  9. Recommendations for the presentation of NMR structures of proteins and nucleic acids - IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy

    International Nuclear Information System (INIS)

    The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards. Much of this document pertains to the reporting of data in journal articles; however, in the interest of the future development of structural biology, it is desirable that the bulk of the reported information be stored in computer-accessible form and be freely accessible to the scientific community in standardized formats for data exchange. These recommendations stem from an IUPAC-IUBMB-IUPAB inter-union venture with the direct involvement of ICSU and CODATA. The Task Group has reviewed previous formal recommendations and has extended them in the light of more recent developments in the field of biomolecular NMR spectroscopy. Drafts of the recommendations presented here have been examined critically by more than 50 specialists in the field and have gone through two rounds of extensive modification to incorporate suggestions and criticisms

  10. Effective cross-section for dimuon production and experimental determination of the hadronic structure functions

    International Nuclear Information System (INIS)

    High mass dimuon hadronic production is studied. This study is aimed at pion structure determination. The device is presented. The accessible luminosity is more than one scale order beyond the preceeding experiment one. The performant beam, the great acceptance and the good high mass dimuon selection are described. Parton model is introduced. Drell-Yann mechanism is reviewed. Hadronic structure, revealed during high mass muon pair production, is presented. In particular, pion structure is determined

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

    OpenAIRE

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

    2015-01-01

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

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

    OpenAIRE

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

    2008-01-01

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

  13. Evaluation of stochastic effects on biomolecular networks using the generalised Nyquist stability criterion

    OpenAIRE

    Kim, J; Bates, D. G.; Postlethwaite, I.

    2008-01-01

    Abstract—Stochastic differential equations are now commonly used to model biomolecular networks in systems biology, and much recent research has been devoted to the development of methods to analyse their stability properties. Stability analysis of such systems may be performed using the Laplace transform, which requires the calculation of the exponential matrix involving time symbolically. However, the calculation of the symbolic exponential matrix is not feasible for problems of even mod...

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

    OpenAIRE

    Bai, Fan; Wang, Wenqing

    2002-01-01

    The origin of chirality, closely related to the evolution of life on the earth, has long been debated. In 1991, Abdus Salam suggested a novel approach to achieve biomolecular homochirality by a phase transition. In his subsequent publication, he predicted that this phase transition could eventually change D-amino acids to L-amino acids as C -H bond would break and H atom became a superconductive atom. Since many experiments denied the configuration change in amino acids, Salam hypothesis arou...

  15. Affinity capillary electrophoresis and density functional theory employed for characterization of (bio)molecular interactions

    Czech Academy of Sciences Publication Activity Database

    Kašička, Václav; Ehala, Sille; Růžička, Martin; Dybal, Jiří; Toman, Petr

    Salzburg: Society of Analytical Chemistry, 2014. OR28. [ISC 2014. International Symposium on Chromatography /30./. 14.09.2014-18.09.2014, Salzburg] R&D Projects: GA ČR(CZ) GAP206/12/0453; GA ČR(CZ) GA13-17224S Institutional support: RVO:61388963 ; RVO:61389013 Keywords : affinity capillary electrophoresis * density functional theory * biomolecular complexes Subject RIV: CB - Analytical Chemistry, Separation

  16. Biomolecular Self-Defense and Futility of High-Specificity Therapeutic Targeting

    OpenAIRE

    Simon Rosenfeld

    2011-01-01

    Robustness has been long recognized to be a distinctive property of living entities. While a reasonably wide consensus has been achieved regarding the conceptual meaning of robustness, the biomolecular mechanisms underlying this systemic property are still open to many unresolved questions. The goal of this paper is to provide an overview of existing approaches to characterization of robustness in mathematically sound terms. The concept of robustness is discussed in various contexts including...

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

    Science.gov (United States)

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

    2016-05-10

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

  18. Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion

    Science.gov (United States)

    Stember, Joseph N.; Wriggers, Willy

    2009-08-01

    The empirical harmonic potential function of elastic network models (ENMs) is augmented by three- and four-body interactions as well as by a parameter-free connection rule. In the new bend-twist-stretch (BTS) model the complexity of the parametrization is shifted from the spatial level of detail to the potential function, enabling an arbitrary coarse graining of the network. Compared to distance cutoff-based Hookean springs, the approach yields a more stable parametrization of coarse-grained ENMs for biomolecular dynamics. Traditional ENMs give rise to unbounded zero-frequency vibrations when (pseudo)atoms are connected to fewer than three neighbors. A large cutoff is therefore chosen in an ENM (about twice the average nearest-neighbor distance), resulting in many false-positive connections that reduce the spatial detail that can be resolved. More importantly, the required three-neighbor connectedness also limits the coarse graining, i.e., the network must be dense, even in the case of low-resolution structures that exhibit few spatial features. The new BTS model achieves such coarse graining by extending the ENM potential to include three-and four-atom interactions (bending and twisting, respectively) in addition to the traditional two-atom stretching. Thus, the BTS model enables reliable modeling of any three-dimensional graph irrespective of the atom connectedness. The additional potential terms were parametrized using continuum elastic theory of elastic rods, and the distance cutoff was replaced by a competitive Hebb connection rule, setting all free parameters in the model. We validate the approach on a carbon-alpha representation of adenylate kinase and illustrate its use with electron microscopy maps of E. coli RNA polymerase, E. coli ribosome, and eukaryotic chaperonin containing T-complex polypeptide 1, which were difficult to model with traditional ENMs. For adenylate kinase, we find excellent reproduction (>90% overlap) of the ENM modes and B factors

  19. X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.

    Science.gov (United States)

    Zhou, X Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Suino-Powell, Kelly M; Boutet, Sébastien; Williams, Garth J; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

    2016-01-01

    Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes. PMID:27070998

  20. Biomolecular pleiomorphism probed by spatial interpolation of coarse models

    OpenAIRE

    Rusu, Mirabela; Birmanns, Stefan; Wriggers, Willy

    2008-01-01

    In low resolution structures of biological assemblies one can often observe conformational deviations that require a flexible rearrangement of structural domains fitted at the atomic level. We are evaluating interpolation methods for the flexible alignment of atomic models based on coarse models. Spatial interpolation is well established in image-processing and visualization to describe the overall deformation or warping of an object or an image. Combined with a coarse representation of the b...

  1. Determinants of Capital Structure A Comparison Between UK and Chinese List Companies

    OpenAIRE

    Hu, Zongyao

    2013-01-01

    For a long time, the choice of capital structure is the decision of corporate financing method has been the core issue of corporate governance; it is also the focus of economists as well as practitioners. It affects not only the governance structure of the company but also determines the characteristics of corporate behaviour and firm value. Reasonable capital structure can regulate corporate behaviour and improve enterprise value. However, the distortions of capital structure may cause the d...

  2. Capital structure determinants of private small and medium-sized enterprises in China

    OpenAIRE

    Newman, Alexander

    2010-01-01

    This thesis examines the capital structure determinants of private SMEs in China and the extent to which financial theories of capital structure adequately explain their financing behaviour. It also investigates whether other theoretical perspectives can be utilised to explain their capital structure decisions. In order to investigate these issues a mixed method approach is utilised, combining analysis of secondary data, with field research in the form of semi-structured interviews and su...

  3. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    CERN Document Server

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  4. Roof structure theory and support resistance determination of longwall face in shallow seam

    Institute of Scientific and Technical Information of China (English)

    HUANG Qing-xiang(黄庆享)

    2003-01-01

    This paper presents the structure models founded in shallow seam, the roof asymmetry arch with three articulations in roof first weighting and the step voussoir beam in roof periodic weighting. These structure models are differ from classic theory, it establishes the new roof control theory of instability structure roof, especially in shallow seam. Based on the new roof structure theory, the support working state of "given sliding load" is put forward, and the factor of load transmitting is introduced to determine the load on roof structure. Therefore, the proper and accurate calculating methods of support resistance are established. Based on this, the dynamic structure theory in shallow seam could be predicted.

  5. SMEs capital structure determinants during severe economic crisis: The case of Greece

    Directory of Open Access Journals (Sweden)

    D. Balios

    2016-12-01

    Full Text Available The objective of this paper was to explore whether and how the main capital structure determinants of SMEs affected capital structure determination in different ways during the years of economic crisis. We used panel data of 8,052 SMEs operating in Greece during 2009–2012. We found that the effect of capital structure determinants on leverage does not change in an environment of economic crisis; larger SMEs continued to show higher debt ratios, the relationship between profitability and tangibility of assets with leverage continued to be negative, and growth was positively related to leverage.

  6. Biomolecular pleiomorphism probed by spatial interpolation of coarse models.

    Science.gov (United States)

    Rusu, Mirabela; Birmanns, Stefan; Wriggers, Willy

    2008-11-01

    In low resolution structures of biological assemblies one can often observe conformational deviations that require a flexible rearrangement of structural domains fitted at the atomic level. We are evaluating interpolation methods for the flexible alignment of atomic models based on coarse models. Spatial interpolation is well established in image-processing and visualization to describe the overall deformation or warping of an object or an image. Combined with a coarse representation of the biological system by feature vectors, such methods can provide a flexible approximation of the molecular structure. We have compared three well-known interpolation techniques and evaluated the results by comparing them with constrained molecular dynamics. One method, inverse distance weighting interpolation, consistently produced models that were nearly indistinguishable on the alpha carbon level from the molecular dynamics results. The method is simple to apply and enables flexing of structures by non-expert modelers. This is useful for the basic interpretation of volumetric data in biological applications such as electron microscopy. The method can be used as a general interpretation tool for sparsely sampled motions derived from coarse models. PMID:18757874

  7. On Explorative and Integrative Modeling of Biomolecular Complexes

    NARCIS (Netherlands)

    van Zundert, G.C.P.

    2015-01-01

    This thesis introduces and showcases novel approaches for explorative and integrative modeling in the presence of cryo-EM data and distance restraints. In it the PowerFit software is presented, a Python package for fast cross correlation based rigid body fitting of high-resolution structures in low-

  8. Co-determination of capital structure and stock returns in banking industry using structural equation modeling

    Directory of Open Access Journals (Sweden)

    Mehdi Taghavi

    2013-08-01

    Full Text Available Capital structure plays essential role on financial strength of business units and there are literally many studies to confirm the relationship between capital structure and return growth. In this paper, we re-examine this relationship by investigating on 12 Iranian private banks using structural equation modelling over the period 2005-2011. The proposed study of this paper designs a questionnaire and distributes it among experts and analyse it use LISREL software package. The result indicates that there is a positive and meaningful relationship, when the level of significance is five percent between capital structure and stock return in private banking industry in Iran. The implementation of Pearson and Spearman correlation tests also validate the findings.

  9. A Study of Characteristics and Determinants of Capital Structure in the UK SMEs Context

    OpenAIRE

    Jin, Menglu

    2011-01-01

    ABSTRACT This dissertation studies the characteristics and determinants of capital structure of the UK small- and medium-sized enterprises (SMEs)- by utilizing a balanced panel data comprising 135 UK SMEs from 2001 to 2010. Specifically, the potential determinants of UK SMEs’ capital structure that will be tested in this paper are profitability, firm size, growth opportunities, tangibility, business risk, non-debt tax shields, industry effects and time effects and economic downturns. To ac...

  10. Automatic Structure Determination of Regular Polysaccharides Based Solely on NMR Spectroscopy

    OpenAIRE

    Lundborg, Magnus; Fontana, Carolina; Widmalm, Göran

    2011-01-01

    The structural analysis of polysaccharides requires that the sugar components and their absolute configurations are determined. We here show that this can be performed based on NMR spectroscopy by utilizing butanolysis with (+)- and (−)-2-butanol that gives the corresponding 2-butyl glycosides with characteristic 1H and 13C NMR chemical shifts. The subsequent computer-assisted structural determination by CASPER can then be based solely on NMR data in a fully automatic way as shown and impleme...

  11. Structural Determinants of Discrimination of NAD+ from NADH in Yeast Mitochondrial NADH Kinase Pos5*

    OpenAIRE

    Ando, Takuya; Ohashi, Kazuto; Ochiai, Akihito; Mikami, Bunzo; Kawai, Shigeyuki; Murata, Kousaku

    2011-01-01

    NAD kinase catalyzes the phosphorylation of NAD+ to synthesize NADP+, whereas NADH kinase catalyzes conversion of NADH to NADPH. The mitochondrial protein Pos5 of Saccharomyces cerevisiae shows much higher NADH kinase than NAD kinase activity and is therefore referred to as NADH kinase. To clarify the structural determinant underlying the high NADH kinase activity of Pos5 and its selectivity for NADH over NAD+, we determined the tertiary structure of Pos5 complexed with NADH at a resolution o...

  12. Unemployment out of nowhere – a structural axiomatic analysis of objective determinants

    OpenAIRE

    Kakarot-Handtke, Egmont

    2011-01-01

    Unemployment is usually explained with reference to the equilibrium of supply and demand in the labour market. This approach rests on specific behavioral assumptions that are formally expressed as axioms. The standard set of axioms is replaced in the present paper by a set of structural axioms. This approach yields the objective determinants of employment. They consist of effective demand, the actual outcome of price formation, structural stress as determined by the heterogeneity within the b...

  13. Determining the velocity fine structure by a laser anemometer with fixed orientation

    Energy Technology Data Exchange (ETDEWEB)

    Kristensen, Leif; Kirkegaard, P.; Mikkelsen, Torben

    2011-02-15

    We have studied the velocity structure functions and spectra which can be determined by a CW-laser anemometer and a (pulsed) lidar anemometer. We have found useful theoretical expressions for both types of anemometers and compared their filtering of the along-beam turbulent velocity. The purpose has been to establish a basis for remote determining of turbulence fine-structure in terms of the rate of dissipation of specific kinetic energy in the atmospheric boundary layer. (Author)

  14. DETERMINANTS OF CAPITAL STRUCTURE OF CROATIAN ENTERPRISES BEFORE AND DURING THE FINANCIAL CRISIS

    OpenAIRE

    Ena Mostarac; Suzana Petrovic

    2013-01-01

    This paper analysis capital structure determinants of Croatian enterprises based on a cross-sectional data for pre-recession 2007 and recession 2010 comprising about 10,000 firms. Determinants are selected with reference to the relevant capital structure theories and include asset tangibility, profitability, firm size and business risk. The results indicate highly positive significant impact of tangibility and negative significant impact of profitability on financial leverage in both observed...

  15. Determinants of Capital Structure: Evidence from UK Listed Company Panel Data

    OpenAIRE

    Trinh, Ngoc Luong

    2012-01-01

    This paper investigates the determinants of the UK listed company capital structure and their impacts on different debt maturity. The analysis was carried out using a panel data set of 230 non-financial companies in the FTSE 350 index from 2002 to 2011. In addition, a set of 6 theoretical determinants as outlined by existing literature including: asset structure, firm size, growth opportunities, profitability, liquidity and non-debt tax shields was used to test their relationships with differ...

  16. EXAFS, Determination of Short Range Order and Local Structures in Materials

    NARCIS (Netherlands)

    Koningsberger, D.C.; Prins, R.

    1981-01-01

    Extended X-ray Absorption Fine Structure (EXAFS) is a powerful method of determining short range order and local structures in materials using X-ray photons produced by a synchrotron light source, or in-house by a high intensity rotating anode X-ray generator. The technique has provided valuable str

  17. Crystal structure determination by powder neutron diffraction at the spallation neutron source, ISIS

    International Nuclear Information System (INIS)

    The paper concerns the determination of crystal structure by powder neutron diffraction at the spallation neutron source, ISIS. The practicability of the technique is illustrated by a study of the crystal structure of ferric arsenate, FeAsO4. (U.K.)

  18. Profitability of Western European banking systems: panel evidence on structural and cyclical determinants

    OpenAIRE

    Beckmann, Rainer

    2007-01-01

    This paper analyses structural and cyclical determinants of banking profitability in 16 Western European countries. We find that financial structure matters, particularly through the beneficial effect of the capital market orientation in the respective national financial system. Furthermore, higher diversification regarding banks' income sources shows a positive effect. The industry concentration of national banking systems, though, does not significantly affect aggregate profitability. Busin...

  19. X-ray interferometric method of determination of super molecular structure parameters of polymers

    International Nuclear Information System (INIS)

    A new method for determining the density of polymeric substances is proposed. It is based on the determination of the path-Iength differences in moire patterns. The method is characterized by simplicity and accuracy of results. The densities of polychloroprene and polystrol are determined with high accuracy. The knowledge of the dependence of polymer density on the stretching degree allows one to reveal the dynamics of changes of the super molecular structure at the deformation of polymer

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-31

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

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

    International Nuclear Information System (INIS)

    The local density of water molecules around a biomolecule is constructed from calculated two- and three-points correlation functions of polar solvents in water using a Potential-of-Mean-Force (PMF) expansion. As a simple approximation, the hydration of all polar (including charged) groups in a biomolecule is represented by the hydration of water oxygen in bulk water, and the effect of non-polar groups on hydration are neglected, except for excluded volume effects. Pair and triplet correlation functions are calculated by molecular dynamics simulations. We present calculations of the structural hydration for ideal A-DNA molecules with sequences [d(CG)5]2 and [d(C5G5)]2. We find that this method can accurately reproduce the hydration patterns of A-DNA observed in neutron diffraction experiments on oriented DNA fibers

  2. Perspectives for quantum interference with biomolecules and biomolecular clusters

    Science.gov (United States)

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

    2016-06-01

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

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

    Science.gov (United States)

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

    2016-03-01

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

  4. Dynamics of biomoleculars studied by Rayleigh scattering of Moessbauer radiation and Moessbauer spectroscopy

    International Nuclear Information System (INIS)

    This paper reports on dynamics of biomoleculars, proteins and DNA that plays a role in the supply and the regulation their functional activity, for example, like transducers of oxygen, like enzymes, in photosynthesis and so on. The Mossbauer spectroscopy (MS) and especially Rayleigh Scattering of Mossbauer Radiation (RSMR) permit to obtain the quantitative data on dimensions and times of complex hierarchy of motion in biopolymers and to create correspondent functional models. The scheme of RSMR includes Mossbauer source 57Co, the scatterer---biopolymer, the detector and Mossbauer analyzer (Black absorber---or one-line absorber), that situated before and after the scatterer on definite angle -2θ

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-10-01

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

  7. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data.

    Science.gov (United States)

    Lee, Woonghee; Petit, Chad M; Cornilescu, Gabriel; Stark, Jaime L; Markley, John L

    2016-06-01

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27-98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models. PMID:27169728

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-11-15

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

  9. Attenuation contrast between biomolecular and inorganic materials at terahertz frequencies

    Science.gov (United States)

    Chan, T. L. J.; Bjarnason, J. E.; Lee, A. W. M.; Celis, M. A.; Brown, E. R.

    2004-09-01

    Wideband photomixing spectroscopy is used in the present work to contrast the transmission spectra of macromolecules commonly found in biomaterials such as potato starch, wheat flour and cornstarch, and proteins (Cytoplex™), and micromolecules such as sucrose, and inorganic materials such as sodium bicarbonate, and calcium sulfate. Powdered samples were measured at 0.1-0.5THz frequencies. A significant difference in attenuation is found between these samples. At 300GHz starch shows an absorption coefficient of ˜6cm-1 whereas Cytoplex shows 1-3cm-1, while inorganic micromolecules have ˜1cm-1. The absorption in starch increases rapidly with frequency tending to follow a power law α =fn with n typically between 1.5 and 2.0. In contrast, protein materials display a slower dependence on frequency with n between 1.0 and 1.5, and simple molecules show the least n among all three categories. The difference between these ubiquitous macromolecular and micromolecular materials is explained in terms of water content and molecular structure.

  10. Immunochemical, biomolecular and biochemical characterization of bovine epithelial intestinal primocultures

    Directory of Open Access Journals (Sweden)

    Mainil Jacques

    2005-12-01

    Full Text Available Abstract Background Cultures of enterocytes and colonocytes represent valuable tools to study growth and differentiation of epithelial cells. In vitro models may be used to evaluate passage or toxicity of drugs, interactions of enteropathogenes bacteria strains with intestinal epithelium and other physiologic or pathologic phenomenon involving the digestive tract. Results Cultures of bovine colonocytes and jejunocytes were obtained from organoid-enriched preparations, using a combination of enzymatic and mechanical disruption of the intestine epithelium, followed by an isopicnic centrifugation discarding most single cells. Confluent cell monolayers arising from plated organoids exhibited epithelium typical features, such as the pavement-like structure, the presence of apical microvilli and tight junctions. Accordingly, cells expressed several markers of enterocyte brush border (i.e. maltase, alkaline phosphatase and fatty acid binding protein as well as an epithelial cytoskeleton component (cytokeratin 18. However, enterocyte primocultures were also positive for the vimentin immunostaining (mesenchyme marker. Vimentin expression studies showed that this gene is constitutively expressed in bovine enterocytes. Comparison of the vimentin expression profile with the pattern of brush border enzymes activities, suggested that the decrease of cell differentiation level observed during the enterocyte isolation procedure and early passages of the primoculture could result from a post-transcriptional de-repression of vimentin synthesis. The low differentiation level of bovine enterocytes in vitro could partly be counteracted adding butyrate (1–2 mM or using a glucose-deprived culture medium. Conclusion The present study describes several complementary approaches to characterize bovine primary cultures of intestinal cells. Cultured cells kept their morphologic and functional characteristics during several generations.

  11. Biomolecular modification of zirconia surfaces for enhanced biocompatibility

    International Nuclear Information System (INIS)

    Yttria-tetragonal zirconia polycrystal (Y-TZP) is a preferred biomaterial due to its good mechanical properties. In order to improve the biocompatibility of zirconia, RGD-peptide derived from extracellular matrix proteins was employed to modify the surface of Y-TZP to promote cell adhesion in this study. The surface of Y-TZP specimens was first modified using a hydrothermal method for different lengths of time. The topographies of modified Y-TZP specimens were analyzed by contact angle, XRD, FTIR, AFM, and FE-SEM. The mechanical properties were evaluated using Vickers hardness and three point bending strength. Then, the RGD-peptide was immobilized on the surface of the Y-TZP by chemical treatment. These RGD-peptide immobilized Y-TZP specimens were characterized by FTIR and AFM, and then were cocultured with MG-63 osteoblast cells for biocompatibility assay. The cell morphology and proliferation were evaluated by SEM, WST-1, and ALP activity assay. The XRD results indicated that the phase transition, from tetragonal phase to monoclinic phase, was increased with a longer incubation time of hydrothermal treatment. However, there were no significant differences in mechanical strengths after RGD-peptide was successfully grafted onto the Y-TZP surface. The SEM images showed that the MG-63 cells appeared polygonal, spindle-shaped, and attached on the RGD-peptide immobilized Y-TZP. The proliferation and cellular activities of MG-63 cells on the RGD-peptide immobilized Y-TZP were better than that on the unmodified Y-TZP. From the above results, the RGD-peptide can be successfully grafted onto the hydrothermal modified Y-TZP surface. The RGD-peptide immobilized Y-TZP can increase cell adhesion, and thus, improve the biocompatibility of Y-TZP. - Highlights: • Covalent bonding between peptide and Y-TZP was proposed. • Stable biomimetic structures produced on the surface of zirconia. • The biocompatibility was improved

  12. A novel strategy for NMR resonance assignment and protein structure determination

    International Nuclear Information System (INIS)

    The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution – especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

  13. Determination Strength of Concrete in-Situ by Seismic Ultrasonic Method in Detecting Risky Structure

    Science.gov (United States)

    Uyanik, O.; Öziçer, S.; Sabbağ, N.

    2014-12-01

    Strength of concrete is important in the analysis of structures. Strength of concrete can be determined as destructive or non destructive. In order to determine to strength of concrete as destructive, core is taken from concrete parts of the structure and uniaxial compressive strength test is applied in the laboratory. In contrast, strength of concrete can be determined as non destructive in situ by seismic ultrasonic technique. In this study, seismic ultrasonic P wave velocity measurements. Schmidt hammer test in situ and core sampling along with uniaxial compressive test are carried out in order to determine the strength of concrete in existing structures in Bornova district of İzmir. Seismic ultrasonic P wave velocity measurements in situ were also applied on the core. The concrete strength values obtained from techniques applied in study were compared and error values are determined. By seismic ultrasonic P wave velocity measurements with error value %5 strength of concrete is determined quickly without any destruction on structures studied.

  14. Biomolecular interactions probed by fluorescence resonance energy transfer

    Science.gov (United States)

    Lange, Daniela Charlotte

    2000-09-01

    trafficking, with emphasis on defining the role of apoD in this disease. In vitro FRET studies on the dynamic structure of apoD and its close relative, β-lactoglobulin, are presented. FRET combined with conventional fluorescence microscopy established a direct association between apoD and cholesterol in situ. No evidence was found for interaction between apoD and the NPC1 protein.

  15. A new protocol for the determination of magnetic structures using simulated annealing and representational analysis. SARAh

    International Nuclear Information System (INIS)

    Complete text of publication follows. The determination of magnetic structures from neutron diffraction data is often carried out by trial and error. Much time is wasted by the examination of structures that are in fact symmetry forbidden. The technique of Representation Analysis (RA) [1] uses simple matrix calculations to provide model magnetic structures, but has fallen into disuse because of its tedious nature. New Windows-based code performs these calculations automatically. Integration with refinement packages based on Simulated Annealing (SA) [2], a.k.a. Reverse Monte Carlo (RMC), algorithms allows these models to be sequentially fitted against diffraction data. Magnetic structures also lend themselves well to the use of Genetic Algorithms (GA) and these techniques can be exploited to increase the symmetry of the refined structures. The best models determined can then be examined using conventional least-squares methods and software. Combination of SA, RA and GA creates a powerful new protocol for the determination of magnetic structures. (author) [1] E.F. Bertaut, Acta Cryst., A 24, 217 (1968); [2] R.L. McGreevy in Structural modelling in Inorganic Crystallography ed. R.A. Catlow, Academic Press (1997)

  16. Determining Orientational Structure of Diamondoid Thiols Attached to Silver Using Near Edge X-ray Absorption Fine Structure Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Willey, T M; Lee, J I; Fabbri, J D; Wang, D; Nielsen, M; Randel, J C; Schreiner, P R; Fokin, A A; Tkachenko, B A; Fokina, N A; Dahl, J P; Carlson, R K; Terminello, L J; Melosh, N A; van Buuren, T

    2008-10-07

    Near-edge x-ray absorption fine structure spectroscopy (NEXAFS) is a powerful tool for determination of molecular orientation in self-assembled monolayers and other surface-attached molecules. A general framework for using NEXAFS to simultaneously determine molecular tilt and twist of rigid molecules attached to surfaces is presented. This framework is applied to self-assembled monolayers of higher diamondoid, hydrocarbon molecules with cubic-diamond-cage structures. Diamondoid monolayers chemisorbed on metal substrates are known to exhibit interesting electronic and surface properties. This work compares molecular orientation in monolayers prepared on silver substrates using two different thiol positional isomers of [121]tetramantane, and thiols derived from two different pentamantane structural isomers, [1212]pentamantane and [1(2,3)4]pentamantane. The observed differences in monolayer structure demonstrate the utility and limitations of NEXAFS spectroscopy and the framework. The results also demonstrate the ability to control diamondoid assembly, in particular the molecular orientational structure, providing a flexible platform for the modification of surface properties with this exciting new class of nanodiamond materials.

  17. The structure of melon necrotic spot virus determined at 2.8 Å resolution

    International Nuclear Information System (INIS)

    The structure of melon necrotic spot virus is reported. The structure of melon necrotic spot virus (MNSV) was determined at 2.8 Å resolution. Although MNSV is classified into the genus Carmovirus of the family Tombusviridae, the three-dimensional structure of MNSV showed a higher degree of similarity to tomato bushy stunt virus (TBSV), which belongs to the genus Tombusvirus, than to carnation mottle virus (CMtV), turnip crinkle virus (TCV) or cowpea mottle virus (CPMtV) from the genus Carmovirus. Thus, the classification of the family Tombusviridae at the genus level conflicts with the patterns of similarity among coat-protein structures. MNSV is one of the viruses belonging to the genera Tombusvirus or Carmovirus that are naturally transmitted in the soil by zoospores of fungal vectors. The X-ray structure of MNSV provides us with a representative structure of viruses transmitted by fungi

  18. Determining complex crystal structures from high pressure single-crystal diffraction data collected on synchrotron sources

    Science.gov (United States)

    McMahon, M. I.; Loa, I.; Stinton, G. W.; Lundegaard, L. F.

    2013-08-01

    As part of a Long Term Project, single-crystal diffraction techniques have been developed for use at the high pressure beamlines ID09 and ID27 at the European Synchrotron Radiation Facility, and have been utilised to determine the crystal structures of various high pressure phases, including those with incommensurate structures, at both high and low temperatures. The same techniques have also been used to determine the structures of high pressure phases at the SRS, Diamond and Petra-III synchrotron sources. In this paper, we describe technical details of the methods developed, and describe some of the considerations necessary for planning experiments and collecting and processing the data. We then illustrate the quality of data that can be obtained, and the complexity of the structures that can be refined, using recent results obtained from complex high pressure phases of N2 and Ba.

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

    Science.gov (United States)

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

    2013-01-01

    After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i) the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii) a model of enzymatic futile cycle and (iii) a genetic toggle switch. In (ii) and (iii) we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises. PMID:23437034

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

    International Nuclear Information System (INIS)

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

  1. Optimizing water hyperpolarization and dissolution for sensitivity-enhanced 2D biomolecular NMR

    Science.gov (United States)

    Olsen, Greg; Markhasin, Evgeny; Szekely, Or; Bretschneider, Christian; Frydman, Lucio

    2016-03-01

    A recent study explored the use of hyperpolarized water, to enhance the sensitivity of nuclei in biomolecules thanks to rapid proton exchanges with labile amide backbone and sidechain groups. Further optimizations of this approach have now allowed us to achieve proton polarizations approaching 25% in the water transferred into the NMR spectrometer, effective water T1 times approaching 40 s, and a reduction in the dilution demanded for the cryogenic dissolution process. Further hardware developments have allowed us to perform these experiments, repeatedly and reliably, in 5 mm NMR tubes. All these ingredients - particularly the ⩾3000× 1H polarization enhancements over 11.7 T thermal counterparts, long T1 times and a compatibility with high-resolution biomolecular NMR setups - augur well for hyperpolarized 2D NMR studies of peptides, unfolded proteins and intrinsically disordered systems undergoing fast exchanges of their protons with the solvent. This hypothesis is here explored by detailing the provisions that lead to these significant improvements over previous reports, and demonstrating 1D coherence transfer experiments and 2D biomolecular HMQC acquisitions delivering NMR spectral enhancements of 100-500× over their optimized, thermally-polarized, counterparts.

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

    Directory of Open Access Journals (Sweden)

    Giulio Caravagna

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

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

    International Nuclear Information System (INIS)

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

  4. Crystal structure determination and reaction pathway of amide-hydride mixtures

    International Nuclear Information System (INIS)

    Combined synchrotron in situ X-ray diffraction and neutron diffraction studies were performed on 2:1 mixtures of lithium amide and magnesium hydride, which have shown promise as solid-state hydrogen storage materials. The dehydrogenated product is a mixed lithium and magnesium imide, Li2Mg(NH)2, whose crystal structure has not heretofore been determined. Furthermore, at elevated temperatures, Li2Mg(NH)2 undergoes two structural transitions from an orthorhombic structure to a primitive cubic structure at intermediate temperature (350 deg. C) followed by a face-centered cubic crystal structure at high temperature (500 deg. C). Disordering of the Li, Mg and cation vacancies as a function of temperature drives the structural transitions. We report the reaction pathway from in situ X-ray diffraction studies and the crystal structures of the three structural variants of Li2Mg(NH)2 as determined by high-resolution X-ray and neutron powder diffraction. We also report the hydrogen storage reaction pathways for mixtures with other cation ratios

  5. Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Yingang, E-mail: fengyg@qibebt.ac.cn [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Song, Xiaxia [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Lin, Jinzhong [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Xuan, Jinsong [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Cui, Qiu [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Wang, Jinfeng [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

    2014-07-18

    Highlights: • The archaea-specific ribosomal protein L46a has no homology to known proteins. • Three dimensional structure and backbone dynamics of L46a were determined by NMR. • The structure of L46a represents a novel protein fold. • A potential rRNA-binding surface on L46a was identified. • The potential position of L46a on the ribosome was proposed. - Abstract: Three archaea-specific ribosomal proteins recently identified show no sequence homology with other known proteins. Here we determined the structure of L46a, the most conserved one among the three proteins, from Sulfolobus solfataricus P2 using NMR spectroscopy. The structure presents a twisted β-sheet formed by the N-terminal part and two helices at the C-terminus. The L46a structure has a positively charged surface which is conserved in the L46a protein family and is the potential rRNA-binding site. Searching homologous structures in Protein Data Bank revealed that the structure of L46a represents a novel protein fold. The backbone dynamics identified by NMR relaxation experiments reveal significant flexibility at the rRNA binding surface. The potential position of L46a on the ribosome was proposed by fitting the structure into a previous electron microscopy map of the ribosomal 50S subunit, which indicated that L46a contacts to domain I of 23S rRNA near a multifunctional ribosomal protein L7ae.

  6. Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold

    International Nuclear Information System (INIS)

    Highlights: • The archaea-specific ribosomal protein L46a has no homology to known proteins. • Three dimensional structure and backbone dynamics of L46a were determined by NMR. • The structure of L46a represents a novel protein fold. • A potential rRNA-binding surface on L46a was identified. • The potential position of L46a on the ribosome was proposed. - Abstract: Three archaea-specific ribosomal proteins recently identified show no sequence homology with other known proteins. Here we determined the structure of L46a, the most conserved one among the three proteins, from Sulfolobus solfataricus P2 using NMR spectroscopy. The structure presents a twisted β-sheet formed by the N-terminal part and two helices at the C-terminus. The L46a structure has a positively charged surface which is conserved in the L46a protein family and is the potential rRNA-binding site. Searching homologous structures in Protein Data Bank revealed that the structure of L46a represents a novel protein fold. The backbone dynamics identified by NMR relaxation experiments reveal significant flexibility at the rRNA binding surface. The potential position of L46a on the ribosome was proposed by fitting the structure into a previous electron microscopy map of the ribosomal 50S subunit, which indicated that L46a contacts to domain I of 23S rRNA near a multifunctional ribosomal protein L7ae

  7. Experimental determination of the π meson structure functions by the Drell-Yan mechanism

    International Nuclear Information System (INIS)

    We have studied high statistics samples of dimuon events (proportional35,000) produced from πsup(+-) on platinum target in the mass interval 4.22 sigma/dx1 dx2 to π+ and π- data. At 200 GeV, the simultaneous use of π+ and π- data allows a separate determination of the valence and sea structure functions of the π. Furthermore, the 150 and 280 GeV data allow an accurate determination of the shape of the valence structure function and give an estimate of its evolution between Q2=25 and 50 GeV2. (orig.)

  8. Determinants of Capital Structure: A case from Textile Industry of Pakistan

    Directory of Open Access Journals (Sweden)

    Aurangzeb

    2012-04-01

    Full Text Available This study examines the determinants of capital structure in Textile industry of Pakistan on a data for the period of 2004 to 2009. Multiple regression technique is used to analyze the relationship between dependent variable (Leverage and independent variables (Firm Size, Tangibility of Assets, Profitability, and Sales Growth. It is concluded all independent variables have significant impact on the balance of leverage. It is concludes that firm size, tangibility of assets and profitability having positive relationship with leverage. On the other hand sales growth has negative relationship with leverage. It is recommended that policy makers should focus on these determinants when making any decisions regarding capital structure.

  9. DETERMINANTS OF CAPITAL STRUCTURE OF CROATIAN ENTERPRISES BEFORE AND DURING THE FINANCIAL CRISIS

    Directory of Open Access Journals (Sweden)

    Ena Mostarac

    2013-06-01

    Full Text Available This paper analysis capital structure determinants of Croatian enterprises based on a cross-sectional data for pre-recession 2007 and recession 2010 comprising about 10,000 firms. Determinants are selected with reference to the relevant capital structure theories and include asset tangibility, profitability, firm size and business risk. The results indicate highly positive significant impact of tangibility and negative significant impact of profitability on financial leverage in both observed years. Firm size seems to be statistically significant at higher level in crisis period, but at the same time no relationship can be found between business risk and financial leverage that is of economic significance.

  10. Organic structure determination using 2-D NMR spectroscopy a problem-based approach

    CERN Document Server

    Simpson, Jeffrey H

    2011-01-01

    Organic Structure Determination Using 2-D NMR Spectroscopy: A Problem-Based Approach, Second Edition, provides an introduction to the use of two-dimensional (2-D) nuclear magnetic resonance (NMR) spectroscopy to determine organic structure. The book begins with a discussion of the NMR technique, while subsequent chapters cover instrumental considerations; data collection, processing, and plotting; chemical shifts; symmetry and topicity; through-bond effects; and through-space effects. The book also covers molecular dynamics; strategies for assigning resonances to atoms within a molecule; s

  11. Scattering pulse of label free fine structure cells to determine the size scale of scattering structures

    Science.gov (United States)

    Zhang, Lu; Chen, Xingyu; Zhang, Zhenxi; Chen, Wei; Zhao, Hong; Zhao, Xin; Li, Kaixing; Yuan, Li

    2016-04-01

    Scattering pulse is sensitive to the morphology and components of each single label-free cell. The most direct detection result, label free cell's scattering pulse is studied in this paper as a novel trait to recognize large malignant cells from small normal cells. A set of intrinsic scattering pulse calculation method is figured out, which combines both hydraulic focusing theory and small particle's scattering principle. Based on the scattering detection angle ranges of widely used flow cytometry, the scattering pulses formed by cell scattering energy in forward scattering angle 2°-5° and side scattering angle 80°-110° are discussed. Combining the analysis of cell's illuminating light energy, the peak, area, and full width at half maximum (FWHM) of label free cells' scattering pulses for fine structure cells with diameter 1-20 μm are studied to extract the interrelations of scattering pulse's features and cell's morphology. The theoretical and experimental results show that cell's diameter and FWHM of its scattering pulse agree with approximate linear distribution; the peak and area of scattering pulse do not always increase with cell's diameter becoming larger, but when cell's diameter is less than about 16 μm the monotone increasing relation of scattering pulse peak or area with cell's diameter can be obtained. This relationship between the features of scattering pulse and cell's size is potentially a useful but very simple criterion to distinguishing malignant and normal cells by their sizes and morphologies in label free cells clinical examinations.

  12. Structure determination of an integral membrane protein at room temperature from crystals in situ

    International Nuclear Information System (INIS)

    The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated. The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates (in situ) is demonstrated. Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling. Essential to the method is the ability to limit radiation damage by recording a small amount of data per sample from many samples and subsequently assembling the resulting data sets using specialized software. The validity of this procedure is established by the structure determination of Haemophilus influenza TehA at 2.3 Å resolution. The method presented offers an effective protocol for the fast and efficient determination of membrane-protein structures at room temperature using third-generation synchrotron beamlines

  13. Structure determination of an integral membrane protein at room temperature from crystals in situ

    Energy Technology Data Exchange (ETDEWEB)

    Axford, Danny [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Hu, Nien-Jen; Choudhury, Hassanul Ghani [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Iwata, So [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Kyoto University, Kyoto 606-8501 (Japan); Beis, Konstantinos [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Alguel, Yilmaz, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom)

    2015-05-14

    The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated. The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates (in situ) is demonstrated. Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling. Essential to the method is the ability to limit radiation damage by recording a small amount of data per sample from many samples and subsequently assembling the resulting data sets using specialized software. The validity of this procedure is established by the structure determination of Haemophilus influenza TehA at 2.3 Å resolution. The method presented offers an effective protocol for the fast and efficient determination of membrane-protein structures at room temperature using third-generation synchrotron beamlines.

  14. An Empirical Study on Capital Structure Determinants of Selected ASEAN Countries

    OpenAIRE

    Ngo, Hoang Anh

    2013-01-01

    Capital structure has been a controversial topic for decades. Conflicting arguments in theories and mixed findings in empirical work require further studies on this subject. More importantly, most previous studies have focused on developed countries and little attention is paid to emerging economies, especially ASEAN. Therefore, this study attempts to fill the gap by examining effects of capital structure's determinants on different measures of leverage of listed manufacturing companies in se...

  15. Accurate determination of crystal structures based on averaged local bond order parameters

    OpenAIRE

    Lechner, Wolfgang; Dellago, Christoph

    2008-01-01

    Local bond order parameters based on spherical harmonics, also known as Steinhardt order parameters, are often used to determine crystal structures in molecular simulations. Here we propose a modification of this method in which the complex bond order vectors are averaged over the first neighbor shell of a given particle and the particle itself. As demonstrated using soft particle systems, this averaging procedure considerably improves the accuracy with which different crystal structures can ...

  16. Identification and determination of solitary wave structures in nonlinear wave propagation

    International Nuclear Information System (INIS)

    Nonlinear wave phenomena are characterized by the appearance of ''solitary wave coherent structures'' traveling at speeds determined by their amplitudes and morphologies. Assuming that these structures are briefly noninteracting, we propose a method for the identification of the number of independent features and their respective speeds. Using data generated from an exact two-soliton solution to the Korteweg-de-Vries equation, we test the method and discuss its strengths and limitations. 41 refs., 2 figs

  17. Crystal structure of dimeric human ciliary neurotrophic factor determined by MAD phasing.

    OpenAIRE

    McDonald, N. Q.; Panayotatos, N; Hendrickson, W A

    1995-01-01

    Ciliary neurotrophic factor (CNTF) promotes the survival and differentiation of developing motor neurons and is a potential therapeutic for treating neurodegeneration and nerve injury. The crystal structure of human CNTF has been determined at 2.4 A resolution using multi-wavelength anomalous diffraction (MAD) phasing from a single Yb3+ ions. The structure reveals that CNTF is dimeric, with a novel anti-parallel arrangement of the subunits, not previously observed for other cytokines. Each su...

  18. The Determinants of Capital Structure: Evidence from the Turkish Manufacturing Sector

    OpenAIRE

    Songul KAKILLI ACARAVCI

    2015-01-01

    This study investigates the determinants of capital structure in Turkey by using panel data methods. The sample period spans from 1993 to 2010 for 79 firms in the manufacturing sector traded on the Istanbul Stock Exchange. The base model was expanded with firm size and sectorspecific effects. This study compares also effects on capital structure according to sectors and firm size of variables used in models. Growth opportunities, size, profitability, tangibility and non-debt tax shields are u...

  19. The Characteristics and Determinants of Capital Structure in Shariah-compliant Firms: Empirical Evidence from Malaysia

    OpenAIRE

    Law, Poh Kim

    2011-01-01

    This study aims to find out whether the prevailing capital structure theories (trade-off, pecking order and agency theory) are applicable on Malaysian Shariah-compliant firms. The impact of Malaysia Shariah Advisory Council (SAC)’s Shariah screening guideline and dual banking system in Malaysia on capital structure will also be examined. The empirical results show that profitability is the most dominant determinant of debt policy with significant negative relationships found with all measures...

  20. Determinants of Firm Affiliation to Pyramid Structure: A Survey from Malaysian Public Listed Firms

    OpenAIRE

    Irfah Najihah Basir Malan; Norhana Salamudin; Noryati Ahmad

    2013-01-01

    This research seeks to examine the determinants of affiliation to pyramid structure of Malaysian public listed firms. A motivation of the research comes from the phenomenon of pyramid structure causing divergence of ultimate owners’ actual ownership and control leading to severe expropriation of minority shareholders’ interest. The method adapts Attig Model and employs Panel Generalised Least Square on 136 Malaysian pyramid firms over a twenty one-year period from 1990 to 2010. There are ten ...

  1. Corporate performance, board structure, and their determinants in the banking industry

    OpenAIRE

    Renée B. Adams; Mehran, Hamid

    2008-01-01

    The subprime crisis highlights how little we know about the governance of banks. This paper addresses a long-standing gap in the literature by analyzing board governance using a sample of banking firm data that spans forty years. We examine the relationship between board structure (size and composition) and bank performance, as well as some determinants of board structure. We document that mergers and acquisitions activity influences bank board composition, and we provide new evidence that or...

  2. Determinants of capital structure in small and medium sized enterprises in Malaysia

    OpenAIRE

    Mat Nawi, Hafizah

    2015-01-01

    This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London This study aims to investigate the determinants of capital structure in small and medium-sized enterprises (SMEs) in Malaysia and their effect on firms’ performance. The study addresses the following primary question: What are the factors that influence the capital structure of SMEs in Malaysia? The sample of this research is SMEs in the east coast region of Malaysia. Adopting a posi...

  3. Determination of damage-free crystal structure of an X-ray sensitive protein using XFEL

    International Nuclear Information System (INIS)

    We report a method of femtosecond crystallography for determining radiation damage-free crystal structures of large proteins at atomic resolution. The name of the method is 'serial femtosecond rotation crystallography' (SF-ROX). Here, we demonstrate experimental details of SF-ROX and 1.9-Å radiation damage-free structure analysis of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein. (author)

  4. The Determinants of Capital Structure-The Comparison/Evidence in China

    OpenAIRE

    Wu, Dan

    2011-01-01

    Capital structure theory has been broadly discussed and studied once it is raised by Modigliani and Miller in 1958. This paper attempts to investigate the determinants of capital structure of Chinese listed companies to compare with western countries. China is one of the rapidly emerging markets in the world, while its market environment varies; research results obtained in western countries are not entirely applicable to China’s situation. Among multiple angles economists have studied in, th...

  5. Phase Structures of Microemulsions Determined by the Steady-State Fluorescence Method

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The steady-state fluorescence method has been tentatively used to determine the phase structures of microemulsion systems consisting of cetyltrimethylammonium bromide (CTAB), n-butanol (n-C4H9OH), octane (n-C5H18), and water. The excimer/monomer intensity ratio (Ie/Im) of pyrene has demonstrated that the various structures in the microemulsion phase region can be distinguished. The results are consistent with electrical conductivity data already reported.

  6. THE DETERMINANTS OF CAPITAL STRUCTURE OF LARGE NON-FINANCIAL LISTED FIRMS IN NIGERIA

    OpenAIRE

    Rafiu Oyesola Salawu; Akinlolu Ayodeji Agboola

    2008-01-01

    This paper examines capital structure determinants of non-financial firms in Nigeria using a panel of 33 large firms. Statistical tests are performed for the period 1990-2004. The results reveal that profitability, tangibility and company size are positively related to total debt and long-term debt, and growth opportunities are negatively associated with total debt. The empirical results indicate that the financing decisions of large firms in Nigeria can be explained by the determinants sugge...

  7. MARKET-STRUCTURE DETERMINANTS OF NATIONAL BRAND-PRIVATE LABEL PRICE DIFFERENCES OF MANUFACTURED FOOD PRODUCTS

    OpenAIRE

    Connor, John M.; Peterson, Everett B.

    1991-01-01

    This paper estimates the relationships between market structure and the Lerner index of monopoly constructed from price data on processed food products sold through grocery stores. A theoretical model of a differentiated oligopoly specifies two determinants of price-cost margins: the Herfindahl-Hirschman index of seller concentration adjusted for the elasticity of demand and the industry advertising-to-sales ratio. The results indicate that the three principal determinants of price-cost margi...

  8. Depressive symptoms and the associations with individual, psychosocial, and structural determinants in Swedish adolescents

    OpenAIRE

    Heléne Zetterström Dahlqvist; Evelina Landstedt; Katja Gillander Gådin

    2012-01-01

    Depressive symptoms in adolescents are an increasing public health issue in Sweden and in most Western countries. Aim: To explore how individual, psychosocial, and structural determinants are associated with depressive symptoms in Swedish adolescents. Methods: A web-based questionnaire was answered by 1193 13- to 16-year-old boys (n = 566) and girls (n = 627). Stepwise logistic regressions were employed to analyse the association between depressive symptoms and various determinants at the ind...

  9. Modernization options for light utility helicopter force structure in the Army National Guard : factors and influences affecting force structure determination

    OpenAIRE

    Bittner, James R.

    2001-01-01

    This thesis assesses the different options for modernizing Army National Guard light utility helicopter aviation assets for future roles and missions. It will review the political process by which Army National Guard aviation structure and modernization are determined. The United States military forces are continually deployed to various regions of the world to perform different missions, in a period characterized by increasingly austere defense budgets. A major budgetary challenge for defens...

  10. Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei

    Energy Technology Data Exchange (ETDEWEB)

    Begley, Darren W.; Hartley, Robert C.; Davies, Douglas R.; Edwards, Thomas E.; Leonard, Jess T.; Abendroth, Jan; Burris, Courtney A.; Bhandari, Janhavi; Myler, Peter J.; Staker, Bart L.; Stewart, Lance J. (UWASH); (Emerald)

    2011-09-28

    As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.

  11. The J-UNIO protocol for automated protein structure determination by NMR in solution

    International Nuclear Information System (INIS)

    The J-UNIO (JCSG protocol using the software UNIO) procedure for automated protein structure determination by NMR in solution is introduced. In the present implementation, J-UNIO makes use of APSY-NMR spectroscopy, 3D heteronuclear-resolved [1H,1H]-NOESY experiments, and the software UNIO. Applications with proteins from the JCSG target list with sizes up to 150 residues showed that the procedure is highly robust and efficient. In all instances the correct polypeptide fold was obtained in the first round of automated data analysis and structure calculation. After interactive validation of the data obtained from the automated routine, the quality of the final structures was comparable to results from interactive structure determination. Special advantages are that the NMR data have been recorded with 6–10 days of instrument time per protein, that there is only a single step of chemical shift adjustments to relate the backbone signals in the APSY-NMR spectra with the corresponding backbone signals in the NOESY spectra, and that the NOE-based amino acid side chain chemical shift assignments are automatically focused on those residues that are heavily weighted in the structure calculation. The individual working steps of J-UNIO are illustrated with the structure determination of the protein YP926445.1 from Shewanella amazonensis, and the results obtained with 17 JCSG targets are critically evaluated.

  12. Evaluation of biomolecular distributions in rat brain tissues by means of ToF-SIMS using a continuous beam of Ar clusters.

    Science.gov (United States)

    Nakano, Shusuke; Yokoyama, Yuta; Aoyagi, Satoka; Himi, Naoyuki; Fletcher, John S; Lockyer, Nicholas P; Henderson, Alex; Vickerman, John C

    2016-06-01

    Time-of-flight secondary ion mass spectrometry (ToF-SIMS) provides detailed chemical structure information and high spatial resolution images. Therefore, ToF-SIMS is useful for studying biological phenomena such as ischemia. In this study, in order to evaluate cerebral microinfarction, the distribution of biomolecules generated by ischemia was measured with ToF-SIMS. ToF-SIMS data sets were analyzed by means of multivariate analysis for interpreting complex samples containing unknown information and to obtain biomolecular mapping indicated by fragment ions from the target biomolecules. Using conventional ToF-SIMS (primary ion source: Bi cluster ion), it is difficult to detect secondary ions beyond approximately 1000 u. Moreover, the intensity of secondary ions related to biomolecules is not always high enough for imaging because of low concentration even if the masses are lower than 1000 u. However, for the observation of biomolecular distributions in tissues, it is important to detect low amounts of biological molecules from a particular area of tissue. Rat brain tissue samples were measured with ToF-SIMS (J105, Ionoptika, Ltd., Chandlers Ford, UK), using a continuous beam of Ar clusters as a primary ion source. ToF-SIMS with Ar clusters efficiently detects secondary ions related to biomolecules and larger molecules. Molecules detected by ToF-SIMS were examined by analyzing ToF-SIMS data using multivariate analysis. Microspheres (45 μm diameter) were injected into the rat unilateral internal carotid artery (MS rat) to cause cerebral microinfarction. The rat brain was sliced and then measured with ToF-SIMS. The brain samples of a normal rat and the MS rat were examined to find specific secondary ions related to important biomolecules, and then the difference between them was investigated. Finally, specific secondary ions were found around vessels incorporating microspheres in the MS rat. The results suggest that important biomolecules related to cerebral

  13. Determination of the Cu(110)-c(6X2)-O structure by x-ray diffraction

    DEFF Research Database (Denmark)

    Feidenhans'l, R.; Grey, F.; Johnson, R.L.; Nielsen, M.

    1991-01-01

    We have performed a structural determination of the Cu(110)-c(6 X 2)-O surface by x-ray diffraction. A model including only copper atoms is found on the basis of the Patterson function; the positions of the oxygen atoms are revealed in an electron-density-difference map. The final structure has a...... as found on the Cu(110)-(2 X 1)-O and Cu(100)-(square-root 2 X 2 square-root 2)R 45-degrees-O surfaces, but they are more densely packed than in the 2 X 1 structure....

  14. Determination of conduction and valence band electronic structure of anatase and rutile TiO2

    Indian Academy of Sciences (India)

    Jakub Szlachetko; Katarzyna Michalow-Mauke; Maarten Nachtegaal; Jacinto Sá

    2014-03-01

    Electronic structures of rutile and anatase polymorph of TiO2 were determined by resonant inelastic X-ray scattering measurements and FEFF9.0 calculations. Difference between crystalline structures led to shifts in the rutile Ti -band to lower energy with respect to anatase, i.e., decrease in band gap. Anatase possesses localized states located in the band gap where electrons can be trapped, which are almost absent in the rutile structure. This could well explain the reported longer lifetimes in anatase. It was revealed that HR-XAS is insufficient to study in-depth unoccupied states of investigated materials because it overlooks the shallow traps.

  15. Use of electrophoretic mobility to determine the secondary structure of a small antisense RNA.

    OpenAIRE

    Jacques, J P; Susskind, M M

    1991-01-01

    Natural antisense RNAs have stem-loop (hairpin) secondary structures that are important for their function. The sar antisense RNA of phage P22 is unusual: the 3' half of the molecule forms an extensive stem-loop, but potential structures for the 5' half are not predicted to be thermodynamically stable. We devised a novel method to determine the secondary structure of sar RNA by examining the electrophoretic mobility on non-denaturing gels of numerous sar mutants. The results show that the wil...

  16. Thermo-responsive cell culture carriers based on poly(vinyl methyl ether)—the effect of biomolecular ligands to balance cell adhesion and stimulated detachment

    Science.gov (United States)

    Teichmann, Juliane; Nitschke, Mirko; Pette, Dagmar; Valtink, Monika; Gramm, Stefan; Härtel, Frauke V.; Noll, Thomas; Funk, Richard H. W.; Engelmann, Katrin; Werner, Carsten

    2015-08-01

    Two established material systems for thermally stimulated detachment of adherent cells were combined in a cross-linked polymer blend to merge favorable properties. Through this approach poly(N-isopropylacrylamide) (PNiPAAm) with its superior switching characteristic was paired with a poly(vinyl methyl ether)-based composition that allows adjusting physico-chemical and biomolecular properties in a wide range. Beyond pure PNiPAAm, the proposed thermo-responsive coating provides thickness, stiffness and swelling behavior, as well as an apposite density of reactive sites for biomolecular functionalization, as effective tuning parameters to meet specific requirements of a particular cell type regarding initial adhesion and ease of detachment. To illustrate the strength of this approach, the novel cell culture carrier was applied to generate transplantable sheets of human corneal endothelial cells (HCEC). Sheets were grown, detached, and transferred onto planar targets. Cell morphology, viability and functionality were analyzed by immunocytochemistry and determination of transepithelial electrical resistance (TEER) before and after sheet detachment and transfer. HCEC layers showed regular morphology with appropriate TEER. Cells were positive for function-associated marker proteins ZO-1, Na+/K+-ATPase, and paxillin, and extracellular matrix proteins fibronectin, laminin and collagen type IV before and after transfer. Sheet detachment and transfer did not impair cell viability. Subsequently, a potential application in ophthalmology was demonstrated by transplantation onto de-endothelialized porcine corneas in vitro. The novel thermo-responsive cell culture carrier facilitates the generation and transfer of functional HCEC sheets. This paves the way to generate tissue engineered human corneal endothelium as an alternative transplant source for endothelial keratoplasty.

  17. Structural and functional conservation of fungal MatA and human SRY sex determining proteins

    OpenAIRE

    Czaja, Wioletta; Miller, Karen Y.; Skinner, Michael K.; Bruce L. Miller

    2014-01-01

    Sex determination in animals and fungi is regulated by specific sex determining genes. The Aspergillus nidulans (A.nidulans) mating type gene matA and the human SRY (Sex Determining Region Y) encode proteins containing a single HMG (High Mobility Group) domain. Analysis of the amino acid sequence of MatA and SRY transcription factors revealed significant structural similarity. The human SRY protein is able to functionally replace MatA and drives the sexual cycle in the fungus A. nidulans. Fun...

  18. Precise equilibrium structure determination of hydrazoic acid (HN3) by millimeter-wave spectroscopy.

    Science.gov (United States)

    Amberger, Brent K; Esselman, Brian J; Stanton, John F; Woods, R Claude; McMahon, Robert J

    2015-09-14

    The millimeter-wave spectrum of hydrazoic acid (HN3) was analyzed in the frequency region of 235-450 GHz. Transitions from a total of 14 isotopologues were observed and fit using the A-reduced or S-reduced Hamiltonian. Coupled-cluster calculations were performed to obtain a theoretical geometry, as well as rotation-vibration interaction corrections. These calculated vibration-rotation correction terms were applied to the experimental rotational constants to obtain mixed theoretical/experimental equilibrium rotational constants (Ae, Be, and Ce). These equilibrium rotational constants were then used to obtain an equilibrium (Re) structure using a least-squares fitting routine. The Re structural parameters are consistent with a previously published Rs structure, largely falling within the uncertainty limits of that Rs structure. The present Re geometric parameters of HN3 are determined with exceptionally high accuracy, as a consequence of the large number of isotopologues measured experimentally and the sophisticated (coupled-cluster theoretical treatment (CCSD(T))/ANO2) of the vibration-rotation interactions. The Re structure exhibits remarkable agreement with the CCSD(T)/cc-pCV5Z predicted structure, validating both the accuracy of the ab initio method and the claimed uncertainties of the theoretical/experimental structure determination. PMID:26374038

  19. Precise equilibrium structure determination of hydrazoic acid (HN{sub 3}) by millimeter-wave spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Amberger, Brent K.; Esselman, Brian J.; Woods, R. Claude; McMahon, Robert J. [Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706 (United States); Stanton, John F. [Institute for Theoretical Chemistry, Department of Chemistry, The University of Texas–Austin, Austin, Texas 78712 (United States)

    2015-09-14

    The millimeter-wave spectrum of hydrazoic acid (HN{sub 3}) was analyzed in the frequency region of 235-450 GHz. Transitions from a total of 14 isotopologues were observed and fit using the A-reduced or S-reduced Hamiltonian. Coupled-cluster calculations were performed to obtain a theoretical geometry, as well as rotation-vibration interaction corrections. These calculated vibration-rotation correction terms were applied to the experimental rotational constants to obtain mixed theoretical/experimental equilibrium rotational constants (A{sub e}, B{sub e}, and C{sub e}). These equilibrium rotational constants were then used to obtain an equilibrium (R{sub e}) structure using a least-squares fitting routine. The R{sub e} structural parameters are consistent with a previously published R{sub s} structure, largely falling within the uncertainty limits of that R{sub s} structure. The present R{sub e} geometric parameters of HN{sub 3} are determined with exceptionally high accuracy, as a consequence of the large number of isotopologues measured experimentally and the sophisticated (coupled-cluster theoretical treatment (CCSD(T))/ANO2) of the vibration-rotation interactions. The R{sub e} structure exhibits remarkable agreement with the CCSD(T)/cc-pCV5Z predicted structure, validating both the accuracy of the ab initio method and the claimed uncertainties of the theoretical/experimental structure determination.

  20. Precise equilibrium structure determination of hydrazoic acid (HN3) by millimeter-wave spectroscopy

    International Nuclear Information System (INIS)

    The millimeter-wave spectrum of hydrazoic acid (HN3) was analyzed in the frequency region of 235-450 GHz. Transitions from a total of 14 isotopologues were observed and fit using the A-reduced or S-reduced Hamiltonian. Coupled-cluster calculations were performed to obtain a theoretical geometry, as well as rotation-vibration interaction corrections. These calculated vibration-rotation correction terms were applied to the experimental rotational constants to obtain mixed theoretical/experimental equilibrium rotational constants (Ae, Be, and Ce). These equilibrium rotational constants were then used to obtain an equilibrium (Re) structure using a least-squares fitting routine. The Re structural parameters are consistent with a previously published Rs structure, largely falling within the uncertainty limits of that Rs structure. The present Re geometric parameters of HN3 are determined with exceptionally high accuracy, as a consequence of the large number of isotopologues measured experimentally and the sophisticated (coupled-cluster theoretical treatment (CCSD(T))/ANO2) of the vibration-rotation interactions. The Re structure exhibits remarkable agreement with the CCSD(T)/cc-pCV5Z predicted structure, validating both the accuracy of the ab initio method and the claimed uncertainties of the theoretical/experimental structure determination

  1. Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials

    Directory of Open Access Journals (Sweden)

    Levin, Igor

    2008-11-01

    Full Text Available The functional responses (e. g., dielectric, magnetic, catalytic, etc. of many industrially-relevant materials are controlled by their local structure-a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale-the so-called "nanostructure problem"-at the center of modern materials development. Today, multiple experimental techniques exist for probing local atomic arrangements; nonetheless, finding accurate comprehensive, and robust structural solutions for the nanostructured materials still remains a formidable challenge because any one of these methods yields only a partial view of the local structure. The primary goal of this 2-day NIST-sponsored workshop was to bring together experts in the key experimental and theoretical areas relevant to local-structure determination to devise a strategy for the collaborative effort required to develop a comprehensive measurement solution on the local scale. The participants unanimously agreed that solving the nanostructure problem-an ultimate frontier in materials characterization-necessitates a coordinated interdisciplinary effort that transcends the existing capabilities of any single institution, including national laboratories, centers, and user facilities. The discussions converged on an institute dedicated to local structure determination as the most viable organizational platform for successfully addressing the nanostructure problem. The proposed "institute" would provide an intellectual infrastructure for local structure determination by (1 developing and maintaining relevant computer software integrated in an open-source global optimization framework (Fig. 2, (2 connecting industrial and academic users with experts in measurement techniques, (3

  2. Biomolecular motors

    Directory of Open Access Journals (Sweden)

    Henry Hess

    2005-12-01

    Here, we give a brief introduction to molecular motors, with an emphasis on motor proteins, describe the challenges in interfacing these bionanomachines with an artificial environment, and provide examples of emerging applications.

  3. Spectroscopic structure and mass determination of plasma cluster accelerated by a coaxial gun

    International Nuclear Information System (INIS)

    The structure of air cluster by spectral line intensities is determined using an unstationary collisional-radiative model. The ratio of filling gas and admixtures is stated. The dependence of cluster mass on the time delay of discharge after admitting of filling gas is calculated at known electron density and cluster volume. (author)

  4. Crystal structure determination from powder diffraction data of the coumarin vanillin chalcone

    Czech Academy of Sciences Publication Activity Database

    Ghouili, A.; Rohlíček, Jan; Ayed, T.B.; Hassen, R.B.

    2014-01-01

    Roč. 29, č. 4 (2014), s. 361-365. ISSN 0885-7156 Grant ostatní: AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : chalcone * absorption spectra * powder diffraction * crystal structure determination * coumarin derivatives Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.636, year: 2014

  5. The determination of the in situ structure by nuclear spin contrast variation

    Energy Technology Data Exchange (ETDEWEB)

    Stuhrmann, H.B. [GKSS Forschungszentrum, Geesthacht (Germany); Nierhaus, K.H. [Max-Planch-Institut fuer Molekulare Genetik, Berlin (Germany)

    1994-12-31

    Polarized neutron scattering from polarized nuclear spins in hydrogenous substances opens a new way of contrast variation. The enhanced contrast due to proton spin polarization was used for the in situ structure determination of tRNA of the functional complex of the E.coli ribosome.

  6. BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

    International Nuclear Information System (INIS)

    We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. All PDB depositions of structures based on NMR data must now be accompanied by experimental restraints. A scheme has been devised that allows depositors to specify a representative structure and to define residues within that structure found experimentally to be largely unstructured. The BMRB now accepts coordinate sets representing three-dimensional structural models based on experimental NMR data of molecules of biological interest that fall outside the guidelines of the Protein Data Bank (i.e., the molecule is a peptide with 23 or fewer residues, a polynucleotide with 3 or fewer residues, a polysaccharide with 3 or fewer sugar residues, or a natural product), provided that the coordinates are accompanied by representation of the covalent structure of the molecule (atom connectivity), assigned NMR chemical shifts, and the structural restraints used in generating model. The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems

  7. Determinants of community structure of zooplankton in heavily polluted river ecosystems

    Science.gov (United States)

    Xiong, Wei; Li, Jie; Chen, Yiyong; Shan, Baoqing; Wang, Weimin; Zhan, Aibin

    2016-02-01

    River ecosystems are among the most affected habitats globally by human activities, such as the release of chemical pollutants. However, it remains largely unknown how and to what extent many communities such as zooplankton are affected by these environmental stressors in river ecosystems. Here, we aim to determine major factors responsible for shaping community structure of zooplankton in heavily polluted river ecosystems. Specially, we use rotifers in the Haihe River Basin (HRB) in North China as a case study to test the hypothesis that species sorting (i.e. species are “filtered” by environmental factors and occur at environmental suitable sites) plays a key role in determining community structure at the basin level. Based on an analysis of 94 sites across the plain region of HRB, we found evidence that both local and regional factors could affect rotifer community structure. Interestingly, further analyses indicated that local factors played a more important role in determining community structure. Thus, our results support the species sorting hypothesis in highly polluted rivers, suggesting that local environmental constraints, such as environmental pollution caused by human activities, can be stronger than dispersal limitation caused by regional factors to shape local community structure of zooplankton at the basin level.

  8. Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

    Science.gov (United States)

    Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

    2016-04-01

    The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

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

    Science.gov (United States)

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

    2013-12-15

    Genetically modified (GM) technique, one of the modern biomolecular engineering technologies, has been deemed as profitable strategy to fight against global starvation. Yet rapid and reliable analytical method is deficient to evaluate the quality and potential risk of such resulting GM products. We herein present a biomolecular analytical system constructed with distinct biochemical activities to expedite the computational detection of genetically modified organisms (GMOs). The computational mechanism provides an alternative to the complex procedures commonly involved in the screening of GMOs. Given that the bioanalytical system is capable of processing promoter, coding and species genes, affirmative interpretations succeed to identify specified GM event in terms of both electrochemical and optical fashions. The biomolecular computational assay exhibits detection capability of genetically modified DNA below sub-nanomolar level and is found interference-free by abundant coexistence of non-GM DNA. This bioanalytical system, furthermore, sophisticates in array fashion operating multiplex screening against variable GM events. Such a biomolecular computational assay and biosensor holds great promise for rapid, cost-effective, and high-fidelity screening of GMO. PMID:23893064

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

    Czech Academy of Sciences Publication Activity Database

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

    2012-01-01

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

  11. Determination and structural elucidation of triacylglycerols in krill oil by chromatographic techniques.

    Science.gov (United States)

    Araujo, Pedro; Zhu, Han; Breivik, Joar Fjørtoft; Hjelle, Jan Idar; Zeng, Yingxu

    2014-02-01

    The content of triacylglycerols (TAG) in krill oil is generally omitted from the labels of commercial supplements and unacknowledged in studies aimed at proving its health benefits. The present study demonstrates that TAG compounds, in addition to phospholipids and lysophospholipids, are an important lipid class in pure krill oil. The fatty acid composition of TAG molecules from krill oil and their distribution on the backbone of TAG structures were determined by gas chromatography and liquid chromatography tandem mass spectrometric, respectively. The content of omega 3 polyunsaturated fatty acids (n-3 PUFA) was similar to those reported in the literature for fish oil. It was estimated that 21 % of n-3 PUFA were at the sn-2 position of TAG structures. To our knowledge, this is the first determination and structural characterization of TAG in pure krill oil supplements. PMID:24190513

  12. Unbiased determination of the proton structure function F2p with faithful uncertainty estimation

    International Nuclear Information System (INIS)

    We construct a parametrization of the deep-inelastic structure function of the proton F2(x,Q2) based on all available experimental information from charged lepton deep-inelastic scattering experiments. The parametrization effectively provides a bias-free determination of the probability measure in the space of structure functions, which retains information on experimental errors and correlations. The result is obtained in the form of a Monte Carlo sample of neural networks trained on an ensemble of replicas of the experimental data. We discuss in detail the techniques required for the construction of bias-free parameterizations of large amounts of structure function data, in view of future applications to the determination of parton distributions based on the same method. (author)

  13. Global epidemiology of HIV among female sex workers: influence of structural determinants.

    Science.gov (United States)

    Shannon, Kate; Strathdee, Steffanie A; Goldenberg, Shira M; Duff, Putu; Mwangi, Peninah; Rusakova, Maia; Reza-Paul, Sushena; Lau, Joseph; Deering, Kathleen; Pickles, Michael R; Boily, Marie-Claude

    2015-01-01

    Female sex workers (FSWs) bear a disproportionately large burden of HIV infection worldwide. Despite decades of research and programme activity, the epidemiology of HIV and the role that structural determinants have in mitigating or potentiating HIV epidemics and access to care for FSWs is poorly understood. We reviewed available published data for HIV prevalence and incidence, condom use, and structural determinants among this group. Only 87 (43%) of 204 unique studies reviewed explicitly examined structural determinants of HIV. Most studies were from Asia, with few from areas with a heavy burden of HIV such as sub-Saharan Africa, Russia, and eastern Europe. To further explore the potential effect of structural determinants on the course of epidemics, we used a deterministic transmission model to simulate potential HIV infections averted through structural changes in regions with concentrated and generalised epidemics, and high HIV prevalence among FSWs. This modelling suggested that elimination of sexual violence alone could avert 17% of HIV infections in Kenya (95% uncertainty interval [UI] 1-31) and 20% in Canada (95% UI 3-39) through its immediate and sustained effect on non-condom use) among FSWs and their clients in the next decade. In Kenya, scaling up of access to antiretroviral therapy among FSWs and their clients to meet WHO eligibility of a CD4 cell count of less than 500 cells per μL could avert 34% (95% UI 25-42) of infections and even modest coverage of sex worker-led outreach could avert 20% (95% UI 8-36) of infections in the next decade. Decriminalisation of sex work would have the greatest effect on the course of HIV epidemics across all settings, averting 33-46% of HIV infections in the next decade. Multipronged structural and community-led interventions are crucial to increase access to prevention and treatment and to promote human rights for FSWs worldwide. PMID:25059947

  14. Use of the CSD program package for structure determination from powder data

    International Nuclear Information System (INIS)

    Although Rietveld's method of full profile structure refinement of powder data is a much-used tool today, ab initio structure solution from powder data is still not a routine task. One of the reasons for this is that fully overlapped peaks usually cannot be handled by routine structure determination programs. This shortcoming is not present in the Crystal Structure Determination (CSD) package which accepts intensities from powder diagrams as well as single crystal data. In order to demonstrate the possibilities of the CSD package, powder diagrams of five substances with already known crystal structure were collected and evaluated with the CSD package. The samples were scheelite (CaWO4), pentaerythritol (C(CH2OH)4), sodium sulfite (Na2SO3), copper sulfate pentahydrate (CuSO4.5H2O) and silver germanium phosphide (Ag6Ge10P12) and showed problems typical for powder work like preferred orientation and heavy peak overlapping. For four of the samples, correct atomic positions for some atoms could be found from the automatic MULTAN solution, which were then used in subsequent least squares- and difference Fourier calculations to locate the remaining atoms. Surprisingly, the cubic Ag6Ge10P12 posed the most problems for the structure solution although one third of the observed intensities was single-indexed and the final R-value was as low as 4%. (orig.)

  15. DETERMINANTS OF CAPITAL STRUCTURE OF INDIAN FIRMS: A STUDY OF BSE 500 COMPANIES

    Directory of Open Access Journals (Sweden)

    Prateek Bedi

    2015-05-01

    Full Text Available Optimizing a company’s capital structure is critical to its ability to achieve near-and long-term growth objectives. The optimal capital structure should ensure companies retain sufficient capital levels during both good times and bad. Most of the companies have p ro b l ems i n c r e a ti n g a n d maintaining a structure that will be viable through multiple business cycles. For such an important and multi-faceted decision, it is useful to study and ascertain the factors that determine this composition. The literature offers competing theories, and empirical studies show diverse results. Hence, the topic still remains an active area of research. To capture the empirical practices with regard to determinants of capital structure in India, an important emerging market, we run OLS regression of six financial variables identified as potential explanatory variables to arrive at the capital structure of 357 nonfinancial companies which are part of BSE 500 group. We find that five of our six independent variables i.e. profitability, size, tangibility, business risk and debt coverage ratio have statistically significant impact on capital structure for an Indian non-financial company.

  16. Effective Method for Determining Environmental Loads on Supporting Structures for Offshore Wind Turbines

    Directory of Open Access Journals (Sweden)

    Dymarski Paweł

    2016-01-01

    Full Text Available This paper presents a description of an effective method for determining loads due to waves and current acting on the supporting structures of the offshore wind turbines. This method is dedicated to the structures consisting of the cylindrical or conical elements as well as (truncates pyramids of polygon with a large number of sides (8 or more. The presented computational method is based on the Morison equation, which was originally developed only for cylindrically shaped structures. The new algorithm shown here uses the coefficients of inertia and drag forces that were calculated for non-cylindrical shapes. The analysed structure consists of segments which are truncated pyramids on the basis of a hex decagon. The inertia coefficients, CM, and drag coefficients, CD, were determined using RANSE-CFD calculations. The CFD simulations were performed for a specific range of variation of the period, and for a certain range of amplitudes of the velocity. In addition, the analysis of influence of the surface roughness on the inertia and drag coefficients was performed. In the next step, the computations of sea wave, current and wind load on supporting structure for the fifty-year storm were carried out. The simulations were performed in the time domain and as a result the function of forces distribution along the construction elements was obtained. The most unfavourable distribution of forces will be used, to analyse the strength of the structure, as the design load.

  17. Magnetic structure determination of amorphous materials using RMC modelling of neutron diffraction data

    International Nuclear Information System (INIS)

    Several difficulties arise when attempting to interpret diffraction data from amorphous magnetic materials. These are due to the increased complexity of the measured structure factors which contain magnetic and nuclear components. In order to determine the magnetic structure from these data it is necessary to isolate the magnetic contribution and use this to produce a satisfactory spin distribution model. This model also relies on information about the disordered nuclear structure. In principle therefore, one data set must yield sufficient information to describe both the disordered atomic and magnetic structure. To complicate things further it is usually not possible to directly transform a magnetic structure factor to a real space spin-spin correlation function in a manner analogous to the production of an atomic radial distribution function from an atomic structure factor. Reverse Monte Carlo (RMC) modelling has been established over the past few years as a method for deducing disordered atomic structures from diffraction data. This paper introduces its application to disordered magnetic systems. Using the family of amorphous magnetic alloys (Dy, Y)7Ni3 as an example, it is demonstrated that RMC can produce three-dimensional spin distributions from structure factor data with remarkably consistent magnetic characteristics. ((orig.))

  18. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes.

    Science.gov (United States)

    Goh, Boon Chong; Hadden, Jodi A; Bernardi, Rafael C; Singharoy, Abhishek; McGreevy, Ryan; Rudack, Till; Cassidy, C Keith; Schulten, Klaus

    2016-07-01

    The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed. PMID:27145875

  19. Determining the Velocity Fine Structure by a Laser Anemometer in VAD operation

    DEFF Research Database (Denmark)

    Kristensen, Leif; Kirkegaard, Peter; Mikkelsen, Torben

    The theoretical basis for determining the dissipation ε, by measuring the velocity structure function with a CW-laser anemometer has been derived in the case of calm wind conditions. If there is a well defined mean wind speed the structure function can be obtained by having the laser beam pointing....... Then it is necessary to “create” a mean wind by turning the laser beam. Since the instrument is not moved the beam will describe a cone which could be a VAD-scanning. In any case the measured velocity components will not be parallel and this implies that the measured structure function will contain a...... term which is proportional to the total variance. The theoretical expression for the line-filtered structure function is derived in two equivalent ways, one in physical space and one in wave-number space, of which the last can be reliably evaluated by numerical integration. Also a practical approximate...

  20. The Determination of Stress State of Structures Considering Sequence of Construction and Load Application

    Directory of Open Access Journals (Sweden)

    Kuroedov Vladimir

    2016-01-01

    Full Text Available For more accurate calculation of structure it is required to apply loads in the process of its construction instead of load application after structure has taken its final form. This action is necessary in order to observe changes in the stress-strain state of the structure under study. This circumstance is important for the massive hydraulic structures, such as hydroelectric dams. It is required to determine tensions, deformations and displacements in solving the building-up tasks. It is necessary to consider the problem for constructions of linear and nonlinear materials and check the principle of superposition on which the method of solving nonlinear problems is based. Also it is necessary to consider the solution of finite element schemes with the help of various iterative methods, such as the method of additional loads and the method of variable.

  1. An Analysis of the Determinants of Voluntary Structural Capital Disclosure by Listed French Companies

    Directory of Open Access Journals (Sweden)

    Inès Kateb

    2012-05-01

    Full Text Available This paper analyzes the characteristics of voluntary structural capital disclosure and points out the factorsexplaining the disclosure of such information, based on a sample of French companies belonging to the SBF 120and observed in 2006.Using manual content analysis, the study shows that firms provide more information on innovation capital withemphasizing on the narrative and descriptive forms. The results confirm that ownership structure, size, debts andthe weight of activated goodwill are the determinants of voluntary structural capital disclosure. Howevervariables apprehending the legitimacy’s level of the firm and the interest in its stakeholders’ pressure seem to benot significant in explaining the level of this disclosure.Accordingly, the structural capital communication strategy does not meet the needs of legitimization that fit intoa vision of corporate citizenship, but in order to mitigate some agency costs and solve the inadequacy offinancial reporting.

  2. Structure determination of the membrane protein-pigment complexes by nuclear magnetic resonance and neutron scattering

    International Nuclear Information System (INIS)

    NMR and neutron scattering were used for the study of three-dimensional structure in a liquid state of a membrane protein-pigment complex (LH1) required for light collection in photosynthesis living things. Three-dimensional structures of α and β polypeptide were determined with a specimen homogeneously labeled with 15N and 13C by multi-dimensional NMR. Here, α and β polypeptides constituted a B820 complex which was the structural unit of LH1. A stable helix structure passing between membranes was evidenced in both polypeptides. Neutron small angle scattering revealed that the B820 complex was composed of one each α and β peptide, and two molecules of pigment Bchl a, and had a gyration radius of about 11A. It is proved that pigment molecules were an essential element for the formation of the stable B820 complex. (Y. Kazumata)

  3. Experimental and theoretical aspects of ab initio structure determination using powder diffraction techniques

    International Nuclear Information System (INIS)

    Neutron powder diffraction has, over the past two decades, developed into a powerful technique for the refinement of moderately complex crystal structures. The advent of a new generation of ultra-high resolution X-ray and neutron powder diffractometers, however, not only permits the refinement of more complex materials but also opens up new areas of research. Perhaps the most exciting development in powder diffraction techniques associated with high resolution is the ab initio determination of crystal structures. This has until recently been possible, in a routine way, only by single crystal studies. The compression of three dimensions of diffraction data to the one dimension of a powder diffraction pattern leads to an unavoidable loss of information. For many, but not all, crystal symmetries high resolution minimises this loss thus allowing the intensities of a sufficient number of resolved Bragg reflections from moderately complex materials to be extracted for use in structure solution by direct methods of phase determination and by Patterson methods. Recent structure determination using the high resolution powder diffractometer, HRPD, at ISIS will be presented. The inherent limitations resulting from crystal and instrumental resolution are discussed along with maximum entropy techniques that seek to optimise the information content of a powder diffraction pattern. (author) 36 refs., 1 fig., 3 tabs

  4. Structure of drug-target proteins determined by both X-ray and neutron diffraction

    International Nuclear Information System (INIS)

    Crystallography enables us to obtain accurate atomic positions within proteins. High resolution X-ray crystallography provides information for most of the atoms comprising a protein, with the exception of hydrogens. Neutron diffraction data can provide information of the location of hydrogen atoms to the structural information determined by X-ray crystallography. Here, we show the recent of the structural determination of drug-target proteins, porcine pancreatic elastase (PPE) and human immuno-deficiency virus type-1 protease (HIV-PR) by both X-ray and neutron diffraction. The structure of porcine pancreatic elastase with its potent inhibitor (FR13080) was determined to 0.94A resolution by X-ray diffraction and 1.75 A resolution by neutron diffraction. It was found that there are two characteristic hydrogen bonding interactions in which hydrogen atoms were confirmed. One is located between a catalytic aspartate and histidine, another is involved in the inhibitor recognition site. The structure of HIV-PR with its potent inhibitor (KNI-272) was also determined to 0.93 A resolution by X-ray diffraction and 2.3 A resolution by neutron diffraction. The ionization state of the catalytic residues were clarified to show that Asp125 is protonated and Asp25 is deprotonated. The ionization state and the location of hydrogen atoms of the catalytic residue in HIV-PR were firstly determined by neutron diffraction. Furthermore, collaborative use of both X-ray and neutron to identify the location of ambiguous hydrogen atoms will be shown. (author)

  5. From X - rays to Biomolecular Structure: D. Hodgkin, R. Franklin and A. Yonath [Dos Raios - X à Estrutura Biomolecular: D. Hodgkin, R. Franklin e A. Yonath

    Directory of Open Access Journals (Sweden)

    Raquel Gonçalves - Maia

    2012-10-01

    Full Text Available Following the discovery of X-rays by Wilhelm Röntgen and Max von Laue’s discovery of X-ray diffraction by crystals, William and Lawrence Bragg made it possible to calculate the positions of the atoms within a crystal from the way in which an X-ray beam is diffracted by a crystal lattice. Since then, several researchers have applied this powerful technique in the study of many molecules of life, such as proteins, vitamins and hormones. In this interdisciplinary field, two women played a very important role, viz. Dorothy Hodgkin (Nobel Prize, 1964 and Rosalind Franklin. Nowadays, Ada Yonath (Nobel Prize, 2009 follows a similar line of research. We will emphasize the extraordinary work of these scientists.

  6. Biomolecular Electrostatics Simulation by an FMM-based BEM on 512 GPUs

    CERN Document Server

    Yokota, Rio; Bardhan, Jaydeep P; Knepley, Matthew G; Barba, L A

    2010-01-01

    We present simulations of biomolecular electrostatics at a scale not reached before, thanks to both algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a boundary element method (BEM) formulation of the continuum electrostatic model. The hardware acceleration is achieved through graphics processors, GPUs. We demonstrate the power of our algorithms and software for the calculation of the electrostatic interactions between biological molecules in solution. Computational experiments are presented simulating the electrostatics of protein--drug binding and several multi-million atom systems consisting of hundreds to thousands of copies of the problems, which models over 20 million atoms and has more than six billion unknowns, one iteration step requires only a few minutes on 512 GPU nodes. We achieved a sustained performance of 34.6TFlops for the entire BEM calculation. We are currently adapting our solver to model the linearized ...

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    In the present study, the conformational changes of bovine submaxillary mucin (BSM) adsorbed on a hydrophobic surface (polystyrene (PS)) as a function of concentration in bulk solution (up to 2mg/mL) have been investigated with biomolecular probe-based approaches, including bicinchoninic acid (BCA...... solution. Adsorbed masses of BSM onto hydrophobic surface, as probe by BCA, showed a continuously increasing trend up to 2mg/mL. But, the signals from EIA and ELLA, which probe the concentration of available unglycosylatedC-terminals and the central glycosylated regions, respectively, showed complicated......),enzyme-linkedimmunosorbentassay(EIA),andenzyme linkedlectinassay(ELLA).Theconformationand hydrodynamic diameter of highly purified BSM molecules, as characterized by circular dichroism (CD) spectroscopy and dynamic light scattering (DLS), respectively, showed a slight, yet gradual coiling and compaction in response to the increase in BSM concentration in bulk...

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

    Science.gov (United States)

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

    2015-06-01

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

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

    Science.gov (United States)

    Sundaram, K; Prasad, C V

    1982-02-01

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

  10. ACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale

    CERN Document Server

    Harvey, M J; De Fabritiis, G

    2009-01-01

    The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation program designed specifically for GPUs which is able to achieve supercomputing scale performance of 40 nanoseconds/day for all-atom protein systems with over 23,000 atoms. We illustrate the characteristics of the code, its validation and performance. We also run a microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. This performance on cost effective hardware allows ACEMD to reach microsecond timescales routinely with important implications in terms of scientific applications.

  11. Biomolecular self-defense and futility of high-specificity therapeutic targeting.

    Science.gov (United States)

    Rosenfeld, Simon

    2011-01-01

    Robustness has been long recognized to be a distinctive property of living entities. While a reasonably wide consensus has been achieved regarding the conceptual meaning of robustness, the biomolecular mechanisms underlying this systemic property are still open to many unresolved questions. The goal of this paper is to provide an overview of existing approaches to characterization of robustness in mathematically sound terms. The concept of robustness is discussed in various contexts including network vulnerability, nonlinear dynamic stability, and self-organization. The second goal is to discuss the implications of biological robustness for individual-target therapeutics and possible strategies for outsmarting drug resistance arising from it. Special attention is paid to the concept of swarm intelligence, a well studied mechanism of self-organization in natural, societal and artificial systems. It is hypothesized that swarm intelligence is the key to understanding the emergent property of chemoresistance. PMID:22272063

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

    CERN Document Server

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

    2010-01-01

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

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

    CERN Document Server

    Bai, F; Bai, Fan; Wang, Wenqing

    2002-01-01

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

  14. Computational Approaches for determination of Most Probable RNA Secondary Structure Using Different Thermodynamics Parameters

    Directory of Open Access Journals (Sweden)

    Binod Kumar,

    2010-03-01

    Full Text Available Many bioinformatics studies require the analysis of RNA structures. More specifically, extensive work is done to elaborate efficient algorithms able to predict the 2-D folding structures of RNA. The core of RNA structure is a dynamic programming algorithm to predict RNA secondary structures from sequence based on the principle of minimizing free energy. In this paper the thermodynamic data have been used for RNA predictions. In this paper the free energy inimization and the partition function code has been used to predictinternal loops of any size in O (N3 time. The free energy table for multibranch loops has been used by Dynalign. Base pair probabilities have been determined by the partition function calculation. Parameters controlling the prediction of suboptimal structures are Max % Energy Difference and Max Number of Structures. The foldmodule provides the basic implementation of RNA secondary structure prediction. A Dynalign dot plot, a separate dot plot is generated foreach of the two sequences involved. OligoScreen calculates the unimolecular and bimolecular folding free energies for a set of RNA oligonucleotides.

  15. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Yuanpeng Janet, E-mail: yphuang@cabm.rutgers.edu; Mao, Binchen; Xu, Fei; Montelione, Gaetano T., E-mail: gtm@rutgers.edu [Rutgers, The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium (United States)

    2015-08-15

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD–NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases {sup 15}N–{sup 1}H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD–NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta.

  16. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score

    International Nuclear Information System (INIS)

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD–NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases 15N–1H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD–NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta

  17. Method of magnetic susceptibility mapping of drilled cores. Experimental measurements for geologic structures determination

    International Nuclear Information System (INIS)

    The evaluation of the safety of a deep geologic repository for dangerous materials requires the knowledge of the interstitial system of the surrounding host rock. A method is proposed for the determination of geologic structures (in particular fractures) from the magnetic susceptibility mapping of drilled cores. The feasibility of the method has been demonstrated using a SQUID magneto-gradient meter. A measurement tool using a new magnetic susceptibility captor and a testing bench have been developed. This tool allows the measurement of rocks with a magnetic susceptibility greater than 10-5 SI units and can generate magnetic susceptibility maps with 4 x 4 mm2 pixels. A magnetic visibility criterion has been defined which allows to foresee if a structure is visible or not. According to the measurements done, it is shown that any centimeter-scale structure with a sufficient magnetic contrast (20%) with respect to the matrix is visible. Therefore, the dip and the orientation of such structure can be determined with a 3 degree and a 5 degree precision, respectively. The position of the structure along the core axis is known with a 4 mm precision. On the other hand, about half of the magnetic contrasts observed do not correspond to the visual analyses and can be explained by very small variations of the mineralogic composition. This last point offers some interesting ways for future research using magnetic susceptibility mapping. (J.S.). 31 refs., 90 figs., 18 tabs., 2 photos., 6 appends

  18. The structure determination of Al20Cu2Mn3 by near atomic resolution chemical mapping

    International Nuclear Information System (INIS)

    Highlights: • The structure of Al20Cu2Mn3 with a space group of Bbmm is completely determined. • The actual formula of Al20Cu2Mn3 is Al31Cu3Mn5. • Al20Cu2Mn3 is formed by a parallel tessellation of hexagon subunits. • Al20Cu2Mn3 is prone to twinning by an alternate tessellation of hexagon subunits. • The Al20Cu2Mn3 is coherent with α-Al along its longitudinal axis. - Abstract: Al20Cu2Mn3 phase is one kind of common dispersoids in aluminum alloys; however, the atomic arrangement of Al20Cu2Mn3 has not yet been clearly identified. Combining the atomic resolution high angle annular dark field and chemical composition quantitative results, three structure models of Al20Cu2Mn3 were derived basing on the isostructural Mn11Ni4Al60. The formation enthalpies and total energy were calculated using the first-principles approach. The structure of the Al20Cu2Mn3 phase with the minimal energy was identified, giving a fully relaxed structure with lattice parameters of a = 23.98 Å, b = 12.54 Å, c = 7.66 Å, which belongs to a space group of Bbmm. The determined structure is in excellent agreement with the near atomic resolution chemical mapping results

  19. Computational tools for experimental determination and theoretical prediction of protein structure

    Energy Technology Data Exchange (ETDEWEB)

    O`Donoghue, S.; Rost, B.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. The authors intend to review the state of the art in the experimental determination of protein 3D structure (focus on nuclear magnetic resonance), and in the theoretical prediction of protein function and of protein structure in 1D, 2D and 3D from sequence. All the atomic resolution structures determined so far have been derived from either X-ray crystallography (the majority so far) or Nuclear Magnetic Resonance (NMR) Spectroscopy (becoming increasingly more important). The authors briefly describe the physical methods behind both of these techniques; the major computational methods involved will be covered in some detail. They highlight parallels and differences between the methods, and also the current limitations. Special emphasis will be given to techniques which have application to ab initio structure prediction. Large scale sequencing techniques increase the gap between the number of known proteins sequences and that of known protein structures. They describe the scope and principles of methods that contribute successfully to closing that gap. Emphasis will be given on the specification of adequate testing procedures to validate such methods.

  20. S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Riley, Kevin Eugene; Hobza, Pavel

    2011-01-01

    Roč. 7, č. 8 (2011), s. 2427-2438. ISSN 1549-9618 R&D Projects: GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : noncovalent interactions * benchmarking * CCSD(T) Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.215, year: 2011

  1. Polarized Raman spectroscopy unravels the biomolecular structural changes in cervical cancer

    Science.gov (United States)

    Daniel, Amuthachelvi; Prakasarao, Aruna; Dornadula, Koteeswaran; Ganesan, Singaravelu

    2016-01-01

    Polarized Raman spectroscopy has emerged as a promising technique giving a wealth of information about the orientation and symmetry of bond vibrations in addition to the general chemical information from the conventional Raman spectroscopy. In this regard, polarized Raman Spectroscopic technique was employed to study the changes in the orientation of biomolecules in normal and cancerous conditions. This technique was compared to the conventional Raman spectroscopic technique and was found to yield additional information about the orientation of tyrosine, collagen and DNA. The statistically analyzed depolarization ratios by Linear Discriminant Analysis yielded better accuracy than the statistical results of conventional Raman spectroscopy. Thus, this study reveals that polarized Raman spectroscopy has better diagnostic potential than the conventional Raman spectroscopic technique.

  2. A Dynamic Analysis of Capital Structure Determinants. Empirical Results for Romanian Capital Market

    Directory of Open Access Journals (Sweden)

    Mihaela Dragota

    2008-04-01

    Full Text Available The analysis of capital structure and its determinants represents an useful approach for the Romanian and foreign investors and for the companies, at the same time. The main conclusion for capital structure analysis was that Romanian listed companies sustained their assets, in this order, on equity, commercial debt and, finally, on financial debt. The four variables used in the regression model are significant. The pecking order theory seemed to be more appropriate for the Romanian capital market, but the signalling theory was not entirely rejected.

  3. Structure Determination of the Nuclear Pore Complex with Three-Dimensional Cryo electron Microscopy.

    Science.gov (United States)

    von Appen, Alexander; Beck, Martin

    2016-05-22

    Determining the structure of the nuclear pore complex (NPC) imposes an enormous challenge due to its size, intricate composition and membrane-embedded nature. In vertebrates, about 1000 protein building blocks assemble into a 110-MDa complex that fuses the inner and outer membranes of a cell's nucleus. Here, we review the recent progress in understanding the in situ architecture of the NPC with a specific focus on approaches using three-dimensional cryo electron microscopy. We discuss technological benefits and limitations and give an outlook toward obtaining a high-resolution structure of the NPC. PMID:26791760

  4. Determination of height of transfer unit at hydrogen isotopic distillation on B7 type structured packing

    International Nuclear Information System (INIS)

    Due to the low pressure drop which that the structured packing introduces it is often used in the case of distillations under vacuum and of the mixture separation when the desired component is present in very low concentration, for example the water, hydrogen and oxygen isotopic distillation. The paper presents a model for the determination of height of transfer unit at hydrogen isotopic distillation plant with structured B7 type packing. The values of HTU calculated with the analogy model between the heat, momentum and mass transfer are compared with the experimental data. (authors)

  5. Height of transfer unit determination at hydrogen isotopic distillation on structured packing, B7 type

    International Nuclear Information System (INIS)

    Due to the low pressure drop that it introduces, the structured packing is often used in the case of distillations under vacuum and of the mixture separation when the desired component is founded in very low concentration, for example the water, hydrogen and oxygen isotopic distillation. The paper presents a model for the determination of height of transfer unit at hydrogen isotopic distillation plant with structured B7 type packing. The values of the height of a transfer unit (HTU) calculated with the analogy model between the heat, momentum and mass transfer are compared with the experimental data

  6. Height of transfer unit determination at hydrogen isotopic distillation on B7 type structured packing

    International Nuclear Information System (INIS)

    Due to the low pressure drop that it introduces, the structured packing is often used in the case of distillation under vacuum and of the mixture separation when the desired component is found in very low concentration, for example the water, hydrogen and oxygen isotopic distillation. The paper presents a model for the determination of height of transfer unit at hydrogen isotopic distillation plant with structured B7 type packing. The values of HTU calculated with the analogy model between the heat, momentum and mass transfer are compared with the experimental data. (authors)

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

    Directory of Open Access Journals (Sweden)

    Zulkifli H Shamsuddin

    2013-08-01

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

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

    KAUST Repository

    Sobhy, M. A.

    2011-11-07

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

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

    Science.gov (United States)

    Wang, Ling; Stumm, Boris; Helms, Volkhard

    2010-03-01

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

  10. Determination of αS from scaling violations of truncated moments of structure functions

    International Nuclear Information System (INIS)

    We determine the strong coupling αS(MZ) from scaling violations of truncated moments of the nonsinglet deep inelastic structure function F2. Truncated moments are determined from BCDMS and NMC data using a neural network parametrization which retains the full experimental information on errors and correlations. Our method minimizes all sources of theoretical uncertainty and bias which characterize extractions of αS from scaling violations. We obtain αS(MZ)=0.124+0.004-0.007 (exp.) +0.003-0.004 (th.)

  11. Determinants of Capital Structure: An Analysis on the Largest 1000 Industrial Firms in Turkey

    OpenAIRE

    H. Aydin OKUYAN; H. Mehmet Tasci

    2010-01-01

    This study aims to explain the determinants of capital structure and find out if static trade off or pecking order is more successful in explaining the debt behaviour of industrial firms in Turkey. For this purpose, the data set of largest 500 and following largest 500 industrial firms determined by ‹stanbul Chamber of Industry have been used. The data set on these firms covers the period of 1993 and 2007. Our findings show that, even though firms that use debt to create more added value, pre...

  12. Advancement and testing of analysis techniques for the determination of the structural dynamic behavior of containment structures. Final report

    International Nuclear Information System (INIS)

    Within the framework of project RS1197, analysis methods have been further developed and tested for the determination of the structural dynamic loading and the maximum load-bearing capacity of containment structures with a focus on the quantification of safety margins against failures due to loads resulting from selected internal and external hazards. The analyses comprised a model containment structure of prestressed reinforced concrete under internal pressure loading until reaching failure pressure, an outer containment structure made of reinforced concrete under local impact loads that may occur during a targeted aircraft crash, and a steel containment under local peak loads from internal pressure and temperature loads due to core melt scenarios with a local hydrogen combustion. GRS participated in the international ''Standard Problem Exercise 3'' on the issue ''Performance of Containment Vessel under Severe Accident Conditions''. Together with the cooperation partners, aspects of the global containment behaviour were considered based on the example of the Sandia 1:4 model containment of prestressed concrete, which was loaded by rising internal pressure until failure. Complex analysis models were developed, calculating the behaviour of the prestressing tendons under consideration of the frictional contact with the cladding tubes. Compared with corresponding measurement values, the analysis results show that the stresses near the tensioning device and the deformation of the inner surface can be realistically modelled as a function of the internal pressure. In the experiment, global structural failure of the containment model was caused by tendon rupture at about 3.64 times the design pressure. With the developed analysis models of a generic structure of an outer reinforced concrete containment, simulations were carried out for various aircraft crash scenarios as contact problems with explicit impactor simulation. For this

  13. An inverse method to determine the dispersion curves of periodic structures based on wave superposition

    Science.gov (United States)

    Junyi, L.; Balint, D. S.

    2015-08-01

    Phononic crystals and acoustic metamaterials have unique properties, such as the existence of band gaps, which give them huge potential in many applications, such as vibration isolation, acoustic cloaking, acoustic lensing, and more. Many methods have been proposed to determine the band structure of these materials but almost all require a model of the structure. In this paper, an inverse method to calculate the band structure of one dimensional periodic structures based on Bloch wave boundary conditions and wave superposition is introduced. The proposed method only requires the frequency responses measured at a small number of points within the structure. This allows the band structures to be determined experimentally using simple equipment, like a shaker and accelerometers. The band structure of a simple bi-material beam was calculated in this study as a demonstration of the method, and the results were found to be in agreement with calculations made using the transfer matrix method. The proposed method was then extended to predict the response of a finite periodic bi-material beam with arbitrary boundary conditions using only the band structure and components of the eigenvectors; some resonance peaks were observed within the band gaps and these were found to be caused by the reflection of the waves at the boundaries. The effects of the number of unit cells on the transmissibility of a beam were investigated. It was found that the transmissibilities within the band gaps can be estimated to be directly proportional to the number of unit cells. Lastly, an attempt was made to extend the method to two and three dimensional periodic structures and the wave superposition method was found to be able to measure a portion of the dispersion surface of two dimensional structures with a fair degree of accuracy, especially at lower bands. Errors and scatter are present at high frequencies caused by more waves significantly affecting the responses of the system. This issue can

  14. Towards the Structure Determination of a Modulated Protein Crystal: The Semicrystalline State of Profilin:Actin

    Science.gov (United States)

    Borgstahl, G.; Lovelace, J.; Snell, E. H.; Bellamy, H.

    2003-01-01

    One of the remaining challenges to structural biology is the solution of modulated structures. While small molecule crystallographers have championed this type of structure, to date, no modulated macromolecular structures have been determined. Modulation of the molecular structures within the crystal can produce satellite reflections or a superlattice of reflections in reciprocal space. We have developed the data collection methods and strategies that are needed to collect and analyze these data. If the macromolecule's crystal lattice is composed of physiologically relevant packing contacts, structural changes induced under physiological conditions can cause distortion relevant to the function and biophysical processes of the molecule making up the crystal. By careful measurement of the distortion, and the corresponding three-dimensional structure of the distorted molecule, we will visualize the motion and mechanism of the biological macromolecule(s). We have measured the modulated diffraction pattern produced by the semicrystalline state of profilin:actin crystals using highly parallel and highly monochromatic synchrotron radiation coupled with fine phi slicing (0.001-0.010 degrees) for structure determination. These crystals present these crystals present a unique opportunity to address an important question in structural biology. The modulation is believed to be due to the formation of actin helical filaments from the actin beta ribbon upon the pH-induced dissociation of profilin. To date, the filamentous state of actin has resisted crystallization and no detailed structures are available. The semicrystalline state profilin:actin crystals provides a unique opportunity to understand the many conformational states of actin. This knowledge is essential for understanding the dynamics underlying shape changes and motility of eukaryotic cells. Many essential processes, such as cytokinesis, phagocytosis, and cellular migration depend upon the capacity of the actin

  15. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

    KAUST Repository

    Li, Jianping

    2013-06-05

    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

  16. Determination of structural disorder in superionic Ag2Te by neutron total scattering

    International Nuclear Information System (INIS)

    The structural disorder in the two high-temperature, superionic phases of Ag2Te has been fully characterized using neutron powder diffraction and two complementary analyses. Rietveld profile refinement of Bragg scattering has been used to determine the most probable average structures and radial distribution functions, determined by Fourier transformation of the total scattering structure factors, have been used to refine local structural models based on these average structures. It is found that the α-phase, which exists between 420 K and 1075 K is best described by a face-centred cubic arrangement of the tellurium ions with the silver ions randomly occupying the tetrahedral and octahedral voids. There is no local ordering of the filled tetrahedral sites and the silver ions in octahedral sites have a broad distribution and preferentially sit off centre in one of the eight directions away from filled tetrahedra. The γ-phase, which exists between 1075 K and the melt, has a body-centred cubic structure similar to α-AgI, and the average structure is best described with silver ions distributed over tetrahedral and trigonal sites and positions which join these two sites. The radial distribution functions in both superionic phases clearly show that silver ions are never closer than ∼2.4 A to each other which means that nearest neighbour 12d tetrahedral sites cannot be simultaneously filled in γ-Ag2Te. The differences in quality of fit to the experimental data between different silver ion ordering schemes are slight and it is proposed that single crystal diffuse scattering may be the only way to distinguish clearly between different models. (author)

  17. Crystallization and X-ray structure determination of a thermoalkalophilic lipase from Geobacillus SBS-4S

    International Nuclear Information System (INIS)

    Crystallization and the structure determination at 1.6 Å resolution of LIPSBS, a thermoalkalophilic lipase from Geobacillus strain SBS-4S, are described. The crystals belonged to orthorhombic space group P212121. A thermoalkalophilic lipase (LIPSBS) from the newly isolated Geobacillus strain SBS-4S which hydrolyzes a wide range of fatty acids has been characterized. In the present study, the crystallization of purified LIPSBS using the sitting-drop vapour-diffusion method and its X-ray diffraction studies are described. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 55.13, b = 71.75, c = 126.26 Å. The structure was determined at 1.6 Å resolution by the molecular-replacement method using the lipase from G. stearothermophilus L1 as a model

  18. Neutron diffraction stress determination in W-laminates for structural divertor applications

    Directory of Open Access Journals (Sweden)

    R. Coppola

    2015-07-01

    Full Text Available Neutron diffraction measurements have been carried out to develop a non-destructive experimental tool for characterizing the crystallographic structure and the internal stress field in W foil laminates for structural divertor applications in future fusion reactors. The model sample selected for this study had been prepared by brazing, at 1085 °C, 13 W foils with 12 Cu foils. A complete strain distribution measurement through the brazed multilayered specimen and determination of the corresponding stresses has been obtained, assuming zero stress in the through-thickness direction. The average stress determined from the technique across the specimen (over both ‘phases’ of W and Cu is close to zero at −17 ± 32 MPa, in accordance with the expectations.

  19. Separation of a Slater determinant wave function with a neck structure into spatially localized subsystems

    OpenAIRE

    Taniguchi, Yasutaka; Kanada-En'yo, Yoshiko

    2011-01-01

    A method to separate a Slater determinant wave function with a two-center neck structure into spatially localized subsystems is proposed, and its potential applications are presented. An orthonormal set of spatially localized single-particle wave functions is obtained by diagonalizing the coordinate operator for the major axis of a necked system. Using the localized single-particle wave functions, the wave function of each subsystem is defined. Therefore, defined subsystem wave functions are ...

  20. System analysis of the extrusion process to determine the objectives and structure of the control system

    OpenAIRE

    Ярощук, Людмила Дем’янівна; Жученко, Олексій Анатолійович

    2013-01-01

    The article is devoted to the system analysis of the extrusion of polymeric materials in order to determine the objectives and structure of a control system. The algorithm of the system analysis of technological objects of different complexity was suggested on the example of the extrusion process.The algorithm provides the definition of the tasks that are formulated for the production system as a whole: productivity and product quality, economic effectiveness, social and environmental tasks.A...

  1. THE INTERNATIONALISATION OF PRODUCTION BY ITALIAN INDUSTRIAL DISTRICTS' FIRMS. STRUCTURAL AND BEHAVIOURAL DETERMINANTS

    OpenAIRE

    Mariotti, Sergio; Mutinelli, Marco; Piscitello, Lucia

    2008-01-01

    International audience The paper argues that structural and behavioural determinants combine to influence internationalisation of production through FDI by industrial districts' firms. As far as the former, leadership effects, represented by the presence of large firms within the district, and Porterian effects, denoted by the intensity of domestic rivalry, positively influence the likelihood that district firms will start internationalise through FDI. Moreover, spillovers induced by the p...

  2. The Internationalization of Production by Italian Industrial Districts' Firms: Structural and Behavioural Determinants

    OpenAIRE

    Mariotti, Sergio; Mutinelli, Marco; Piscitello, Lucia

    2008-01-01

    Abstract The paper argues that structural and behavioural determinants combine to influence internationalisation of production through FDI by industrial districts? firms. As far as the former, leadership effects, represented by the presence of large firms within the district, and Porterian effects, denoted by the intensity of domestic rivalry, positively influence the likelihood that district firms will start internationalise through FDI. Moreover, spillovers induced by the presenc...

  3. Structural Determinants of the Total Loans Volume in the Czech Republic

    OpenAIRE

    Řepková, Iveta

    2010-01-01

    The aim of this paper is to analyze the structural determinants of the total loans volume in the Czech banking sector. Analysis of five selected characteristics is realized in period 2000-2008. It used the OLS regression analysis for estimate of model. The regression analysis showed that the concentration of the credit market and the profitability calculated as the return on assets (ROA) has positive impact to total loans and the quality of portfolio has negative impact to total loans. If the...

  4. High-resolution structure determination by continuous rotation data collection in MicroED

    OpenAIRE

    Nannenga, Brent L; Shi, Dan; Leslie, Andrew G W; Gonen, Tamir

    2014-01-01

    MicroED uses very small three-dimensional protein crystals and electron diffraction for structure determination. An improved data collection protocol for MicroED called “continuous rotation” is presented. Here microcrystals are continuously rotated during data collection yielding improved data, and allowing data processing with MOSFLM resulting in improved resolution for the model protein lysozyme. These improvements pave the way for the implementation and application of MicroED with wide app...

  5. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    Science.gov (United States)

    Craig, George D.; Glass, Robert; Rupp, Bernhard

    1997-01-01

    A method for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10.sup.6 V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved.

  6. Crystal structure determination of thymoquinone by high-resolution X-ray powder diffraction

    OpenAIRE

    Pagola, S.; Benavente, A; Raschi, A.; Romano, E; Molina, M. A. A.; Stephens, P.W.

    2004-01-01

    The crystal structure of 2-isopropyl-5-methyl-1,4-benzoquinone (thymoquinone) and its thermal behavior—as necessary physical and chemical properties—were determined in order to enhance the current understanding of thymoquinone chemical action by using high resolution x-ray powder diffraction, Fourier transform infrared spectroscopy (FTIR), and 3 thermo-analytical techniques thermogravimetric analysis (TGA), differential thermal analysis (DTA), and differential scanning calorimetry (DSC). The ...

  7. Structural insights into viral determinants of nematode mediated grapevine fanleaf virus transmission

    OpenAIRE

    Schellenberger, Pascale; Sauter, Claude; Lorber, Bernard; Bron, Patrick; Trapani, Stefano; Bergdoll, Marc; Marmonier, Aurelie; Schmitt-Keichinger, Corinne; Lemaire, Olivier; Demangeat, Gerard; Ritzenthaler, Christophe

    2011-01-01

    Many animal and plant viruses rely on vectors for their transmission from host to host. Grapevine fanleaf virus (GFLV), a picorna-like virus from plants, is transmitted specifically by the ectoparasitic nematode Xiphinema index. The icosahedral capsid of GFLV, which consists of 60 identical coat protein subunits (CP), carries the determinants of this specificity. Here, we provide novel insight into GFLV transmission by nematodes through a comparative structural and functional analysis of two ...

  8. Determinants of the Capital Structure of Small and Medium Sized Brazilian Enterprises

    OpenAIRE

    Denis Forte; Lucas Ayres Barros; Wilson Toshiro Nakamura

    2013-01-01

    This research investigates the determinants of the capital structure of small and medium enterprises (SMEs) using a unique database that includes over 19,000 Brazilian firms and spans 13 years of data. The econometric analysis employs the System Generalized Method of Moments estimator (GMM-Sys) and two strong results emerge: (a) profitability is negatively related to leverage, and (b) asset growth is positively related to leverage. Both results are consistent with the pecking order theory of ...

  9. Determinants of capital structure in UK and Chinese consumer service industry

    OpenAIRE

    Feng, Chun

    2013-01-01

    This paper aims to investigate the determinants of capital structure in Chinese and UK consumer service industry. This research use panel data to investigate 1618 observations of the Chinese companies and 835 observations of the UK companies in consumer service industry from 2003 to 2012. This test is run on total, long-term and short-term leverage as dependent variables. Profitability, size, growth opportunity, volatility, non-debt tax shields, collateral value of assets, uniqueness is deter...

  10. Determinants of Capital Structure: A case from Textile Industry of Pakistan

    OpenAIRE

    Aurangzeb; Anwar ul Haq

    2012-01-01

    This study examines the determinants of capital structure in Textile industry of Pakistan on a data for the period of 2004 to 2009. Multiple regression technique is used to analyze the relationship between dependent variable (Leverage) and independent variables (Firm Size, Tangibility of Assets, Profitability, and Sales Growth). It is concluded all independent variables have significant impact on the balance of leverage. It is concludes that firm size, tangibility of assets and profitability ...

  11. Calibration of a Computation Model for a Reinforced Concrete Structure Against the Experimentally Determined Dynamic Characteristics

    OpenAIRE

    Gavriloaia, Constantin; Budescu, Mihai; Ţăranu, Nicolae; Hohan, Raluca

    2013-01-01

    The dynamic characteristics of the structures range are depending on their mass and lateral stiffness. In the present paper a method for improving the computation model is proposed, thus creating a link between the dynamic characteristics obtained with the computation model based on the finite element method and the experimentally determined dynamic characteristics. The finite element model was obtained using the program ETABS and the experimental dynamic characteristics were obtained on a lo...

  12. A pipeline for structure determination of in vivo-grown crystals using in cellulo diffraction

    OpenAIRE

    Boudes, Marion; Garriga, Damià; Fryga, Andrew; Caradoc-Davies, Tom; Coulibaly, Fasséli

    2016-01-01

    While structure determination from micrometre-sized crystals used to represent a challenge, serial X-ray crystallography on microfocus beamlines at synchrotron and free-electron laser facilities greatly facilitates this process today for microcrystals and nanocrystals. In addition to typical microcrystals of purified recombinant protein, these advances have enabled the analysis of microcrystals produced inside living cells. Here, a pipeline where crystals are grown in insect cells, sorted by ...

  13. Three-dimensional structure determination of capsid of Aedes albopicus C6/36 cell densovirus

    Institute of Scientific and Technical Information of China (English)

    CHENG; Lingpeng; CHEN; Senxiong; Jenifer; M.Brannan; Joa

    2004-01-01

    The three-dimensional structure of capsid of Aedes albopictus C6/36 densovirus was determined to 14-(A) resolution by electron cryomicroscopy and computer reconstruction. The triangulation number of the capsid is 1. There are 12 holes in each triangular face and a spike on each 5-fold vertex. The validity of the capsid and nucleic acid densities in the reconstructions was discussed.

  14. Structure determination of cyclo pentane terpene derivatives by crossed NMR and MS techniques

    International Nuclear Information System (INIS)

    3 of the 4 stereoisomers of the 1-isopropenyl 2,3-dimethylcyclopentane, obtained from the cracking of 3,7-dimethylocta-1,6-diene, were purified and characterized. Dihedral angles, between the protons of the substituted carbons, have been determined by molecular modelling. Analysis of the NMR and mass spectra allowed us to access to the structure of the different isomers. (authors). 6 refs., 2 tabs

  15. NMR structural determination of unique invertebrate glycosaminoglycans endowed with medical properties.

    Science.gov (United States)

    Pomin, Vitor H

    2015-09-01

    Glycosaminoglycans (GAGs) are sulfated polysaccharides of complex structure endowed with numerous biomedical functions. Although ubiquitously distributed in vertebrates, GAGs can also occur in certain terrestrial or marine invertebrates. Solution nuclear magnetic resonance (NMR) spectroscopy has been the analytical technique mostly employed in structural characterization of GAGs from any source. This review aims at illustrating the application of NMR in structural determination of few representative invertebrate GAG examples of unique structures and endowed with therapeutic actions. They are the holothurian fucosylated chondroitin sulfate, the acharan sulfate isolated from the snail Achatina fulica, the dermatan sulfates with distinct sulfation patterns extracted from ascidian species, the sulfated glucuronic acid-containing heparan sulfate isolated from the gastropode Nodipecten nodosum, and the hybrid heparin/heparan sulfate molecule obtained from the shrimp Litopenaeus vannamei. These invertebrate GAGs exhibit distinct structures when compared to those extracted from mammalian GAGs. The distinct structures of the invertebrate GAGs lead also to different mechanisms of actions as compared to the mammalian GAG standards. Invertebrate GAGs comprise promising therapeutic candidates in fights against diseases. Solution NMR has been playing a pivotal role in this carbohydrate-based drug research, discovery and development. PMID:26083200

  16. SHELXT – Integrated space-group and crystal-structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Sheldrick, George M., E-mail: gsheldr@shelx.uni-ac.gwdg.de [Georg-August Universität Göttingen, Tammannstrasse 4, Göttingen, 37077 (Germany)

    2015-01-01

    SHELXT automates routine small-molecule structure determination starting from single-crystal reflection data, the Laue group and a reasonable guess as to which elements might be present. The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.

  17. Structure determination in 55-atom Li-Na and Na-K nanoalloys.

    Science.gov (United States)

    Aguado, Andrés; López, José M

    2010-09-01

    The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions. PMID:20831313

  18. Determining the Structure of Biomaterials Interfaces using Synchrotron-based X-ray Diffraction

    Energy Technology Data Exchange (ETDEWEB)

    McBride, M

    2002-01-24

    The purpose of this project is to explore the feasibility of using surface X-ray diffraction (SXRD) to determine the structure of biomineral surfaces in electrolyte solutions and of the adsorbed layer of acidic amino acids that are believed to play a central role in the control of biomineral formation and function. The work is a critical component in the development of an integrated picture of the physical and chemical basis for deposition and dissolution at solid-liquid interfaces in biological systems, and brings a new and very powerful surface-sensitive capability to LLNL. We have chosen as our model systems calcium carbonate and calcium phosphate in aspartic and glutamic acid-bearing solutions. The calcium compounds are ubiquitous among biomineral structures, both those that are beneficial such as bones and teeth, and those that are pathological such as kidney stones, while the two acidic amino acids--both as simple and poly-amino acids--are the dominant constituents of protein mixtures implicated in the control of biomineralization. The goals of the work are: (1) to determine the surface structure of pure calcium phosphate and calcium carbonate surfaces in aqueous solution using SXRD; (2) to determine how those surfaces are modified by the presence of aspartic and glutamic acid, both as the simple amino acids and as poly-aspartate and poly-glutamate and (3) to model the interactions of acidic amino acids with calcite.

  19. Feasibility of one-shot-per-crystal structure determination using Laue diffraction

    International Nuclear Information System (INIS)

    Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used

  20. Oscillation Laue Analysis (OLA) - A new crystal structure determination method for mineral physics

    Science.gov (United States)

    Dera, P.; Downs, R. T.; Liermann, H.; Yang, W.

    2006-12-01

    We present a new approach for collection and interpretation of polychromatic radiation diffraction images, called Oscillation Laue Analysis, which combines capabilities of single crystal X-ray diffraction and X-ray absorption spectroscopy. The method is based on smearing Laue reflections into variable-energy curves by slight oscillation of the crystal during the exposure. The OLA method allows for simple and precise peak energy determination and harmonic overlap deconvolution through measurement of X-ray attenuation coefficient of metal foils inserted into incident beam. The method provides an easy reliable way of determining unit cells of unknown single-crystal phases, yields multiple monochromatic structure factor sets covering wide range of energies, which can be used for Multiple Anomalous Dispersion (MAD) based structure solution or enhancement of contrast between neighboring elements in the periodic table, and allows the routine ab initio solution of unknown structures. The results of our first experiments, performed at sector 16 of the Advanced Photon Source Laboratory, and aimed at determination of the compression mechanism of escolite (Cr2O3) will be presented and discussed in the context of application of the new approach in micromineralogy, characterization of meteoritic samples, and high-pressure mineral physics.