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Sample records for structural refinement method

  1. Towards automated crystallographic structure refinement with phenix.refine

    Afonine, Pavel V., E-mail: pafonine@lbl.gov; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel; Headd, Jeffrey J.; Moriarty, Nigel W. [Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720 (United States); Mustyakimov, Marat; Terwilliger, Thomas C. [Los Alamos National Laboratory, M888, Los Alamos, NM 87545 (United States); Urzhumtsev, Alexandre [CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France); Université Henri Poincaré, Nancy 1, BP 239, 54506 Vandoeuvre-lès-Nancy (France); Zwart, Peter H. [Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720 (United States); University of California Berkeley, Berkeley, CA 94720 (United States)

    2012-04-01

    phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods. phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

  2. Using high-order methods on adaptively refined block-structured meshes - discretizations, interpolations, and filters.

    Ray, Jaideep; Lefantzi, Sophia; Najm, Habib N.; Kennedy, Christopher A.

    2006-01-01

    Block-structured adaptively refined meshes (SAMR) strive for efficient resolution of partial differential equations (PDEs) solved on large computational domains by clustering mesh points only where required by large gradients. Previous work has indicated that fourth-order convergence can be achieved on such meshes by using a suitable combination of high-order discretizations, interpolations, and filters and can deliver significant computational savings over conventional second-order methods at engineering error tolerances. In this paper, we explore the interactions between the errors introduced by discretizations, interpolations and filters. We develop general expressions for high-order discretizations, interpolations, and filters, in multiple dimensions, using a Fourier approach, facilitating the high-order SAMR implementation. We derive a formulation for the necessary interpolation order for given discretization and derivative orders. We also illustrate this order relationship empirically using one and two-dimensional model problems on refined meshes. We study the observed increase in accuracy with increasing interpolation order. We also examine the empirically observed order of convergence, as the effective resolution of the mesh is increased by successively adding levels of refinement, with different orders of discretization, interpolation, or filtering.

  3. Structural refinement of artificial superlattices by the X-ray diffraction method

    Ishibashi, Y; Tsurumi, T

    1999-01-01

    This paper reports a structural refinement of BaTiO sub 3 (BTO)/SrTiO sub 3 (STO) artificially superstructured thin films. The refinement was achieved by taking into account the effect of interdiffusion between BTO and STO. The samples were prepared by a molecular-beam epitaxy method on SrTiO sub 3 (001) substrate at 600 .deg. C. The phonon model was employed to simulate the X-ray diffraction (XRD) profiles. A discrepancy was observed in the intensities of the satellite peaks when the effect of the interdiffusion between BTO and STO was not incorporated in the simulation. In successive simulations, the concentration profile due to the interdiffusion was first calculated according to Fick's second law, and then the coefficients of the Fourier series describing the lattice distortion and the modulation of the structure factor were determined. The XRD profiles thus simulated almost completely agreed with those observed. This indicates that XRD analysis with the calculation process proposed in this study will ena...

  4. Crystal structure refinement with SHELXL

    Sheldrick, George M., E-mail: gsheldr@shelx.uni-ac.gwdg.de [Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstraße 4, Göttingen 37077 (Germany)

    2015-01-01

    New features added to the refinement program SHELXL since 2008 are described and explained. The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

  5. Structure of incommensurate ammonium tetrafluoroberyllate studied by structure refinements and the maximum entropy method

    Palatinus, Lukáš; Amami, M.; van Smaalen, S.

    2004-01-01

    Roč. 60, - (2004), s. 127-137 ISSN 0108-7681 Grant - others:DFG(DE) XX Institutional research plan: CEZ:AV0Z1010914 Keywords : incommensurate modulation * superspace * maximum entropy method Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 5.418, year: 2004

  6. Towards automated crystallographic structure refinement with phenix.refine

    Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel; Headd, Jeffrey J.; Moriarty, Nigel W.; Mustyakimov, Marat; Terwilliger, Thomas C.; Urzhumtsev, Alexandre; Zwart, Peter H.; Adams, Paul D.

    2012-01-01

    phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An i...

  7. Molecular Structure-Based Methods of Property Prediction in Application to Lipids: A Review and Refinement

    Cunico, Larissa; Hukkerikar, Amol; Ceriani, Roberta

    2013-01-01

    The paper is a review of the combined group contribution (GC)–atom connectivity index (CI) approachfor prediction of physical and thermodynamic properties of organic chemicals and their mixtures withspecial emphasis on lipids. The combined approach employs carefully selected datasets of different...... dependent, have been developed. For mixtures, properties related to phase equilibria aremodeled with GE-based models (UNIQUAC, UNIFAC, NRTL, and combined UNIFAC-CI method). The col-lected phase equilibrium data for VLE and SLE have been tested for thermodynamic consistency togetherwith a performance...... evaluation of the GE-models. The paper also reviews the role of the databases andthe mathematical and thermodynamic consistency of the measured/estimated data and the predictivenature of the developed models....

  8. A method for refining oil

    Bruskin, Yu.A.; Gorokhov, V.V.; Kotler, L.D.; Kovalenko, N.F.; Spasskiy, Yu.B.; Titov, A.M.; Vlasenko, V.Ye.; Vytnov, V.A.

    1983-01-01

    In the method for refining oil through its distillation with the isolation of directly distilled gases and a benzine fraction (BS) with the use of a benzine fraction pyrolysis, in order to increase the output of the lower olefines and to reduce the energy expenditures, the distillation is conducted with the isolation of 10 to 40 percent of the benzine fraction from its potential content along with the directly distilled gases. The obtained mixture of the remaining part of the benzine fraction is absorbed at a pressure of 1.5 to 6 atmospheres with the feeding of the obtained saturated absorbent to pyrolysis and subsequent mixing of the obtained pyrolysis gas with the unabsorbed product and their joint gas division. As compared to the known method, the proposed method makes it possible to reduce the energy expenditures which is achieved through a reduction in the volume of irrigation in the tower, and to increase the output of the olefines through processing of the steam and gas mixture of the benzine and the directly distilled gases.

  9. Refinement of the crystal structure of lead titanate with different degrees of imperfection of cationic and anionic sublattices by the Rietveld method

    Akimov, A.I.; Savchuk, G.K.; Rubtsov, V.A.; Letko, A.K.

    2003-01-01

    The parameters of the crystal structure of lead titanate with different degrees of imperfection of the anionic and cationic sublattices are refined by the Rietveld method. The experiments are carried out on a DRON-4 diffractometer (CuK α radiation; 20 deg. d 5.0-6.0%

  10. Protein Structure Refinement by Optimization

    Carlsen, Martin

    on whether the three-dimensional structure of a homologous sequence is known. Whether or not a protein model can be used for industrial purposes depends on the quality of the predicted structure. A model can be used to design a drug when the quality is high. The overall goal of this project is to assess...... that correlates maximally to a native-decoy distance. The main contribution of this thesis is methods developed for analyzing the performance of metrically trained knowledge-based potentials and for optimizing their performance while making them less dependent on the decoy set used to define them. We focus...... being at-least a local minimum of the potential. To address how far the current functional form of the potential is from an ideal potential we present two methods for finding the optimal metrically trained potential that simultaneous has a number of native structures as a local minimum. Our results...

  11. Structural refinement and coarsening in deformed metals

    Hansen, N.; Huang, X.; Xing, Q.

    2005-01-01

    The microstructural refinement by plastic deformation is analysed in terms of key parameters, the spacing between and the misorientation angle across the boundaries subdividing the structure. Coarsening of such structures by annealing is also characterised. For both deformed and annealed structur...

  12. Structure refinement of polycrystalline orthorhombic yttrium ...

    The perovskite ceramic phases with composition Ca1−YTiO3+ (where = 0.1, 0.2 and 0.3; hereafter CYT-10, CYT-20 and CYT-30) have been synthesized by solid state reaction at 1050°C. The structure refinement using general structure analysis system (GSAS) software converges to satisfactory profile indicators ...

  13. Biomolecular structure refinement using the GROMOS simulation software

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

    2011-01-01

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

  14. Biomolecular structure refinement using the GROMOS simulation software

    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.

  15. Rare earths refining by vacuum sublimation method

    Rytus, N.N.

    1983-01-01

    The process of rare earths refining by the sUblimation; method in high and superhigh oil-free vacuum, is investigated. The method is effective for rare earths obtaining and permits to prepare metal samples with a high value of electric resistance ratio γ=RsUb(298 K)/Rsub(4.2 K). The estimation of general purity is performed for Sm, Eu, Yb, Tm, Dy, Ho, Er and Se

  16. Refining glass structure in two dimensions

    Sadjadi, Mahdi; Bhattarai, Bishal; Drabold, D. A.; Thorpe, M. F.; Wilson, Mark

    2017-11-01

    Recently determined atomistic scale structures of near-two dimensional bilayers of vitreous silica (using scanning probe and electron microscopy) allow us to refine the experimentally determined coordinates to incorporate the known local chemistry more precisely. Further refinement is achieved by using classical potentials of varying complexity: one using harmonic potentials and the second employing an electrostatic description incorporating polarization effects. These are benchmarked against density functional calculations. Our main findings are that (a) there is a symmetry plane between the two disordered layers, a nice example of an emergent phenomena, (b) the layers are slightly tilted so that the Si-O-Si angle between the two layers is not 180∘ as originally thought but rather 175 ±2∘ , and (c) while interior areas that are not completely imagined can be reliably reconstructed, surface areas are more problematic. It is shown that small crystallites that appear are just as expected statistically in a continuous random network. This provides a good example of the value that can be added to disordered structures imaged at the atomic level by implementing computer refinement.

  17. A self-consistent MoD-WM/MM structural refinement method: characterization of hydrogen bonding in the orytricha nova G-1uar

    Batista, Enrique R [Los Alamos National Laboratory; Newcomer, Micharel B [YALE UNIV; Raggin, Christina M [YALE UNIV; Gascon, Jose A [YALE UNIV; Loria, J Patrick [YALE UNIV; Batista, Victor S [YALE UNIV

    2008-01-01

    This paper generalizes the MoD-QM/MM hybrid method, developed for ab initio computations of protein electrostatic potentials [Gasc6n, l.A.; Leung, S.S.F.; Batista, E.R.; Batista, V.S. J. Chem. Theory Comput. 2006,2, 175-186], as a practical algorithm for structural refinement of extended systems. The computational protocol involves a space-domain decomposition scheme for the formal fragmentation of extended systems into smaller, partially overlapping, molecular domains and the iterative self-consistent energy minimization of the constituent domains by relaxation of their geometry and electronic structure. The method accounts for mutual polarization of the molecular domains, modeled as Quantum-Mechanical (QM) layers embedded in the otherwise classical Molecular-Mechanics (MM) environment according to QM/MM hybrid methods. The method is applied to the description of benchmark models systems that allow for direct comparisons with full QM calculations, and subsequently applied to the structural characterization of the DNA Oxytricha nova Guanine quadruplex (G4). The resulting MoD-QM/MM structural model of the DNA G4 is compared to recently reported highresolution X-ray diffraction and NMR models, and partially validated by direct comparisons between {sup 1}H NMR chemical shifts that are highly sensitive to hydrogen-bonding and stacking interactions and the corresponding theoretical values obtained at the density functional theory DFT QM/MM (BH&H/6-31 G*:Amber) level in conjunction with the gauge independent atomic orbital (GIAO) method for the ab initio self consistent-field (SCF) calculation of NMR chemical shifts.

  18. Structural refinement of vitreous silica bilayers

    Sadjadi, Mahdi; Wilson, Mark; Thorpe, M. F.

    The importance of glasses resides not only in their applications but in fundamental questions that they put forth. The continuous random network model can successfully describe the glass structure, but determining details, like ring statistics, has always been difficult using only diffraction data. But recent atomic images of 2D vitreous silica bilayers can offer valuable new insights which are hard to be observed directly in 3D silica models/experiments (for references see). However, the experimental results are prone to uncertainty in atomic positions, systematic errors, and being finite. We employ special boundary conditions developed for such networks to refine the experimental structures. We show the best structure can be found by using various potentials to maximize information gained from the experimental samples. We find a range of densities, the so-called flexibility window, in which tetrahedra are perfect. We compare results from simulations using harmonic potentials, MD with atomic polarizabilities included and DFT. We should thank David Drabold and Bishal Bhattarai for useful discussions. Support through NSF Grant # DMS 1564468 is gratefully acknowledged.

  19. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1

    Dolenc, Jozica; Missimer, John H.; Steinmetz, Michel O.; Gunsteren, Wilfred F. van

    2010-01-01

    The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 φ torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular α-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured 3 J(H N -H Cα )-coupling constants, indicating that different conformers of GCN4p16-31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and 3 J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and 3 J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16-31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16-31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.

  20. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1.

    Dolenc, Jozica; Missimer, John H; Steinmetz, Michel O; van Gunsteren, Wilfred F

    2010-07-01

    The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 phi torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular alpha-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured (3)J(H(N)-H(Calpha))-coupling constants, indicating that different conformers of GCN4p16-31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and (3)J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and (3)J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16-31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16-31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.

  1. Mathematical aspects of Rietveld refinement and crystal structure ...

    Administrator

    The core mathematics, goodness-of-fit parameters of Rietveld refinement technique is introduced for structural ... transducers in medical and solar applications (Obmann ..... Prince 1985 in Structure and statistics in crystallography (ed.).

  2. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1

    Dolenc, Jozica [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH (Switzerland); Missimer, John H.; Steinmetz, Michel O. [Paul Scherrer Institut, Biomolecular Research (Switzerland); Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.c [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH (Switzerland)

    2010-07-15

    The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 {phi} torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular {alpha}-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured {sup 3}J(H{sub N}-H{sub C{alpha}})-coupling constants, indicating that different conformers of GCN4p16-31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and {sup 3}J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and {sup 3}J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16-31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16-31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.

  3. Method of optimization of the natural gas refining process

    Sadykh-Zade, E.S.; Bagirov, A.A.; Mardakhayev, I.M.; Razamat, M.S.; Tagiyev, V.G.

    1980-01-01

    The SATUM (automatic control system of technical operations) system introduced at the Shatlyk field should assure good quality of gas refining. In order to optimize the natural gas refining processes and experimental-analytical method is used in compiling the mathematical descriptions. The program, compiled in Fortran language, in addition to parameters of optimal conditions gives information on the yield of concentrate and water, concentration and consumption of DEG, composition and characteristics of the gas and condensate. The algorithm for calculating optimum engineering conditions of gas refining is proposed to be used in ''advice'' mode, and also for monitoring progress of the gas refining process.

  4. i3Drefine software for protein 3D structure refinement and its assessment in CASP10.

    Bhattacharya, Debswapna; Cheng, Jianlin

    2013-01-01

    Protein structure refinement refers to the process of improving the qualities of protein structures during structure modeling processes to bring them closer to their native states. Structure refinement has been drawing increasing attention in the community-wide Critical Assessment of techniques for Protein Structure prediction (CASP) experiments since its addition in 8(th) CASP experiment. During the 9(th) and recently concluded 10(th) CASP experiments, a consistent growth in number of refinement targets and participating groups has been witnessed. Yet, protein structure refinement still remains a largely unsolved problem with majority of participating groups in CASP refinement category failed to consistently improve the quality of structures issued for refinement. In order to alleviate this need, we developed a completely automated and computationally efficient protein 3D structure refinement method, i3Drefine, based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique. In the recent community-wide blind experiment, CASP10, i3Drefine (as 'MULTICOM-CONSTRUCT') was ranked as the best method in the server section as per the official assessment of CASP10 experiment. Here we provide the community with free access to i3Drefine software and systematically analyse the performance of i3Drefine in strict blind mode on the refinement targets issued in CASP10 refinement category and compare with other state-of-the-art refinement methods participating in CASP10. Our analysis demonstrates that i3Drefine is only fully-automated server participating in CASP10 exhibiting consistent improvement over the initial structures in both global and local structural quality metrics. Executable version of i3Drefine is freely available at http://protein.rnet.missouri.edu/i3drefine/.

  5. i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10

    Bhattacharya, Debswapna; Cheng, Jianlin

    2013-01-01

    Protein structure refinement refers to the process of improving the qualities of protein structures during structure modeling processes to bring them closer to their native states. Structure refinement has been drawing increasing attention in the community-wide Critical Assessment of techniques for Protein Structure prediction (CASP) experiments since its addition in 8th CASP experiment. During the 9th and recently concluded 10th CASP experiments, a consistent growth in number of refinement targets and participating groups has been witnessed. Yet, protein structure refinement still remains a largely unsolved problem with majority of participating groups in CASP refinement category failed to consistently improve the quality of structures issued for refinement. In order to alleviate this need, we developed a completely automated and computationally efficient protein 3D structure refinement method, i3Drefine, based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique. In the recent community-wide blind experiment, CASP10, i3Drefine (as ‘MULTICOM-CONSTRUCT’) was ranked as the best method in the server section as per the official assessment of CASP10 experiment. Here we provide the community with free access to i3Drefine software and systematically analyse the performance of i3Drefine in strict blind mode on the refinement targets issued in CASP10 refinement category and compare with other state-of-the-art refinement methods participating in CASP10. Our analysis demonstrates that i3Drefine is only fully-automated server participating in CASP10 exhibiting consistent improvement over the initial structures in both global and local structural quality metrics. Executable version of i3Drefine is freely available at http://protein.rnet.missouri.edu/i3drefine/. PMID:23894517

  6. Refinement of RAIM via Implementation of Implicit Euler Method

    Lee, Yoonhee; Kim, Han-Chul [Korea Institute of Nuclear and Safety, Daejeon (Korea, Republic of)

    2016-10-15

    The first approach is a mechanistic approach which is used in LIRIC in which more than 200 reactions are modeled in detail. This approach enables to perform the detailed analysis. However, it requires huge computation burden. The other approach is a simplified model approach which is used in the IMOD, ASTEC/IODE, and etc. Recently, KINS has developed RAIM (Radio-Active Iodine chemistry Model) based on the simplified model approach. Since the numerical analysis module in RAIM is based on the explicit Euler method, there are major issues on the stability of the module. Therefore, implementation of a stable numerical method becomes essential. In this study, RAIM is refined via implementation of implicit Euler method in which the Newton method is used to find the solutions at each time step. The refined RAIM is tested by comparing to RAIM based on the explicit Euler method. In this paper, RAIM was refined by implementing the implicit Euler method. At each time step of the method in the refined RAIM, the reaction kinetics equations are solved by the Newton method in which elements of the Jacobian matrix are expressed analytically. With the results of OECD-BIP P10T2 test, the refined RAIM was compared to RAIM with the explicit Euler method. The refined RAIM shows better agreement with the experimental data than those from the explicit Euler method. For the rapid change of pH during the experiment, the refined RAIM gives more realistic changes in the concentrations of chemical species than those from the explicit Euler method. In addition, in terms of computing time, the refined RAIM shows comparable computing time to that with explicit Euler method. These comparisons are attributed to ⁓10 times larger time step size used in the implicit Euler method, even though computation burden at each time step in the refined RAIM is much higher than that of the explicit Euler method. Compared to the experimental data, the refined RAIM still shows discrepancy, which are attributed

  7. Refinement of RAIM via Implementation of Implicit Euler Method

    Lee, Yoonhee; Kim, Han-Chul

    2016-01-01

    The first approach is a mechanistic approach which is used in LIRIC in which more than 200 reactions are modeled in detail. This approach enables to perform the detailed analysis. However, it requires huge computation burden. The other approach is a simplified model approach which is used in the IMOD, ASTEC/IODE, and etc. Recently, KINS has developed RAIM (Radio-Active Iodine chemistry Model) based on the simplified model approach. Since the numerical analysis module in RAIM is based on the explicit Euler method, there are major issues on the stability of the module. Therefore, implementation of a stable numerical method becomes essential. In this study, RAIM is refined via implementation of implicit Euler method in which the Newton method is used to find the solutions at each time step. The refined RAIM is tested by comparing to RAIM based on the explicit Euler method. In this paper, RAIM was refined by implementing the implicit Euler method. At each time step of the method in the refined RAIM, the reaction kinetics equations are solved by the Newton method in which elements of the Jacobian matrix are expressed analytically. With the results of OECD-BIP P10T2 test, the refined RAIM was compared to RAIM with the explicit Euler method. The refined RAIM shows better agreement with the experimental data than those from the explicit Euler method. For the rapid change of pH during the experiment, the refined RAIM gives more realistic changes in the concentrations of chemical species than those from the explicit Euler method. In addition, in terms of computing time, the refined RAIM shows comparable computing time to that with explicit Euler method. These comparisons are attributed to ⁓10 times larger time step size used in the implicit Euler method, even though computation burden at each time step in the refined RAIM is much higher than that of the explicit Euler method. Compared to the experimental data, the refined RAIM still shows discrepancy, which are attributed

  8. Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

    Smart, Oliver S., E-mail: osmart@globalphasing.com; Womack, Thomas O.; Flensburg, Claus; Keller, Peter; Paciorek, Włodek; Sharff, Andrew; Vonrhein, Clemens; Bricogne, Gérard [Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom)

    2012-04-01

    Local structural similarity restraints (LSSR) provide a novel method for exploiting NCS or structural similarity to an external target structure. Two examples are given where BUSTER re-refinement of PDB entries with LSSR produces marked improvements, enabling further structural features to be modelled. Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct ‘target’ structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and @@target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -target enables the correct ligand-binding structure to be found, and http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.

  9. Refining waste hardmetals into tungsten oxide nanosheets via facile method

    Li, Zhifei; Zheng, Guangwei; Wang, Jinshu, E-mail: wangjsh@bjut.edu.cn; Li, Hongyi, E-mail: lhy06@bjut.edu.cn; Wu, Junshu; Du, Yucheng [Beijing University of Technology, Key Laboratory of Advanced Functional Materials, School of Materials Science and Engineering (China)

    2016-04-15

    A new hydrothermal system has been designed to recycle waste WC–Co hardmetal with low cobalt (Co) content (3 %). In the solution system, nitric acid was designed to dissolve Co, H{sub 2}O{sub 2} served as oxidant to accelerate the oxidation of the WC–Co hardmetals, and fluorine (F{sup −}) was designed to dissolve and recrystallize generated tungsten oxides, which were found to possess a layered structure using scanning electron microscopy and transmission electron microscopy. The obtained tungsten oxides were identified as WO{sub 3}·0.33H{sub 2}O by X-ray diffraction and their specific surface area was measured as 89.2 m{sup 2} g{sup −1} via N{sub 2} adsorption–desorption techniques. The present layered structure tungsten oxides exhibited a promising capability for removing lead ion (Pb{sup 2+}) and organic species, such as methyl blue. The adsorption model was found to be in agreement with Langmuir isotherm model. Given the facile synthesis procedure and promising properties of final products, this new approach should have great potential for refining some other waste hardmetals or tungsten products.Graphical AbstractA new hydrothermal system was designed to recycle waste hardmetal with low cobalt content. Through this method, waste hardmetal was refined into WO{sub 3}·0.33H{sub 2}O nanosheets which shows excellent adsorption capacities toward methylene blue and lead ion (Pb{sup 2+}).

  10. Crystal structure of vanadite: Refinement of anisotropic displacement parameters

    Laufek, F.; Skála, Roman; Haloda, J.; Císařová, I.

    2006-01-01

    Roč. 51, 3-4 (2006), s. 271-275 ISSN 1210-8197 Institutional research plan: CEZ:AV0Z30130516 Keywords : anisotropic displacement parameter * crystal structure * single-crystal X-ray refinement * vanadinite Subject RIV: DB - Geology ; Mineralogy

  11. Trajectory Optimization Based on Multi-Interval Mesh Refinement Method

    Ningbo Li

    2017-01-01

    Full Text Available In order to improve the optimization accuracy and convergence rate for trajectory optimization of the air-to-air missile, a multi-interval mesh refinement Radau pseudospectral method was introduced. This method made the mesh endpoints converge to the practical nonsmooth points and decreased the overall collocation points to improve convergence rate and computational efficiency. The trajectory was divided into four phases according to the working time of engine and handover of midcourse and terminal guidance, and then the optimization model was built. The multi-interval mesh refinement Radau pseudospectral method with different collocation points in each mesh interval was used to solve the trajectory optimization model. Moreover, this method was compared with traditional h method. Simulation results show that this method can decrease the dimensionality of nonlinear programming (NLP problem and therefore improve the efficiency of pseudospectral methods for solving trajectory optimization problems.

  12. SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

    Tong, Jing; Pei, Jimin; Grishin, Nick V

    2015-09-03

    Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

  13. Refinement of NMR structures using implicit solvent and advanced sampling techniques.

    Chen, Jianhan; Im, Wonpil; Brooks, Charles L

    2004-12-15

    NMR biomolecular structure calculations exploit simulated annealing methods for conformational sampling and require a relatively high level of redundancy in the experimental restraints to determine quality three-dimensional structures. Recent advances in generalized Born (GB) implicit solvent models should make it possible to combine information from both experimental measurements and accurate empirical force fields to improve the quality of NMR-derived structures. In this paper, we study the influence of implicit solvent on the refinement of protein NMR structures and identify an optimal protocol of utilizing these improved force fields. To do so, we carry out structure refinement experiments for model proteins with published NMR structures using full NMR restraints and subsets of them. We also investigate the application of advanced sampling techniques to NMR structure refinement. Similar to the observations of Xia et al. (J.Biomol. NMR 2002, 22, 317-331), we find that the impact of implicit solvent is rather small when there is a sufficient number of experimental restraints (such as in the final stage of NMR structure determination), whether implicit solvent is used throughout the calculation or only in the final refinement step. The application of advanced sampling techniques also seems to have minimal impact in this case. However, when the experimental data are limited, we demonstrate that refinement with implicit solvent can substantially improve the quality of the structures. In particular, when combined with an advanced sampling technique, the replica exchange (REX) method, near-native structures can be rapidly moved toward the native basin. The REX method provides both enhanced sampling and automatic selection of the most native-like (lowest energy) structures. An optimal protocol based on our studies first generates an ensemble of initial structures that maximally satisfy the available experimental data with conventional NMR software using a simplified

  14. Iterative Refinement Methods for Time-Domain Equalizer Design

    Evans Brian L

    2006-01-01

    Full Text Available Commonly used time domain equalizer (TEQ design methods have been recently unified as an optimization problem involving an objective function in the form of a Rayleigh quotient. The direct generalized eigenvalue solution relies on matrix decompositions. To reduce implementation complexity, we propose an iterative refinement approach in which the TEQ length starts at two taps and increases by one tap at each iteration. Each iteration involves matrix-vector multiplications and vector additions with matrices and two-element vectors. At each iteration, the optimization of the objective function either improves or the approach terminates. The iterative refinement approach provides a range of communication performance versus implementation complexity tradeoffs for any TEQ method that fits the Rayleigh quotient framework. We apply the proposed approach to three such TEQ design methods: maximum shortening signal-to-noise ratio, minimum intersymbol interference, and minimum delay spread.

  15. A method of refining aromatic hydrocarbons from coal chemical production

    Zieborak, K.; Koprowski, A.; Ratajczak, W.

    1979-10-01

    A method is disclosed for refining aromatic hydrocarbons of coal chemical production by contact of liquid aromatic hydrocarbons and their mixtures with a strongly acid macroporous sulfocationite in the H-form at atmospheric pressure and high temperature. The method is distinguished in that the aromatic hydrocarbons and their mixtures, from which alkali compounds have already been removed, are supplied for refinement with the sulfocationite with simultaneous addition of olefin derivatives of aromatic hydrocarbons, followed by separation of pure hydrocarbons by rectification. Styrene or alpha-methylstyrene is used as the olefin derivatives of the aromatic hydrocarbons. The method is performed in several stages with addition of olefin derivatives of aromatic hydrocarbons at each stage.

  16. PREFMD: a web server for protein structure refinement via molecular dynamics simulations.

    Heo, Lim; Feig, Michael

    2018-03-15

    Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git. feig@msu.edu. Supplementary data are available at Bioinformatics online.

  17. Refining developmental coordination disorder subtyping with multivariate statistical methods

    Lalanne Christophe

    2012-07-01

    Full Text Available Abstract Background With a large number of potentially relevant clinical indicators penalization and ensemble learning methods are thought to provide better predictive performance than usual linear predictors. However, little is known about how they perform in clinical studies where few cases are available. We used Random Forests and Partial Least Squares Discriminant Analysis to select the most salient impairments in Developmental Coordination Disorder (DCD and assess patients similarity. Methods We considered a wide-range testing battery for various neuropsychological and visuo-motor impairments which aimed at characterizing subtypes of DCD in a sample of 63 children. Classifiers were optimized on a training sample, and they were used subsequently to rank the 49 items according to a permuted measure of variable importance. In addition, subtyping consistency was assessed with cluster analysis on the training sample. Clustering fitness and predictive accuracy were evaluated on the validation sample. Results Both classifiers yielded a relevant subset of items impairments that altogether accounted for a sharp discrimination between three DCD subtypes: ideomotor, visual-spatial and constructional, and mixt dyspraxia. The main impairments that were found to characterize the three subtypes were: digital perception, imitations of gestures, digital praxia, lego blocks, visual spatial structuration, visual motor integration, coordination between upper and lower limbs. Classification accuracy was above 90% for all classifiers, and clustering fitness was found to be satisfactory. Conclusions Random Forests and Partial Least Squares Discriminant Analysis are useful tools to extract salient features from a large pool of correlated binary predictors, but also provide a way to assess individuals proximities in a reduced factor space. Less than 15 neuro-visual, neuro-psychomotor and neuro-psychological tests might be required to provide a sensitive and

  18. Crystal structure refinement of α-Si3N4 using synchrotron radiation powder diffraction data: unbiased refinement strategy

    Toraya, H.

    2000-01-01

    The crystal structure of α-silicon nitride (Si 3 N 4 ) was refined by the Rietveld method using synchrotron radiation powder diffraction data (wavelength = 1.2 A) collected at station BL-4B2 in the photon factory. A refinement procedure that adopted a new weight function, w = 1/Y o e (Y o is the observed profile intensity and e ≅ 2), for the least-squares fitting [Toraya (1998). J. Appl. Cryst. 31, 333-343] was studied. The most reasonable structural parameters were obtained with e = 1.7. Crystal data of α-Si 3 N 4 : trigonal, P31c, a = 7.75193 (3), c = 5.61949 (4) A, V = 292.447 (3) A 3 , Z = 4; R p = 5.08, R wp = 6.50, R B = 3.36, R F = 2.26%. The following five factors are considered equally important for deriving accurate structural parameters from powder diffraction data: (i) sufficiently large sin θ/λ range of >0.8 A -1 ; (ii) adequate counting statistics; (iii) correct profile model; (iv) proper weighting on observations to give a uniform distribution of the mean weighted squared residuals; (v) high-angular-resolution powder diffraction data. (orig.)

  19. 3Drefine: an interactive web server for efficient protein structure refinement.

    Bhattacharya, Debswapna; Nowotny, Jackson; Cao, Renzhi; Cheng, Jianlin

    2016-07-08

    3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Parallel Block Structured Adaptive Mesh Refinement on Graphics Processing Units

    Beckingsale, D. A. [Atomic Weapons Establishment (AWE), Aldermaston (United Kingdom); Gaudin, W. P. [Atomic Weapons Establishment (AWE), Aldermaston (United Kingdom); Hornung, R. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gunney, B. T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gamblin, T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Herdman, J. A. [Atomic Weapons Establishment (AWE), Aldermaston (United Kingdom); Jarvis, S. A. [Atomic Weapons Establishment (AWE), Aldermaston (United Kingdom)

    2014-11-17

    Block-structured adaptive mesh refinement is a technique that can be used when solving partial differential equations to reduce the number of zones necessary to achieve the required accuracy in areas of interest. These areas (shock fronts, material interfaces, etc.) are recursively covered with finer mesh patches that are grouped into a hierarchy of refinement levels. Despite the potential for large savings in computational requirements and memory usage without a corresponding reduction in accuracy, AMR adds overhead in managing the mesh hierarchy, adding complex communication and data movement requirements to a simulation. In this paper, we describe the design and implementation of a native GPU-based AMR library, including: the classes used to manage data on a mesh patch, the routines used for transferring data between GPUs on different nodes, and the data-parallel operators developed to coarsen and refine mesh data. We validate the performance and accuracy of our implementation using three test problems and two architectures: an eight-node cluster, and over four thousand nodes of Oak Ridge National Laboratory’s Titan supercomputer. Our GPU-based AMR hydrodynamics code performs up to 4.87× faster than the CPU-based implementation, and has been scaled to over four thousand GPUs using a combination of MPI and CUDA.

  1. Refinement of Bayesian Network Structures upon New Data

    Zeng, Yifeng; Xiang, Yanping; Pacekajus, Saulius

    2010-01-01

    Refinement of Bayesian network (BN) structures using new data becomes more and more relevant. Some work has been done there; however, one problem has not been considered yet – what to do when new data have fewer or more attributes than the existing model. In both cases, data contain important...... knowledge and every effort must be made in order to extract it. In this paper, we propose a general merging algorithm to deal with situations when new data have different set of attributes. The merging algorithm updates sufficient statistics when new data are received. It expands the flexibility of BN...

  2. An efficient method for model refinement in diffuse optical tomography

    Zirak, A. R.; Khademi, M.

    2007-11-01

    Diffuse optical tomography (DOT) is a non-linear, ill-posed, boundary value and optimization problem which necessitates regularization. Also, Bayesian methods are suitable owing to measurements data are sparse and correlated. In such problems which are solved with iterative methods, for stabilization and better convergence, the solution space must be small. These constraints subject to extensive and overdetermined system of equations which model retrieving criteria specially total least squares (TLS) must to refine model error. Using TLS is limited to linear systems which is not achievable when applying traditional Bayesian methods. This paper presents an efficient method for model refinement using regularized total least squares (RTLS) for treating on linearized DOT problem, having maximum a posteriori (MAP) estimator and Tikhonov regulator. This is done with combination Bayesian and regularization tools as preconditioner matrices, applying them to equations and then using RTLS to the resulting linear equations. The preconditioning matrixes are guided by patient specific information as well as a priori knowledge gained from the training set. Simulation results illustrate that proposed method improves the image reconstruction performance and localize the abnormally well.

  3. Frequency-restrained structure-factor refinement. Pt. 1

    Lunin, V.Yu.; Skovoroda, T.P.

    1991-01-01

    An analysis of the frequencies of different values encountered in protein electron-density syntheses reveals characteristic shapes for their distributions (histograms). This property can be used to refine ill-defined phases (and, perhaps, some of the moduli) of structure factors, and thus to obtain more-interpretable electron-density maps. A simple empirical model is designed which can predict the histogram for a protein with an undetermined structure provided its unit-cell volume and charge are known. The parameters of the histogram model are derived from a set of proteins with known spatial structures. The application of the simulated histogram is illustrated by an improved electron-density map for the 'dry' form of the protein γ-crystallin IIIb. (orig.)

  4. Refining the structure and content of clinical genomic reports.

    Dorschner, Michael O; Amendola, Laura M; Shirts, Brian H; Kiedrowski, Lesli; Salama, Joseph; Gordon, Adam S; Fullerton, Stephanie M; Tarczy-Hornoch, Peter; Byers, Peter H; Jarvik, Gail P

    2014-03-01

    To effectively articulate the results of exome and genome sequencing we refined the structure and content of molecular test reports. To communicate results of a randomized control trial aimed at the evaluation of exome sequencing for clinical medicine, we developed a structured narrative report. With feedback from genetics and non-genetics professionals, we developed separate indication-specific and incidental findings reports. Standard test report elements were supplemented with research study-specific language, which highlighted the limitations of exome sequencing and provided detailed, structured results, and interpretations. The report format we developed to communicate research results can easily be transformed for clinical use by removal of research-specific statements and disclaimers. The development of clinical reports for exome sequencing has shown that accurate and open communication between the clinician and laboratory is ideally an ongoing process to address the increasing complexity of molecular genetic testing. © 2014 Wiley Periodicals, Inc.

  5. Adaptive mesh refinement and adjoint methods in geophysics simulations

    Burstedde, Carsten

    2013-04-01

    It is an ongoing challenge to increase the resolution that can be achieved by numerical geophysics simulations. This applies to considering sub-kilometer mesh spacings in global-scale mantle convection simulations as well as to using frequencies up to 1 Hz in seismic wave propagation simulations. One central issue is the numerical cost, since for three-dimensional space discretizations, possibly combined with time stepping schemes, a doubling of resolution can lead to an increase in storage requirements and run time by factors between 8 and 16. A related challenge lies in the fact that an increase in resolution also increases the dimensionality of the model space that is needed to fully parametrize the physical properties of the simulated object (a.k.a. earth). Systems that exhibit a multiscale structure in space are candidates for employing adaptive mesh refinement, which varies the resolution locally. An example that we found well suited is the mantle, where plate boundaries and fault zones require a resolution on the km scale, while deeper area can be treated with 50 or 100 km mesh spacings. This approach effectively reduces the number of computational variables by several orders of magnitude. While in this case it is possible to derive the local adaptation pattern from known physical parameters, it is often unclear what are the most suitable criteria for adaptation. We will present the goal-oriented error estimation procedure, where such criteria are derived from an objective functional that represents the observables to be computed most accurately. Even though this approach is well studied, it is rarely used in the geophysics community. A related strategy to make finer resolution manageable is to design methods that automate the inference of model parameters. Tweaking more than a handful of numbers and judging the quality of the simulation by adhoc comparisons to known facts and observations is a tedious task and fundamentally limited by the turnaround times

  6. Block-structured Adaptive Mesh Refinement - Theory, Implementation and Application

    Deiterding Ralf

    2011-12-01

    Full Text Available Structured adaptive mesh refinement (SAMR techniques can enable cutting-edge simulations of problems governed by conservation laws. Focusing on the strictly hyperbolic case, these notes explain all algorithmic and mathematical details of a technically relevant implementation tailored for distributed memory computers. An overview of the background of commonly used finite volume discretizations for gas dynamics is included and typical benchmarks to quantify accuracy and performance of the dynamically adaptive code are discussed. Large-scale simulations of shock-induced realistic combustion in non-Cartesian geometry and shock-driven fluid-structure interaction with fully coupled dynamic boundary motion demonstrate the applicability of the discussed techniques for complex scenarios.

  7. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

    Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.; Moriarty, Nigel W.; Zwart, Peter H.; Hung, Li-Wei; Read, Randy J.; Adams, Paul D.

    2008-01-01

    The highly automated PHENIX AutoBuild wizard is described. The procedure can be applied equally well to phases derived from isomorphous/anomalous and molecular-replacement methods. The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 Å, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution

  8. Method of refining mineral and shale oils, etc

    1950-12-06

    A method is described for refining mineral oils, shale oils, tar oil. The oil is preferably treated with concentrated sulphuric acid, of not less than 90% by weight concentration or with chloro-sulphonic acid in order to extract the more reactive components of the oil. The solution (extract phase) is separated from the treated oil (raffinate phase) by centrifuging, characterised by centrifugally separating the extract phase from the raffinate phase before any noticeable chemical reaction with subsequent solution of acid reaction products in the raffinate phase has taken place. The acid remaining in the raffinate phase is allowed to react chemically with the more reactive constituents. The sludge formed is removed from the raffinate phase by centrifuging.

  9. Structural heredity of TiC and its influences on refinement behaviors of AlTiC master alloy

    王振卿; 刘相法; 柳延辉; 张均燕; 于丽娜; 边秀房

    2003-01-01

    Heredity of microstructure in AlTiC master alloy, grain refiners, was analyzed. It is found that, for morphologies and distributions of TiC particles, there are visible heredity which originates from raw materials or processing methods of Al melt, and will ultimately be transferred to the solid state structure through the melt stage, and this phenomenon can cause hereditary influences on refinement: formation of chain-like TiC morphology results in rapid refinement fading behavior; distribution of TiC along grain boundaries greatly reduces refinement efficiency. Controlling of structural heredity through proper selections of raw materials and processing parameters is of great importance in obtaining ideal microstructures and improving refinement behaviors of AlTiC master alloys.

  10. A skeleton model for the MJO with refined vertical structure

    Thual, Sulian; Majda, Andrew J.

    2016-05-01

    The Madden-Julian oscillation (MJO) is the dominant mode of variability in the tropical atmosphere on intraseasonal timescales and planetary spatial scales. The skeleton model is a minimal dynamical model that recovers robustly the most fundamental MJO features of (I) a slow eastward speed of roughly 5 {ms}^{-1}, (II) a peculiar dispersion relation with dω /dk ≈ 0, and (III) a horizontal quadrupole vortex structure. This model depicts the MJO as a neutrally-stable atmospheric wave that involves a simple multiscale interaction between planetary dry dynamics, planetary lower-tropospheric moisture and the planetary envelope of synoptic-scale activity. Here we propose and analyse an extended version of the skeleton model with additional variables accounting for the refined vertical structure of the MJO in nature. The present model reproduces qualitatively the front-to-rear vertical structure of the MJO found in nature, with MJO events marked by a planetary envelope of convective activity transitioning from the congestus to the deep to the stratiform type, in addition to a front-to-rear structure of moisture, winds and temperature. Despite its increased complexity the present model retains several interesting features of the original skeleton model such as a conserved energy and similar linear solutions. We further analyze a model version with a simple stochastic parametrization for the unresolved details of synoptic-scale activity. The stochastic model solutions show intermittent initiation, propagation and shut down of MJO wave trains, as in previous studies, in addition to MJO events with a front-to-rear vertical structure of varying intensity and characteristics from one event to another.

  11. Protein structure refinement using a quantum mechanics-based chemical shielding predictor

    Bratholm, Lars Andersen; Jensen, Jan Halborg

    2017-01-01

    The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor...... of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic...

  12. Synthesis, characterization and structural refinement of polycrystalline uranium substituted zirconolite

    Shrivastava, O.P.; Narendra Kumar; Sharma, I.B.

    2005-01-01

    Ceramic precursors of Zirconolite (CaZrTi 2 O 7 ) family have a remarkable property of substitution Zr 4+ cationic sites. This makes them potential material for nuclear waste management in 'synroc' technology. In order to simulate the mechanism of partial substitution of zirconium by tetravalent actinides, a solid phase of composition CaZr 0.95 U 0.5 Ti 2 O 7 has been synthesized through ceramic route by taking calculated quantities of oxides of Ca, Ti and nitrates of uranium and zirconium respectively. Solid state synthesis has been carried out by repeated pelletizing and sintering the finely powdered oxide mixture in a muffle furnace at 1050 degC. The polycrystalline solid phase has been characterized by its typical powder diffraction pattern. Step analysis data has been used for ab initio calculation of structural parameters. The uranium substituted zirconolite crystallizes in monoclinic symmetry with space group C2/c (15). The following unit cell parameters have been calculated: a =12.4883(15), b =7.2448(5), c 11.3973(10) and β = 100.615(9)0. The structure was refined to satisfactory completion. The Rp and Rwp are found to be 7.48% and 9.74% respectively. (author)

  13. Conforming to interface structured adaptive mesh refinement: 3D algorithm and implementation

    Nagarajan, Anand; Soghrati, Soheil

    2018-03-01

    A new non-iterative mesh generation algorithm named conforming to interface structured adaptive mesh refinement (CISAMR) is introduced for creating 3D finite element models of problems with complex geometries. CISAMR transforms a structured mesh composed of tetrahedral elements into a conforming mesh with low element aspect ratios. The construction of the mesh begins with the structured adaptive mesh refinement of elements in the vicinity of material interfaces. An r-adaptivity algorithm is then employed to relocate selected nodes of nonconforming elements, followed by face-swapping a small fraction of them to eliminate tetrahedrons with high aspect ratios. The final conforming mesh is constructed by sub-tetrahedralizing remaining nonconforming elements, as well as tetrahedrons with hanging nodes. In addition to studying the convergence and analyzing element-wise errors in meshes generated using CISAMR, several example problems are presented to show the ability of this method for modeling 3D problems with intricate morphologies.

  14. A refined method for creating saccular aneurysms in the rabbit

    Krings, Timo [Department of Neuroradiology, University Hospital of the University of Technology Aachen, Pauwelsstrase 30, 52057, Aachen (Germany); Department of Neurosurgery, University Hospital of the University of Technology Aachen, Pauwelsstrase 30, 52057, Aachen (Germany); Moeller-Hartmann, Walter; Meetz, Alexander; Dreeskamp, Heiko; Stein, Klaus-Peter; Thron, Armin [Department of Neuroradiology, University Hospital of the University of Technology Aachen, Pauwelsstrase 30, 52057, Aachen (Germany); Hans, Franz-Josef; Thiex, Ruth; Gilsbach, Joachim M. [Department of Neurosurgery, University Hospital of the University of Technology Aachen, Pauwelsstrase 30, 52057, Aachen (Germany); Brunn, Anna [Department of Neuropathology, University Hospital of the University of Technology Aachen, Pauwelsstrase 30, 52057, Aachen (Germany); Scherer, Kira [Department of Laboratory Animal Science, University Hospital of the University of Technology Aachen, Pauwelsstrase 30, 52057, Aachen (Germany)

    2003-07-01

    We describe a refined animal model of human intracerebral aneurysms for testing endovascular devices for interventional neuroradiological procedures. Saccular aneurysms resulting from a stump of the right common carotid artery (CCA) were created in 15 New Zealand White rabbits by intraluminal incubation of elastase that was applied to the CCA after distal ligation of the CCA and proximal occlusion of the vessel using a pliable balloon. Subsequently a microcatheter was advanced to a position cranial to the balloon and the elastase was infused under fluoroscopic guidance to avoid retrograde flow to the trachea via aberrant vessels. Contrast-enhanced (CE) MRA at 1.5 T and conventional digital subtraction angiography was performed to test for aneurysm size, morphology and neck anatomy. In all 15 animals aneurysms resulted from the stump of the right CCA, ranging in size from 2.0 to 9.9 mm (mean 6.3 mm) in craniocaudal direction, 1.0 to 5.5 mm (mean 3.8 mm) in mediolateral direction and 1.0 to 3.8 mm (mean 2.4 mm) in neck diameter. Aneurysm morphology could be adequately demonstrated using CE MRA. On histological evaluation a loss of the internal elastic lamina was noted. The described method represents an easy, reliable, and reproducible method of aneurysm creation in the rabbit in an area of high shear stress. These aneurysms can be used for testing new endovascular devices for embolization of intracranial aneurysms. (orig.)

  15. A refined method for creating saccular aneurysms in the rabbit

    Krings, Timo; Moeller-Hartmann, Walter; Meetz, Alexander; Dreeskamp, Heiko; Stein, Klaus-Peter; Thron, Armin; Hans, Franz-Josef; Thiex, Ruth; Gilsbach, Joachim M.; Brunn, Anna; Scherer, Kira

    2003-01-01

    We describe a refined animal model of human intracerebral aneurysms for testing endovascular devices for interventional neuroradiological procedures. Saccular aneurysms resulting from a stump of the right common carotid artery (CCA) were created in 15 New Zealand White rabbits by intraluminal incubation of elastase that was applied to the CCA after distal ligation of the CCA and proximal occlusion of the vessel using a pliable balloon. Subsequently a microcatheter was advanced to a position cranial to the balloon and the elastase was infused under fluoroscopic guidance to avoid retrograde flow to the trachea via aberrant vessels. Contrast-enhanced (CE) MRA at 1.5 T and conventional digital subtraction angiography was performed to test for aneurysm size, morphology and neck anatomy. In all 15 animals aneurysms resulted from the stump of the right CCA, ranging in size from 2.0 to 9.9 mm (mean 6.3 mm) in craniocaudal direction, 1.0 to 5.5 mm (mean 3.8 mm) in mediolateral direction and 1.0 to 3.8 mm (mean 2.4 mm) in neck diameter. Aneurysm morphology could be adequately demonstrated using CE MRA. On histological evaluation a loss of the internal elastic lamina was noted. The described method represents an easy, reliable, and reproducible method of aneurysm creation in the rabbit in an area of high shear stress. These aneurysms can be used for testing new endovascular devices for embolization of intracranial aneurysms. (orig.)

  16. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

    Rong Shen

    2015-10-01

    Full Text Available The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels, each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good

  17. Bureaucratic Structure in Schools: A Refinement and Synthesis in Measurement.

    Sousa, David A.; Hoy, Wayne K.

    1981-01-01

    Compares two methods of measuring bureaucratic structure, Hall's organizational inventory and the University of Aston (England) approach, and tests them using data from 55 public high schools in New Jersey. Factor analysis reveals four underlying dimensions of school structure, including organizational control, rational specialization, system…

  18. A refined method for calculating equivalent effective stratospheric chlorine

    Engel, Andreas; Bönisch, Harald; Ostermöller, Jennifer; Chipperfield, Martyn P.; Dhomse, Sandip; Jöckel, Patrick

    2018-01-01

    Chlorine and bromine atoms lead to catalytic depletion of ozone in the stratosphere. Therefore the use and production of ozone-depleting substances (ODSs) containing chlorine and bromine is regulated by the Montreal Protocol to protect the ozone layer. Equivalent effective stratospheric chlorine (EESC) has been adopted as an appropriate metric to describe the combined effects of chlorine and bromine released from halocarbons on stratospheric ozone. Here we revisit the concept of calculating EESC. We derive a refined formulation of EESC based on an advanced concept of ODS propagation into the stratosphere and reactive halogen release. A new transit time distribution is introduced in which the age spectrum for an inert tracer is weighted with the release function for inorganic halogen from the source gases. This distribution is termed the release time distribution. We show that a much better agreement with inorganic halogen loading from the chemistry transport model TOMCAT is achieved compared with using the current formulation. The refined formulation shows EESC levels in the year 1980 for the mid-latitude lower stratosphere, which are significantly lower than previously calculated. The year 1980 is commonly used as a benchmark to which EESC must return in order to reach significant progress towards halogen and ozone recovery. Assuming that - under otherwise unchanged conditions - the EESC value must return to the same level in order for ozone to fully recover, we show that it will take more than 10 years longer than estimated in this region of the stratosphere with the current method for calculation of EESC. We also present a range of sensitivity studies to investigate the effect of changes and uncertainties in the fractional release factors and in the assumptions on the shape of the release time distributions. We further discuss the value of EESC as a proxy for future evolution of inorganic halogen loading under changing atmospheric dynamics using simulations from

  19. Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

    Bratholm, Lars A; Jensen, Jan H

    2017-03-01

    The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural

  20. Study of the crystallite size of nitrosylpentacyanoferrate through refinement of structures

    Jimenez G, J.A.; Yee M, H.T.; Balmaceda E, J.; Reguera R, E.

    2006-01-01

    The development reached in the instrumentation and in the computer science of the diffraction of rays X, it has enlarged the reach of the method of powders considerably, in the resolution of crystalline structures of polycrystalline material converting it in a potent tool that, attended by spectroscopic techniques, it allows the fine characterization to atomic scale of having been accustomed to crystalline. In the thesis it is developed an effective methodology of determination of the crystallite size and structural refinement starting from data of diffraction of powders, based on the use of the equation of Sherrer for the estimate of the crystallite size and the method of Rietveld for the structural refinement; supplemented with the employment of the spectroscopic methods (IR and Moessbauer). The combined use of these techniques in the structural study of having been accustomed to crystalline lens of high complexity provides a novel and advanced work. The estimate of the crystallite size, it has been little explored to study accustomed to crystalline such as the pentacyanonitrosyl ferrates. One of the reasons for the which have intended to study the glass size in these structures it is due to that the molecular materials have attracted the attention of the international scientific community for their promissory properties in fields so diverse as: the absorption, desorption and separation of gases among others. Of the entreated information by means of databases and articles of scientific popularization were refined the structures of two compounds (NPCo and NPNi) obtained by powders diffraction; offering the possibility to develop a titled work: 'Physical description of the desorption of the water in nano structured material of nitrosyl penta cyano ferrates' which is carried out in parallel way to this thesis. This tools supplemented with the spectroscopic methods, potent the reach of the methods of diffraction of powders for the structural study of having been

  1. Summary of structural refinement in hi-silicon aluminium piston alloy with phosphorous as grain refiner

    Malik, F.A.; Sheikh, S.T.; Choudhry, A.A.

    2003-01-01

    Aluminium Silicon Alloys are extensively used in a wide variety of applications. There are numerous variables in composition, production control, final structure which can influence the mechanical properties of Hi - Silicon Piston alloys. Hypereutectic AlSi alloys develop coarse grain primary silicon crystals, which have a strong negative effect on the tensile strength, the ductility, and the hardness. These crystals slow machining and reduce the tool life considerably. Phosphorous addition produce a fine, evenly spread crystal structure, lamellar structure of the silicon changes into a granular structure. (author)

  2. Multilevel local refinement and multigrid methods for 3-D turbulent flow

    Liao, C.; Liu, C. [UCD, Denver, CO (United States); Sung, C.H.; Huang, T.T. [David Taylor Model Basin, Bethesda, MD (United States)

    1996-12-31

    A numerical approach based on multigrid, multilevel local refinement, and preconditioning methods for solving incompressible Reynolds-averaged Navier-Stokes equations is presented. 3-D turbulent flow around an underwater vehicle is computed. 3 multigrid levels and 2 local refinement grid levels are used. The global grid is 24 x 8 x 12. The first patch is 40 x 16 x 20 and the second patch is 72 x 32 x 36. 4th order artificial dissipation are used for numerical stability. The conservative artificial compressibility method are used for further improvement of convergence. To improve the accuracy of coarse/fine grid interface of local refinement, flux interpolation method for refined grid boundary is used. The numerical results are in good agreement with experimental data. The local refinement can improve the prediction accuracy significantly. The flux interpolation method for local refinement can keep conservation for a composite grid, therefore further modify the prediction accuracy.

  3. Grid refinement for aeroacoustics in the lattice Boltzmann method: A directional splitting approach

    Gendre, Félix; Ricot, Denis; Fritz, Guillaume; Sagaut, Pierre

    2017-08-01

    This study focuses on grid refinement techniques for the direct simulation of aeroacoustics, when using weakly compressible lattice Boltzmann models, such as the D3Q19 athermal velocity set. When it comes to direct noise computation, very small errors on the density or pressure field may have great negative consequences. Even strong acoustic density fluctuations have indeed a clearly lower amplitude than the hydrodynamic ones. This work deals with such very weak spurious fluctuations that emerge when a vortical structure crosses a refinement interface, which may contaminate the resulting aeroacoustic field. We show through an extensive literature review that, within the framework described above, this issue has never been addressed before. To tackle this problem, we develop an alternative algorithm and compare its behavior to a classical one, which fits our in-house vertex-centered data structure. Our main idea relies on a directional splitting of the continuous discrete velocity Boltzmann equation, followed by an integration over specific characteristics. This method can be seen as a specific coupling between finite difference and lattice Boltzmann, locally on the interface between the two grids. The method is assessed considering two cases: an acoustic pulse and a convected vortex. We show how very small errors on the density field arise and propagate throughout the domain when a vortical flow crosses the refinement interface. We also show that an increased free stream Mach number (but still within the weakly compressible regime) strongly deteriorates the situation, although the magnitude of the errors may remain negligible for purely aerodynamic studies. A drastically reduced level of error for the near-field spurious noise is obtained with our approach, especially for under-resolved simulations, a situation that is crucial for industrial applications. Thus, the vortex case is proved useful for aeroacoustic validations of any grid refinement algorithm.

  4. Unstructured Cartesian refinement with sharp interface immersed boundary method for 3D unsteady incompressible flows

    Angelidis, Dionysios; Chawdhary, Saurabh; Sotiropoulos, Fotis

    2016-11-01

    A novel numerical method is developed for solving the 3D, unsteady, incompressible Navier-Stokes equations on locally refined fully unstructured Cartesian grids in domains with arbitrarily complex immersed boundaries. Owing to the utilization of the fractional step method on an unstructured Cartesian hybrid staggered/non-staggered grid layout, flux mismatch and pressure discontinuity issues are avoided and the divergence free constraint is inherently satisfied to machine zero. Auxiliary/hanging nodes are used to facilitate the discretization of the governing equations. The second-order accuracy of the solver is ensured by using multi-dimension Lagrange interpolation operators and appropriate differencing schemes at the interface of regions with different levels of refinement. The sharp interface immersed boundary method is augmented with local near-boundary refinement to handle arbitrarily complex boundaries. The discrete momentum equation is solved with the matrix free Newton-Krylov method and the Krylov-subspace method is employed to solve the Poisson equation. The second-order accuracy of the proposed method on unstructured Cartesian grids is demonstrated by solving the Poisson equation with a known analytical solution. A number of three-dimensional laminar flow simulations of increasing complexity illustrate the ability of the method to handle flows across a range of Reynolds numbers and flow regimes. Laminar steady and unsteady flows past a sphere and the oblique vortex shedding from a circular cylinder mounted between two end walls demonstrate the accuracy, the efficiency and the smooth transition of scales and coherent structures across refinement levels. Large-eddy simulation (LES) past a miniature wind turbine rotor, parameterized using the actuator line approach, indicates the ability of the fully unstructured solver to simulate complex turbulent flows. Finally, a geometry resolving LES of turbulent flow past a complete hydrokinetic turbine illustrates

  5. Protein structure modeling and refinement by global optimization in CASP12.

    Hong, Seung Hwan; Joung, InSuk; Flores-Canales, Jose C; Manavalan, Balachandran; Cheng, Qianyi; Heo, Seungryong; Kim, Jong Yun; Lee, Sun Young; Nam, Mikyung; Joo, Keehyoung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

    2018-03-01

    For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain re-modeling. For better template selection and model selection, we updated our model quality assessment (QA) method with the newly developed SVMQA (support vector machine for quality assessment). For 3D chain building, we updated our energy function by including restraints generated from predicted residue-residue contacts. New energy terms for the predicted secondary structure and predicted solvent accessible surface area were also introduced. For difficult targets, we proposed a new method, LEEab, where the template term played a less significant role than it did in LEE, complemented by increased contributions from other terms such as the predicted contact term. For TBM (template-based modeling) targets, LEE performed better than LEEab, but for FM targets, LEEab was better. For model refinement, we modified our CASP11 molecular dynamics (MD) based protocol by using explicit solvents and tuning down restraint weights. Refinement results from MD simulations that used a new augmented statistical energy term in the force field were quite promising. Finally, when using inaccurate information (such as the predicted contacts), it was important to use the Lorentzian function for which the maximal penalty arising from wrong information is always bounded. © 2017 Wiley Periodicals, Inc.

  6. Ab initio structure determination and refinement of a scorpion protein toxin.

    Smith, G D; Blessing, R H; Ealick, S E; Fontecilla-Camps, J C; Hauptman, H A; Housset, D; Langs, D A; Miller, R

    1997-09-01

    The structure of toxin II from the scorpion Androctonus australis Hector has been determined ab initio by direct methods using SnB at 0.96 A resolution. For the purpose of this structure redetermination, undertaken as a test of the minimal function and the SnB program, the identity and sequence of the protein was withheld from part of the research team. A single solution obtained from 1 619 random atom trials was clearly revealed by the bimodal distribution of the final value of the minimal function associated with each individual trial. Five peptide fragments were identified from a conservative analysis of the initial E-map, and following several refinement cycles with X-PLOR, a model was built of the complete structure. At the end of the X-PLOR refinement, the sequence was compared with the published sequence and 57 of the 64 residues had been correctly identified. Two errors in sequence resulted from side chains with similar size while the rest of the errors were a result of severe disorder or high thermal motion in the side chains. Given the amino-acid sequence, it is estimated that the initial E-map could have produced a model containing 99% of all main-chain and 81% of side-chain atoms. The structure refinement was completed with PROFFT, including the contributions of protein H atoms, and converged at a residual of 0.158 for 30 609 data with F >or= 2sigma(F) in the resolution range 8.0-0.964 A. The final model consisted of 518 non-H protein atoms (36 disordered), 407 H atoms, and 129 water molecules (43 with occupancies less than unity). This total of 647 non-H atoms represents the largest light-atom structure solved to date.

  7. Structure of bound water and refinement of acid metmyoglobin

    Raghaven, N.V.; Schoenborn, B.P.

    1982-06-01

    The structure of myoglobin has been determined by x-ray diffraction for the acidmet, deoxy, and the oxy forms. Neutron diffraction work, done in this laboratory, has demonstrated that hydrogen and deuterium positions can be located. In addition to the localization of H and D, neutron diffraction provides a unique method for studying the water structure because of the strong scattering ability of D 2 O. The scattering factor of deuterium is nearly twice as large as that of hydrogen, and it increases the visibility of water molecules in Fourier maps, so that in a neutron map a water molecule appears about three times as strong as in an equivalent electron-density map. (DT)

  8. NMR structural refinement of an extrahelical adenosine tridecamer d(CGCAGAATTCGCG)2 via a hybrid relaxation matrix procedure

    Nikonowicz, E.P.; Meadows, R.P.; Gorenstein, D.G.

    1990-01-01

    Until very recently interproton distances from NOESY experiments have been derived solely from the two-spin approximation method. Unfortunately, even at short mixing times, there is a significant error in many of these distances. A complete relaxation matrix approach employing a matrix eigenvalue/eigenvector solution to the Bloch equations avoids the approximation of the two-spin method. The authors calculated the structure of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex, d-(CGCAGAATTCGCG) 2 , by an iterative refinement approach using a hybrid relaxation matrix method combined with restrained molecular dynamics calculations. Distances from the 2D NOESY spectra have been calculated from the relaxation rate matrix which has been evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix derived distances have then been used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure is then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete. Although the crystal structure of the tridecamer clearly shows the extrahelical adenosine looped out way from the duplex, the NOESY distance restrained hybrid matrix/molecular dynamics structural refinement establishes that the extrahelical adenosine stacks into the duplex

  9. Hybrid-hybrid matrix structural refinement of a DNA three-way junction from 3D NOESY-NOESY

    Thiviyanathan, Varatharasa; Luxon, Bruce A.; Leontis, Neocles B.; Illangasekare, Nishantha; Donne, David G.; Gorenstein, David G.

    1999-01-01

    Homonuclear 3D NOESY-NOESY has shown great promise for the structural refinement of large biomolecules. A computationally efficient hybrid-hybrid relaxation matrix refinement methodology, using 3D NOESY-NOESY data, was used to refine the structure of a DNA three-way junction having two unpaired bases at the branch point of the junction. The NMR data and the relaxation matrix refinement confirm that the DNA three-way junction exists in a folded conformation with two of the helical stems stacked upon each other. The third unstacked stem extends away from the junction, forming an acute angle (∼60 deg.) with the stacked stems. The two unpaired bases are stacked upon each other and are exposed to the solvent. Helical parameters for the bases in all three strands show slight deviations from typical values expected for right-handed B-form DNA. Inter-nucleotide imino-imino NOEs between the bases at the branch point of the junction show that the junction region is well defined. The helical stems show mobility (± 20 deg.) indicating dynamic processes around the junction region. The unstacked helical stem adjacent to the unpaired bases shows greater mobility compared to the other two stems. The results from this study indicate that the 3D hybrid-hybrid matrix MORASS refinement methodology, by combining the spectral dispersion of 3D NOESY-NOESY and the computational efficiency of 2D refinement programs, provides an accurate and robust means for structure determination of large biomolecules. Our results also indicate that the 3D MORASS method gives higher quality structures compared to the 2D complete relaxation matrix refinement method

  10. The Refining Mechanism of Super Gravity on the Solidification Structure of Al-Cu Alloys

    Yuhou Yang

    2016-12-01

    Full Text Available There is far less study of the refining effect of super gravity fields on solidification structures of metals than of the effects of electrical currents, magnetic and ultrasonic fields. Moreover, the refining mechanisms of super gravity are far from clear. This study applied a super gravity field to Al-Cu alloys to investigate its effect on refining their structures and the mechanism of interaction. The experimental results showed that the solidification structure of Al-Cu alloys can be greatly refined by a super gravity field. The major refining effect was mainly achieved when super gravity was applied at the initial solidification stage; only slight refinement could be obtained towards the end of solidification. No refinement was obtained by the super gravity treatment on pure liquid or solid stages. The effectiveness of super gravity results from its promoting the multiplication of crystal nuclei, which we call “Heavy Crystal Rain”, thereby greatly strengthening the migration of crystal nuclei within the alloy. Increasing the solute Cu content can increase nucleation density and restrict the growth of crystals, which further increases the refining effect of super gravity. Within this paper, we also discuss the motile behavior of crystals in a field of super gravity.

  11. A grid-enabled web service for low-resolution crystal structure refinement.

    O'Donovan, Daniel J; Stokes-Rees, Ian; Nam, Yunsun; Blacklow, Stephen C; Schröder, Gunnar F; Brunger, Axel T; Sliz, Piotr

    2012-03-01

    Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low-resolution X-ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.

  12. Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement

    Chen, Xiaorui; Lu, Mingyang; Poon, Billy K.; Wang, Qinghua; Ma, Jianpeng

    2009-01-01

    The structural model of the unliganded and fully glycosylated simian immunodeficiency virus gp120 core determined to 4.0 Å resolution was substantially improved using a recently developed normal-mode-based anisotropic B-factor refinement method. The envelope protein gp120/gp41 of simian and human immunodeficiency viruses plays a critical role in viral entry into host cells. However, the extraordinarily high structural flexibility and heavy glycosylation of the protein have presented enormous difficulties in the pursuit of high-resolution structural investigation of some of its conformational states. An unliganded and fully glycosylated gp120 core structure was recently determined to 4.0 Å resolution. The rather low data-to-parameter ratio limited refinement efforts in the original structure determination. In this work, refinement of this gp120 core structure was carried out using a normal-mode-based refinement method that has been shown in previous studies to be effective in improving models of a supramolecular complex at 3.42 Å resolution and of a membrane protein at 3.2 Å resolution. By using only the first four nonzero lowest-frequency normal modes to construct the anisotropic thermal parameters, combined with manual adjustments and standard positional refinement using REFMAC5, the structural model of the gp120 core was significantly improved in many aspects, including substantial decreases in R factors, better fitting of several flexible regions in electron-density maps, the addition of five new sugar rings at four glycan chains and an excellent correlation of the B-factor distribution with known structural flexibility. These results further underscore the effectiveness of this normal-mode-based method in improving models of protein and nonprotein components in low-resolution X-ray structures

  13. Topology Synthesis of Structures Using Parameter Relaxation and Geometric Refinement

    Hull, P. V.; Tinker, M. L.

    2007-01-01

    Typically, structural topology optimization problems undergo relaxation of certain design parameters to allow the existence of intermediate variable optimum topologies. Relaxation permits the use of a variety of gradient-based search techniques and has been shown to guarantee the existence of optimal solutions and eliminate mesh dependencies. This Technical Publication (TP) will demonstrate the application of relaxation to a control point discretization of the design workspace for the structural topology optimization process. The control point parameterization with subdivision has been offered as an alternative to the traditional method of discretized finite element design domain. The principle of relaxation demonstrates the increased utility of the control point parameterization. One of the significant results of the relaxation process offered in this TP is that direct manufacturability of the optimized design will be maintained without the need for designer intervention or translation. In addition, it will be shown that relaxation of certain parameters may extend the range of problems that can be addressed; e.g., in permitting limited out-of-plane motion to be included in a path generation problem.

  14. Refinement of the Fe4Al13 structure and its relationship to the quasihomological homeotypical structures

    Grin, J.; Burkhardt, U.; Ellner, M.; Peters, K.

    1994-01-01

    The crystal structure of Fe 4 Al 13 was refined using single crystal diffractometer data: pearson symbol mC102, space group C2/m; a=15.492(2) A, b=8.078(2) A, c=12.471(1) A, β=107.69(1) ; R F =0.053, R F (w)=0.044 for 1127 reflections and 137 refined parameters. The coordination numbers of atoms are 9, 10, 11 for iron and 10, 12, 13, 14 for aluminium. The shortest interatomic distances are: Fe-Fe - 2.902 A, Fe-Al - 2.374 A, Al-Al - 2.533 A. A preferred occupation of pentagonal prismatic coordinated positions by aluminium was found. The structural relationship between the Fe 4 Al 13 structure and chemically homologous and homeotypical structures of aluminium and gallium containing systems with the 3d transition metals is discussed. The greatest similarity was found concerning the coordination polyhedra, especially that of transition metal atoms. The main common feature of these homeotypical structures is the presence of pentagonal ''channels'', which is strongly dependent on the chemical composition. With increasing atomic number of the 3d transition metal, the stability range of these structures shifts to the transition metal-rich concentration. It is concluded that there is a connection between the occurrence of aluminium and gallium-containing decagonal and icosahedral phases and the existence of the infinite one-dimensional pentagonal channels in the intermetallic compounds showing a similar chemical composition. (orig.)

  15. Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures

    2014-01-01

    We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5–22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solution and in the crystal, all of the restrained Rosetta refined NMR structures were sufficiently accurate to be used for solving the corresponding X-ray crystal structures by molecular replacement. The protocol for restrained refinement of protein NMR structures was also compared with restrained CS-Rosetta calculations. For proteins smaller than 10 kDa, restrained CS-Rosetta, starting from extended conformations, provides slightly more accurate structures, while for proteins in the size range of 10–25 kDa the less CPU intensive restrained Rosetta refinement protocols provided equally or more accurate structures. The restrained Rosetta protocols described here can improve the accuracy of protein NMR structures and should find broad and general for studies of protein structure and function. PMID:24392845

  16. Lattice-Boltzmann Method with Dynamic Grid Refinement for Simulating Particle Deposition on a Single Fibre

    Helmut Schomburg

    2013-03-01

    Full Text Available In this work a numerical approach to predict the deposition behaviour of nano-scale particles on the surface of a single fibre by resolving the resulting dendrite-like particle structures in detail is presented. The gas flow simulation is carried out by a two-dimensional Lattice-Boltzmann method, which is coupled with a Lagrangian approach for the particle motion. To decrease calculation time and system requirements the Lattice-Boltzmann model is extended to allow for local grid refinement. Because of the a priori unknown location of deposition, the simulation procedure starts on a coarse mesh which is then locally refined in a fully adaptive way in regions of accumulated particles. After each deposition the fluid flow is recalculated in order to resolve the coupling of the flow with the growing particle structures correctly. For the purpose of avoiding unphysical blocking of flow by growing particle dendrites the Lattice-Boltzmann method is extended to permeable cells in these regions using the Brinkmann equation. This extended deposition model is compared to simpler approaches, where the deposit has no retroaction on the flow or is treated as a solid structure. It is clear that the permeable model is most realistic and allows considering the particle deposition on a fibre as two-dimensional problem. Comprehensive simulations were conducted for analysing the importance of different parameters, i.e. free-stream velocity and particle diameter on the deposit structure. The results of this sensitivity analysis agree qualitatively well with former published numerical and experimental results. Finally the structure of the particle deposit was quantitatively characterised by using a modified fractal dimension.

  17. A melt refining method for uranium-contaminated aluminum

    Uda, T.; Iba, H.; Hanawa, K.

    1986-01-01

    Melt refining of uranium-contaminated aluminum which has been difficult to decontaminate because of the high reactivity of aluminum, was experimentally studied. Samples of contaminated aluminum and its alloys were melted after adding various halide fluxes at various melting temperatures and various melting times. Uranium concentration in the resulting ingots was determined. Effective flux compositions were mixtures of chlorides and fluorides, such as LiF, KCl, and BaCl 2 , at a fluoride/chloride mole ratio of 1 to 1.5. The removal of uranium from aluminum (the ''decontamination effect'') increased with decreasing melting temperature, but the time allowed for reaction had little influence. Pure aluminum was difficult to decontaminate from uranium; however, uranium could be removed from alloys containing magnesium. This was because the activity of the aluminum was decreased by formation of the intermetallic compound Al-Mg. With a flux of LiF-KCl-BaCl 2 and a temperature of 800 0 C, uranium added to give an initial concentration of 500 ppm was removed from a commercial alloy of aluminum, A5056, which contains 5% magnesium, to a final concentration of 0.6 ppm, which is near that in the initial aluminum alloy

  18. Repetitive Identification of Structural Systems Using a Nonlinear Model Parameter Refinement Approach

    Jeng-Wen Lin

    2009-01-01

    Full Text Available This paper proposes a statistical confidence interval based nonlinear model parameter refinement approach for the health monitoring of structural systems subjected to seismic excitations. The developed model refinement approach uses the 95% confidence interval of the estimated structural parameters to determine their statistical significance in a least-squares regression setting. When the parameters' confidence interval covers the zero value, it is statistically sustainable to truncate such parameters. The remaining parameters will repetitively undergo such parameter sifting process for model refinement until all the parameters' statistical significance cannot be further improved. This newly developed model refinement approach is implemented for the series models of multivariable polynomial expansions: the linear, the Taylor series, and the power series model, leading to a more accurate identification as well as a more controllable design for system vibration control. Because the statistical regression based model refinement approach is intrinsically used to process a “batch” of data and obtain an ensemble average estimation such as the structural stiffness, the Kalman filter and one of its extended versions is introduced to the refined power series model for structural health monitoring.

  19. Solid state synthesis and structural refinement of polycrystalline La ...

    Perovskite structure based ceramic precursors have a characteristic property of substitution in the ``A" site of the ABO3 structure. This makes them a potential material for nuclear waste management in synthetic rock (SYNROC) technology. In order to simulate the mechanism of rare earth fixation in perovskite, La ...

  20. Refinement of grain structure in 20 MnNiMo (SA508C) steel

    Sheng Zhongqi; Xiao Hong; Peng Feng; Zou Min

    1997-04-01

    The size of prior austenite grains and bainitic colonies of 20 MnNiMo (SA508C) steel (a reactor pressure vessel steel) after normal heat treatment is measured and its controlling factors are discussed. Results show that low aluminium content can induce serious mixed structure with fine and coarse grains in prior austenite. Fast cooling rate can promote refinement of bainitic colonies. Further refinement of grains can be obtained by inter-critical quenching. (5 figs., 1 tab.)

  1. Spatially adaptive hp refinement approach for PN neutron transport equation using spectral element method

    Nahavandi, N.; Minuchehr, A.; Zolfaghari, A.; Abbasi, M.

    2015-01-01

    Highlights: • Powerful hp-SEM refinement approach for P N neutron transport equation has been presented. • The method provides great geometrical flexibility and lower computational cost. • There is a capability of using arbitrary high order and non uniform meshes. • Both posteriori and priori local error estimation approaches have been employed. • High accurate results are compared against other common adaptive and uniform grids. - Abstract: In this work we presented the adaptive hp-SEM approach which is obtained from the incorporation of Spectral Element Method (SEM) and adaptive hp refinement. The SEM nodal discretization and hp adaptive grid-refinement for even-parity Boltzmann neutron transport equation creates powerful grid refinement approach with high accuracy solutions. In this regard a computer code has been developed to solve multi-group neutron transport equation in one-dimensional geometry using even-parity transport theory. The spatial dependence of flux has been developed via SEM method with Lobatto orthogonal polynomial. Two commonly error estimation approaches, the posteriori and the priori has been implemented. The incorporation of SEM nodal discretization method and adaptive hp grid refinement leads to high accurate solutions. Coarser meshes efficiency and significant reduction of computer program runtime in comparison with other common refining methods and uniform meshing approaches is tested along several well-known transport benchmarks

  2. “Best fit” framework synthesis: refining the method

    2013-01-01

    Background Following publication of the first worked example of the “best fit” method of evidence synthesis for the systematic review of qualitative evidence in this journal, the originators of the method identified a need to specify more fully some aspects of this particular derivative of framework synthesis. Methods and Results We therefore present a second such worked example in which all techniques are defined and explained, and their appropriateness is assessed. Specified features of the method include the development of new techniques to identify theories in a systematic manner; the creation of an a priori framework for the synthesis; and the “testing” of the synthesis. An innovative combination of existing methods of quality assessment, analysis and synthesis is used to complete the process. This second worked example was a qualitative evidence synthesis of employees’ views of workplace smoking cessation interventions, in which the “best fit” method was found to be practical and fit for purpose. Conclusions The method is suited to producing context-specific conceptual models for describing or explaining the decision-making and health behaviours of patients and other groups. It offers a pragmatic means of conducting rapid qualitative evidence synthesis and generating programme theories relating to intervention effectiveness, which might be of relevance both to researchers and policy-makers. PMID:23497061

  3. Refining a Heuristic for Constructing Bayesian Networks from Structured Arguments

    Wieten, G.M.; Bex, F.J.; van der Gaag, L.C.; Prakken, H.; Renooij, S.

    2018-01-01

    Recently, a heuristic was proposed for constructing Bayesian networks (BNs) from structured arguments. This heuristic helps domain experts who are accustomed to argumentation to transform their reasoning into a BN and subsequently weigh their case evidence in a probabilistic manner. While the

  4. TOWARDS A REFINED STRUCTURE OF PERSONALITY-TRAITS

    DERAAD, B; HENDRIKS, AAJ; HOFSTEE, WKB

    1992-01-01

    In this article we pursue two goals. The first is a further articulation of the dimensionality of the Dutch trait domain. The second is a detailed mapping of the factorial trait structure, one which includes intelligible and proper niches for various nuances of the trait language and for different

  5. Refining femtosecond laser induced periodical surface structures with liquid assist

    Jiao, L.S.; Ng, E.Y.K.; Zheng, H.Y.

    2013-01-01

    Highlights: ► LIPSS on silicon wafer was made in air and in ethanol environment. ► Ethanol environment produce cleaner surface ripples. ► Ethanol environment decrease spatial wavelength of the LIPSS by 30%. ► More number of pulses produce smaller spatial wavelength in air. ► Number of pulses do not influence spatial wavelength in ethanol environment. - Abstract: Laser induced periodic surface structures were generated on silicon wafer using femtosecond laser. The medium used in this study is both air and ethanol. The laser process parameters such as wavelength, number of pulse, laser fluence were kept constant for both the mediums. The focus of the study is to analyze spatial wavelength. When generating surface structures with air as a medium and same process parameter of the laser, spatial wavelength results showed a 30% increase compared to ethanol. The cleanliness of the surface generated using ethanol showed considerably less debris than in air. The results observed from the above investigation showed that the medium plays a predominant role in the generation of surface structures.

  6. Synthesis of Al-5Ti-1B Refiner by Melt Reaction Method

    LI He; CHAI Li-hua; MA Teng-fei; CHEN Zi-yong

    2017-01-01

    Al-5Ti-1B refiner was successfully prepared by melt reaction method. Through the thermodynamics calculation, the initial reaction temperature was determined. The influence of reaction temperature on microstructure and absorption rate of the alloy was investigated. The phase and microstructure of the alloy were observed by X-ray diffraction, scanning electron microscope and energy dispersive spectrometer. The Al-5Ti-1B refiner was extruded at high temperature to wire with the diameter of 9.5mm...

  7. Methods of refining natural oils, and methods of producing fuel compositions

    Firth, Bruce E.; Kirk, Sharon E.

    2015-10-27

    A method of refining a natural oil includes: (a) providing a feedstock that includes a natural oil; (b) reacting the feedstock in the presence of a metathesis catalyst to form a metathesized product that includes olefins and esters; (c) passivating residual metathesis catalyst with an agent that comprises nitric acid; (d) separating the olefins in the metathesized product from the esters in the metathesized product; and (e) transesterifying the esters in the presence of an alcohol to form a transesterified product and/or hydrogenating the olefins to form a fully or partially saturated hydrogenated product. Methods for suppressing isomerization of olefin metathesis products produced in a metathesis reaction, and methods of producing fuel compositions are described.

  8. Automating crystallographic structure solution and refinement of protein–ligand complexes

    Echols, Nathaniel; Moriarty, Nigel W.; Klei, Herbert E.; Afonine, Pavel V.; Bunkóczi, Gábor; Headd, Jeffrey J.; McCoy, Airlie J.; Oeffner, Robert D.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

    2013-01-01

    A software system for automated protein–ligand crystallography has been implemented in the Phenix suite. This significantly reduces the manual effort required in high-throughput crystallographic studies. High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation

  9. Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.

    Mark A Olson

    Full Text Available A central problem of computational structural biology is the refinement of modeled protein structures taken from either comparative modeling or knowledge-based methods. Simulations are commonly used to achieve higher resolution of the structures at the all-atom level, yet methodologies that consistently yield accurate results remain elusive. In this work, we provide an assessment of an adaptive temperature-based replica exchange simulation method where the temperature clients dynamically walk in temperature space to enrich their population and exchanges near steep energetic barriers. This approach is compared to earlier work of applying the conventional method of static temperature clients to refine a dataset of conformational decoys. Our results show that, while an adaptive method has many theoretical advantages over a static distribution of client temperatures, only limited improvement was gained from this strategy in excursions of the downhill refinement regime leading to an increase in the fraction of native contacts. To illustrate the sampling differences between the two simulation methods, energy landscapes are presented along with their temperature client profiles.

  10. Usability Testing as a Method to Refine a Health Sciences Library Website.

    Denton, Andrea H; Moody, David A; Bennett, Jason C

    2016-01-01

    User testing, a method of assessing website usability, can be a cost-effective and easily administered process to collect information about a website's effectiveness. A user experience (UX) team at an academic health sciences library has employed user testing for over three years to help refine the library's home page. Test methodology used in-person testers using the "think aloud" method to complete tasks on the home page. Review of test results revealed problem areas of the design and redesign; further testing was effective in refining the page. User testing has proved to be a valuable method to engage users and provide feedback to continually improve the library's home page.

  11. Detecting Difference between Process Models Based on the Refined Process Structure Tree

    Jing Fan

    2017-01-01

    Full Text Available The development of mobile workflow management systems (mWfMS leads to large number of business process models. In the meantime, the location restriction embedded in mWfMS may result in different process models for a single business process. In order to help users quickly locate the difference and rebuild the process model, detecting the difference between different process models is needed. Existing detection methods either provide a dissimilarity value to represent the difference or use predefined difference template to generate the result, which cannot reflect the entire composition of the difference. Hence, in this paper, we present a new approach to solve this problem. Firstly, we parse the process models to their corresponding refined process structure trees (PSTs, that is, decomposing a process model into a hierarchy of subprocess models. Then we design a method to convert the PST to its corresponding task based process structure tree (TPST. As a consequence, the problem of detecting difference between two process models is transformed to detect difference between their corresponding TPSTs. Finally, we obtain the difference between two TPSTs based on the divide and conquer strategy, where the difference is described by an edit script and we make the cost of the edit script close to minimum. The extensive experimental evaluation shows that our method can meet the real requirements in terms of precision and efficiency.

  12. A simple nodal force distribution method in refined finite element meshes

    Park, Jai Hak [Chungbuk National University, Chungju (Korea, Republic of); Shin, Kyu In [Gentec Co., Daejeon (Korea, Republic of); Lee, Dong Won [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Cho, Seungyon [National Fusion Research Institute, Daejeon (Korea, Republic of)

    2017-05-15

    In finite element analyses, mesh refinement is frequently performed to obtain accurate stress or strain values or to accurately define the geometry. After mesh refinement, equivalent nodal forces should be calculated at the nodes in the refined mesh. If field variables and material properties are available at the integration points in each element, then the accurate equivalent nodal forces can be calculated using an adequate numerical integration. However, in certain circumstances, equivalent nodal forces cannot be calculated because field variable data are not available. In this study, a very simple nodal force distribution method was proposed. Nodal forces of the original finite element mesh are distributed to the nodes of refined meshes to satisfy the equilibrium conditions. The effect of element size should also be considered in determining the magnitude of the distributing nodal forces. A program was developed based on the proposed method, and several example problems were solved to verify the accuracy and effectiveness of the proposed method. From the results, accurate stress field can be recognized to be obtained from refined meshes using the proposed nodal force distribution method. In example problems, the difference between the obtained maximum stress and target stress value was less than 6 % in models with 8-node hexahedral elements and less than 1 % in models with 20-node hexahedral elements or 10-node tetrahedral elements.

  13. Modeling and optimization of the european oil refining capacities and structures on the horizons 1995, 2000 and 2010

    Khebri, S.

    1993-04-01

    This thesis is a study on petroleum refining. In a first part, the author describes the existing refining processes and the structure of refining units, the structure of petroleum consumption and the interfaces with petroleum chemistry industry and gives a retrospect on world and european petroleum refining. In a second part, the author describes the models used to realize the simulation of supplies, market and refining scheme. Four scenarios are developed (conventional wisdom, driving into tensions, sustaining a high economic growth, high prices) and a forecasting on the horizons 1995, 2000 and 2010 is given. 54 refs

  14. Grid refinement model in lattice Boltzmann method for stream function-vorticity formulations

    Shin, Myung Seob [Dept. of Mechanical Engineering, Dongyang Mirae University, Seoul (Korea, Republic of)

    2015-03-15

    In this study, we present a grid refinement model in the lattice Boltzmann method (LBM) for two-dimensional incompressible fluid flow. That is, the model combines the desirable features of the lattice Boltzmann method and stream function-vorticity formulations. In order to obtain an accurate result, very fine grid (or lattice) is required near the solid boundary. Therefore, the grid refinement model is used in the lattice Boltzmann method for stream function-vorticity formulation. This approach is more efficient in that it can obtain the same accurate solution as that in single-block approach even if few lattices are used for computation. In order to validate the grid refinement approach for the stream function-vorticity formulation, the numerical simulations of lid-driven cavity flows were performed and good results were obtained.

  15. Analysis and development of spatial hp-refinement methods for solving the neutron transport equation

    Fournier, D.

    2011-01-01

    The different neutronic parameters have to be calculated with a higher accuracy in order to design the 4. generation reactor cores. As memory storage and computation time are limited, adaptive methods are a solution to solve the neutron transport equation. The neutronic flux, solution of this equation, depends on the energy, angle and space. The different variables are successively discretized. The energy with a multigroup approach, considering the different quantities to be constant on each group, the angle by a collocation method called SN approximation. Once the energy and angle variable are discretized, a system of spatially-dependent hyperbolic equations has to be solved. Discontinuous finite elements are used to make possible the development of hp-refinement methods. Thus, the accuracy of the solution can be improved by spatial refinement (h-refinement), consisting into subdividing a cell into sub-cells, or by order refinement (p-refinement), by increasing the order of the polynomial basis. In this thesis, the properties of this methods are analyzed showing the importance of the regularity of the solution to choose the type of refinement. Thus, two error estimators are used to lead the refinement process. Whereas the first one requires high regularity hypothesis (analytical solution), the second one supposes only the minimal hypothesis required for the solution to exist. The comparison of both estimators is done on benchmarks where the analytic solution is known by the method of manufactured solutions. Thus, the behaviour of the solution as a regard of the regularity can be studied. It leads to a hp-refinement method using the two estimators. Then, a comparison is done with other existing methods on simplified but also realistic benchmarks coming from nuclear cores. These adaptive methods considerably reduces the computational cost and memory footprint. To further improve these two points, an approach with energy-dependent meshes is proposed. Actually, as the

  16. Refinement of homology-based protein structures by molecular dynamics simulation techniques

    Fan, H; Mark, AE

    The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to

  17. Iterative model-building, structure refinement, and density modification with the PHENIX AutoBuild Wizard

    Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720, USA; Department of Haematology, University of Cambridge, Cambridge CB2 0XY, England; Terwilliger, Thomas; Terwilliger, T.C.; Grosse-Kunstleve, Ralf Wilhelm; Afonine, P.V.; Moriarty, N.W.; Zwart, P.H.; Hung, L.-W.; Read, R.J.; Adams, P.D.

    2007-04-29

    The PHENIX AutoBuild Wizard is a highly automated tool for iterative model-building, structure refinement and density modification using RESOLVE or TEXTAL model-building, RESOLVE statistical density modification, and phenix.refine structure refinement. Recent advances in the AutoBuild Wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model completion algorithms, and automated solvent molecule picking. Model completion algorithms in the AutoBuild Wizard include loop-building, crossovers between chains in different models of a structure, and side-chain optimization. The AutoBuild Wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 {angstrom} to 3.2 {angstrom}, resulting in a mean R-factor of 0.24 and a mean free R factor of 0.29. The R-factor of the final model is dependent on the quality of the starting electron density, and relatively independent of resolution.

  18. Valence electron structure analysis of refining mecha-nism of Sc and Ti additions on aluminum

    LI PieJie; YE YiCong; HE LiangJu

    2009-01-01

    The mechanism of the difference of refining effect between Sc and Ti adding to aluminum can not be explained substantially with traditional theory. Valence electron structures of AI-Ti and Al-Sc alloys have been studied by using the empirical electron theory of solids and molecules (EET). The covalent bond electron numbers and interfacial electron density differences are calculated. The conclusion is that, in the two alloys, different covalent bond electron numbers of nucleation particles, and different electron densities on the interface between the second phase particles and the matrix, fundamentally lead to the difference of refining effect between Sc and Ti adding to aluminum.

  19. Wavelet-based Adaptive Mesh Refinement Method for Global Atmospheric Chemical Transport Modeling

    Rastigejev, Y.

    2011-12-01

    Numerical modeling of global atmospheric chemical transport presents enormous computational difficulties, associated with simulating a wide range of time and spatial scales. The described difficulties are exacerbated by the fact that hundreds of chemical species and thousands of chemical reactions typically are used for chemical kinetic mechanism description. These computational requirements very often forces researches to use relatively crude quasi-uniform numerical grids with inadequate spatial resolution that introduces significant numerical diffusion into the system. It was shown that this spurious diffusion significantly distorts the pollutant mixing and transport dynamics for typically used grid resolution. The described numerical difficulties have to be systematically addressed considering that the demand for fast, high-resolution chemical transport models will be exacerbated over the next decade by the need to interpret satellite observations of tropospheric ozone and related species. In this study we offer dynamically adaptive multilevel Wavelet-based Adaptive Mesh Refinement (WAMR) method for numerical modeling of atmospheric chemical evolution equations. The adaptive mesh refinement is performed by adding and removing finer levels of resolution in the locations of fine scale development and in the locations of smooth solution behavior accordingly. The algorithm is based on the mathematically well established wavelet theory. This allows us to provide error estimates of the solution that are used in conjunction with an appropriate threshold criteria to adapt the non-uniform grid. Other essential features of the numerical algorithm include: an efficient wavelet spatial discretization that allows to minimize the number of degrees of freedom for a prescribed accuracy, a fast algorithm for computing wavelet amplitudes, and efficient and accurate derivative approximations on an irregular grid. The method has been tested for a variety of benchmark problems

  20. Synthesis of Al-5Ti-1B Refiner by Melt Reaction Method

    LI He

    2017-02-01

    Full Text Available Al-5Ti-1B refiner was successfully prepared by melt reaction method. Through the thermodynamics calculation, the initial reaction temperature was determined. The influence of reaction temperature on microstructure and absorption rate of the alloy was investigated. The phase and microstructure of the alloy were observed by X-ray diffraction, scanning electron microscope and energy dispersive spectrometer. The Al-5Ti-1B refiner was extruded at high temperature to wire with the diameter of 9.5mm, and then the refinement experiment was carried out on pure aluminium. The results indicate that the refiner consists of TiB2, TiAl3 and α-Al, and the microstructure prepared at 850℃ is the optimum and the absorption rate of Ti and B matches the best. The TiAl3 and TiB2 phases distribute homogeneously in the matrix after extrusion. When adding 0.2%(mass fraction of Al-5Ti-1B refiner, the grain size of pure aluminium reduces from 3.99mm to 0.45mm.

  1. Refining Nodes and Edges of State Machines

    Hallerstede, Stefan; Snook, Colin

    2011-01-01

    State machines are hierarchical automata that are widely used to structure complex behavioural specifications. We develop two notions of refinement of state machines, node refinement and edge refinement. We compare the two notions by means of examples and argue that, by adopting simple conventions...... refinement theory and UML-B state machine refinement influences the style of node refinement. Hence we propose a method with direct proof of state machine refinement avoiding the detour via Event-B that is needed by UML-B....

  2. Fluid bilayer structure determination: Joint refinement in composition space using X-ray and neutron diffraction data

    White, S.H. [Univ. of California, Irvine, CA (United States); Wiener, M.C. [Univ. of California, San Francisco, CA (United States)

    1994-12-31

    Experimentally-determined structural models of fluid lipid bilayers are essential for verifying molecular dynamics simulations of bilayers and for understanding the structural consequences of peptide interactions. The extreme thermal motion of bilayers precludes the possibility of atomic-level structural models. Defining {open_quote}the structure{close_quote} of a bilayer as the time-averaged transbilayer distribution of the water and the principal lipid structural groups such as the carbonyls and double-bonds (quasimolecular fragments), one can represent the bilayer structure as a sum of Gaussian functions referred to collectively as the quasimolecular structure. One method of determining the structure is by neutron diffraction combined with exhaustive specific deuteration. This method is impractical because of the expense of the chemical syntheses and the limited amount of neutron beam time currently available. We have therefore developed the composition space refinement method for combining X-ray and minimal neutron diffraction data to arrive at remarkably detailed and accurate structures of fluid bilayers. The composition space representation of the bilayer describes the probability of occupancy per unit length across the width of the bilayer of each quasimolecular component and permits the joint refinement of X-ray and neutron lamellar diffraction data by means of a single quasimolecular structure that is fitted simultaneously to both data sets. Scaling of each component by the appropriate neutron or X-ray scattering length maps the composition-space profile to the appropriate scattering length space for comparison to experimental data. The difficulty with the method is that fluid bilayer structures are generally only marginally determined by the experimental data. This means that the space of possible solutions must be extensively explored in conjunction with a thorough analysis of errors.

  3. Fluid bilayer structure determination: Joint refinement in composition space using X-ray and neutron diffraction data

    White, S.H.; Wiener, M.C.

    1994-01-01

    Experimentally-determined structural models of fluid lipid bilayers are essential for verifying molecular dynamics simulations of bilayers and for understanding the structural consequences of peptide interactions. The extreme thermal motion of bilayers precludes the possibility of atomic-level structural models. Defining open-quote the structure close-quote of a bilayer as the time-averaged transbilayer distribution of the water and the principal lipid structural groups such as the carbonyls and double-bonds (quasimolecular fragments), one can represent the bilayer structure as a sum of Gaussian functions referred to collectively as the quasimolecular structure. One method of determining the structure is by neutron diffraction combined with exhaustive specific deuteration. This method is impractical because of the expense of the chemical syntheses and the limited amount of neutron beam time currently available. We have therefore developed the composition space refinement method for combining X-ray and minimal neutron diffraction data to arrive at remarkably detailed and accurate structures of fluid bilayers. The composition space representation of the bilayer describes the probability of occupancy per unit length across the width of the bilayer of each quasimolecular component and permits the joint refinement of X-ray and neutron lamellar diffraction data by means of a single quasimolecular structure that is fitted simultaneously to both data sets. Scaling of each component by the appropriate neutron or X-ray scattering length maps the composition-space profile to the appropriate scattering length space for comparison to experimental data. The difficulty with the method is that fluid bilayer structures are generally only marginally determined by the experimental data. This means that the space of possible solutions must be extensively explored in conjunction with a thorough analysis of errors

  4. Neutron powder diffraction and theory-aided structure refinement of rubidium and cesium ureate

    Sterri, Kjersti B.; Deringer, Volker L.; Houben, Andreas; Jacobs, Philipp [RWTH Aachen Univ. (Germany). Inst. of Inorganic Chemistry; Kumar, Chogondahalli M.N. [Forschungszentrum Juelich GmbH, Juelich Centre for Neutron Science (JCNS), Outstation at SNS, Oak Ridge National Laboratory, Oak Ridge, TN (United States); Oak Ridge National Laboratory, TN (United States). Chemical and Engineering Materials Div.; Dronskowski, Richard [RWTH Aachen Univ. (Germany). Inst. of Inorganic Chemistry; RWTH Aachen Univ. (Germany). Juelich-Aachen Research Alliance (JARA-HPC)

    2016-08-01

    Urea (CN{sub 2}H{sub 4}O) is a fundamental biomolecule whose derivatives are abundant throughout chemistry. Among the latter, rubidium ureate (RbCN{sub 2}H{sub 3}O) and its cesium analog (CsCN{sub 2}H{sub 3}O) have been described only very recently and form the first structurally characterized salts of deprotonated urea. Here, we report on a neutron diffraction study on the aforementioned alkaline-metal ureates, which affords the positions for all hydrogen atoms (including full anisotropic displacement tensors) and thus allows us to gain fundamental insights into the hydrogen-bonding networks in the title compounds. The structure refinements of the experimental neutron data proceeded successfully using starting parameters from ab initio simulations of atomic positions and anisotropic displacement parameters. Such joint experimental-theoretical refinement procedures promise significant practical potential in cases where complex solids (organic, organometallic, framework materials) are studied by powder diffraction.

  5. Dense and refined microstructure 3D measurement method based on an optical microscope and varying illuminations

    Li, Zhongwei; Li, Y F

    2011-01-01

    We propose a novel microscopic photometric stereo (MPS) method based on a conventional optical microscope and varying illuminations for dense and refined microstructure 3D measurement. To guarantee the flexibility of the MPS, an uncalibrated photometric stereo (UPS) method, which does not require a priori knowledge of the light-source direction or the light-source intensity, is employed to recover surface normals and albedos from the captured multiple micro-images. Although the UPS has been studied before, there are some particular issues to be addressed to make it suitable for microscopic cases. For resolving the inherent generalized bas-relief (GBR) ambiguity of the UPS, we present a GBR disambiguation method based on a framework of entropy minimization, and extend it using a graph-cut energy minimization to decrease the influence of noise and further refine the recovered surface normal. The proposed MPS method has been tested on synthetic as well as real images and very encouraging results have been obtained. The experimental results show that this novel method can reconstruct dense and refined 3D points for the microstructure. It is an easy-to-implement yet effective alternative method for microstructure 3D measurement and can be applied to many potential fields

  6. Latest Developments in Data Analysis and Structure Determination and Refinement: Software for Chemical Crystallography

    Dix, I.; Adam, M.; Jacob, H. F.; Roter, A.

    2003-01-01

    The introduction of a two-dimensional CCD X-ray detector nearly 10 years ago by Bruker started a revolution in chemical crystallography. Since then, crystallographers can accomplish a complete data collection even of small and poorly scattering crystals in a few hours instead of days. The launch of the kappa geometry by Nonius a few years ago beforehand equally revolutionized the field of single crystal diffractometry. Currently Bruker Nonius has far more than 500 CCD systems installed. The latest development of Bruker Nonius, the X8 APEX, is the powerful combination of both: the APEX CCD detector and the unique Kappa four-circle goniometer. The APEX 4K CCD detector provides the utmost sensitivity, while the Kappa four-circle goniometer offers a very open geometry, granting all the flexibility to align any crystallographic axis. This provides a more efficient data collection for axial photographs to investigate e.g. diffuse scattering or incommensurate structures. Even the crystal-detector distance is computer-controlled for precise and superior data collection. The X8 APEX software suite gives a whole new look to the CCD users interface. It not only has improved data collection abilities, but also guides the chemist or mineralogist through gathering the raw crystal data to producing the final crystal structure. It provides context-dependent menus, which are well-known from business software packages such as Outlook. The tools for unit cell determination, views into reciprocal space, optimisation of the data collection strategy, data integration, scaling and correcting (SADABS) as well as tools for structure solving and refining (SHELXTL package) will be presented. Low temperature work has become an essential tool for challenging samples. The Bruker Nonius Kryo-Flex cryogenic device makes chemical crystallography at low temperatures a routine method in your laboratory. Of course, the Kryo-Flex is fully controlled by the new graphical user interface of the X8 APEX

  7. A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs.

    Kumbhar, Sadhana; Johannsen, Silke; Sigel, Roland K O; Waller, Mark P; Müller, Jens

    2013-10-01

    A series of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations was performed on models of a DNA duplex with artificial silver(I)-mediated imidazole base pairs. The optimized structures were compared to the original experimental NMR structure (Nat. Chem. 2 (2010) 229-234). The metal⋯metal distances are significantly shorter (~0.5Å) in the QM/MM model than in the original NMR structure. As a result, argentophilic interactions are feasible between the silver(I) ions of neighboring metal-mediated base pairs. Using the computationally determined metal⋯metal distances, a re-refined NMR solution structure of the DNA duplex was obtained. In this new NMR structure, all experimental constraints remain fulfilled. The new NMR structure shows less deviation from the regular B-type conformation than the original one. This investigation shows that the application of QM/MM models to generate additional constraints to be used during NMR structural refinements represents an elegant approach to obtaining high-resolution NMR structures. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Modulation wave approach to the structural parameterization and Rietveld refinement of low carnegieite

    Withers, R.L.; Thompson, J.G.

    1993-01-01

    The crystal structure of low carnegieite, NaAlSiO 4 [M r =142.05, orthorhombic, Pb2 1 a, a=10.261(1), b=14.030(2), c=5.1566(6) A, D x =2.542 g cm -3 , Z=4, Cu Kα 1 , λ=1.5406 A, μ=77.52 cm -1 , F(000)=559.85], is determined via Rietveld refinement from powder data, R p =0.057, R wp =0.076, R Bragg =0.050. Given that there are far too many parameters to be determined via unconstrained Rietveld refinement, a group theoretical or modulation wave approach is used in order to parameterize the structural deviation of low carnegieite from its underlying C9 aristotype. Appropriate crystal chemical constraints are applied in order to provide two distinct plausible starting models for the structure of the aluminosilicate framework. The correct starting model for the aluminosilicate framework as well as the ordering and positions of the non-framework Na atoms are then determined via Rietveld refinement. At all stages, chemical plausibility is checked via the use of the bond-length-bond-valence formalism. The JCPDS file number for low carnegieite is 44-1496. (orig.)

  9. Refined algebraic quantisation in a system with nonconstant gauge invariant structure functions

    Martínez-Pascual, Eric

    2013-01-01

    In a previous work [J. Louko and E. Martínez-Pascual, “Constraint rescaling in refined algebraic quantisation: Momentum constraint,” J. Math. Phys. 52, 123504 (2011)], refined algebraic quantisation (RAQ) within a family of classically equivalent constrained Hamiltonian systems that are related to each other by rescaling one momentum-type constraint was investigated. In the present work, the first steps to generalise this analysis to cases where more constraints occur are developed. The system under consideration contains two momentum-type constraints, originally abelian, where rescalings of these constraints by a non-vanishing function of the coordinates are allowed. These rescalings induce structure functions at the level of the gauge algebra. Providing a specific parametrised family of real-valued scaling functions, the implementation of the corresponding rescaled quantum momentum-type constraints is performed using RAQ when the gauge algebra: (i) remains abelian and (ii) undergoes into an algebra of a nonunimodular group with nonconstant gauge invariant structure functions. Case (ii) becomes the first example known to the author where an open algebra is handled in refined algebraic quantisation. Challenging issues that arise in the presence of non-gauge invariant structure functions are also addressed

  10. An assessment of dietary exposure to glyphosate using refined deterministic and probabilistic methods.

    Stephenson, C L; Harris, C A

    2016-09-01

    Glyphosate is a herbicide used to control broad-leaved weeds. Some uses of glyphosate in crop production can lead to residues of the active substance and related metabolites in food. This paper uses data on residue levels, processing information and consumption patterns, to assess theoretical lifetime dietary exposure to glyphosate. Initial estimates were made assuming exposure to the highest permitted residue levels in foods. These intakes were then refined using median residue levels from trials, processing information, and monitoring data to achieve a more realistic estimate of exposure. Estimates were made using deterministic and probabilistic methods. Exposures were compared to the acceptable daily intake (ADI)-the amount of a substance that can be consumed daily without an appreciable health risk. Refined deterministic intakes for all consumers were at or below 2.1% of the ADI. Variations were due to cultural differences in consumption patterns and the level of aggregation of the dietary information in calculation models, which allows refinements for processing. Probabilistic exposure estimates ranged from 0.03% to 0.90% of the ADI, depending on whether optimistic or pessimistic assumptions were made in the calculations. Additional refinements would be possible if further data on processing and from residues monitoring programmes were available. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. Noise bias in the refinement of structures derived from single particles

    Stewart, Alex; Grigorieff, Nikolaus

    2004-01-01

    One of the main goals in the determination of three-dimensional macromolecular structures from electron microscope images of individual molecules and complexes (single particles) is a sufficiently high spatial resolution, about 4 A, at which the interpretation with an atomic model becomes possible. To reach high resolution, an iterative refinement procedure using an expectation maximization algorithm is often used that leads to a more accurate alignment of the positional and orientational parameters for each particle. We show here the results of refinement algorithms that use a phase residual, a linear correlation coefficient, or a weighted correlation coefficient to align individual particles. The algorithms were applied to computer-generated data sets that contained projections from model structures, as well as noise. The algorithms show different degrees of over-fitting, especially at high resolution where the signal is weak. We demonstrate that the degree of over-fitting is reduced with a weighting scheme that depends on the signal-to-noise ratio in the data. The weighting also improves the accuracy of resolution measurement by the commonly used Fourier shell correlation. The performance of the refinement algorithms is compared to that using a maximum likelihood approach. The weighted correlation coefficient was implemented in the computer program FREALIGN

  12. Structural refinement, photoluminescence and Raman spectroscopy of wurtzite Mn-doped Zn O pellets

    Marquina, J.; Martin, J.; Luengo, J.; Vera, F.; Roa, L. [Centro de Estudios Avanzados en Optica, Universidad de los Andes, Merida 5101 (Venezuela, Bolivarian Republic of); Gonzalez, J. [Centro de Estudios de Semiconductores, Universidad de los Andes, Merida 5101 (Venezuela, Bolivarian Republic of); Rodriguez, F.; Renero L, C.; Valiente, R. [Malta-Consolider Team, CITIMAC, Facultad de Ciencias, Universidad de Cantabria, Santander 69005 (Spain); Delgado, G. E., E-mail: marquinajesus@gmail.com [Laboratorio de Cristalografia, Facultad de Ciencias, Universidad de los Andes, Merida 5101 (Venezuela, Bolivarian Republic of)

    2017-11-01

    We report the results of the Rietveld refinement, photoluminescence and Raman spectroscopy of Mn-doped Zn O ceramic pellets. Rietveld refinement shows that samples crystallize in the wurtzite structure and for the Mn-doped sample indicated that the Mn atoms substitute the Zn tetrahedral crystallographic sites in the Zn O host lattice. The emission and absorption spectra of Mn-doped Zn O have been investigated in the visible-UV region and the data have been interpreted in terms of the wurtzite Zn O electronic structure. Two broad bands, one due to superposition between donor bound excitons (DX) and free excitons (FX) and other due free-to bond excitonic recombination (FB) dominates the low-temperature photoluminescence spectra of Mn-doped Zn O bulk. In the Raman spectrum, an extra mode at ∼520 cm{sup -1} has been observed in agreement with earlier works, and it is an indicator for the incorporation of Mn{sup +2} ions into the Zn O host matrix since it is not is observed in Zn O pristine. Rietveld refinement of the X-ray diffraction patterns, energy-dispersive X-ray spectroscopy (EDS) technique, and Raman spectroscopies were performed to study these effects. (Author)

  13. Rietveld refinement of magnetic structures from pulsed-neutron-source powder-diffraction data

    Robinson, R.A.; Lawson, A.C.; Larson, A.C.; Von Dreele, R.B.; Goldstone, J.A.

    1994-01-01

    The General Structure Analysis System, GSAS, has recently been modified to include magnetic neutron- scattering cross-sections. Low-temperature diffraction data have been taken on the hexagonal noncollinear antiferromagnet UPdSn on both the HIPD and the NPD powder diffractometers ail LANSCE. The low-resolution data reveal that the magnetic structure has orthorhombic symmetry (magnetic space group P c m'c2 1 ) between 25K and 40K, and monoclinic symmetry (magnetic space group PC 1121 ) below 25K. The high-resolution data reveal that there are structural distortions with corresponding symmetry changes in each of these phases, to give chemical space groups Cmc2 1 and P2 1 , respectively, while the paramagnetic phase above 40K has space group P6 3 mc. Using GSAS, we have refined data sets from both diffractometers simultaneously, including both magnetic and structural cross-sections. Magnetoelastic coefficients for the distortions have been extracted and we have determined the sign of the coupling between the structural monoclinicity and the magnetic monoclinicity. The magnetic results from Rietveld refinement are in good agreement with model fitting to the integrated intensities of seven independent magnetic reflections and these, in turn, agree with measurements made on the same sample using the constant-wavelength reactor technique. Our results therefore validate, to some level, both the technique of using spallation sources for complicated magnetic structures and the specifics of the GSAS Rietveld code

  14. Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

    Shi, Jade; Schwantes, Christian; Bilsel, Osman

    2017-01-01

    The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.

  15. An adaptive mesh refinement approach for average current nodal expansion method in 2-D rectangular geometry

    Poursalehi, N.; Zolfaghari, A.; Minuchehr, A.

    2013-01-01

    Highlights: ► A new adaptive h-refinement approach has been developed for a class of nodal method. ► The resulting system of nodal equations is more amenable to efficient numerical solution. ► The benefit of the approach is reducing computational efforts relative to the uniform fine mesh modeling. ► Spatially adaptive approach greatly enhances the accuracy of the solution. - Abstract: The aim of this work is to develop a spatially adaptive coarse mesh strategy that progressively refines the nodes in appropriate regions of domain to solve the neutron balance equation by zeroth order nodal expansion method. A flux gradient based a posteriori estimation scheme has been utilized for checking the approximate solutions for various nodes. The relative surface net leakage of nodes has been considered as an assessment criterion. In this approach, the core module is called in by adaptive mesh generator to determine gradients of node surfaces flux to explore the possibility of node refinements in appropriate regions and directions of the problem. The benefit of the approach is reducing computational efforts relative to the uniform fine mesh modeling. For this purpose, a computer program ANRNE-2D, Adaptive Node Refinement Nodal Expansion, has been developed to solve neutron diffusion equation using average current nodal expansion method for 2D rectangular geometries. Implementing the adaptive algorithm confirms its superiority in enhancing the accuracy of the solution without using fine nodes throughout the domain and increasing the number of unknown solution. Some well-known benchmarks have been investigated and improvements are reported

  16. A new adaptive mesh refinement data structure with an application to detonation

    Ji, Hua; Lien, Fue-Sang; Yee, Eugene

    2010-11-01

    A new Cell-based Structured Adaptive Mesh Refinement (CSAMR) data structure is developed. In our CSAMR data structure, Cartesian-like indices are used to identify each cell. With these stored indices, the information on the parent, children and neighbors of a given cell can be accessed simply and efficiently. Owing to the usage of these indices, the computer memory required for storage of the proposed AMR data structure is only {5}/{8} word per cell, in contrast to the conventional oct-tree [P. MacNeice, K.M. Olson, C. Mobary, R. deFainchtein, C. Packer, PARAMESH: a parallel adaptive mesh refinement community toolkit, Comput. Phys. Commun. 330 (2000) 126] and the fully threaded tree (FTT) [A.M. Khokhlov, Fully threaded tree algorithms for adaptive mesh fluid dynamics simulations, J. Comput. Phys. 143 (1998) 519] data structures which require, respectively, 19 and 2{3}/{8} words per cell for storage of the connectivity information. Because the connectivity information (e.g., parent, children and neighbors) of a cell in our proposed AMR data structure can be accessed using only the cell indices, a tree structure which was required in previous approaches for the organization of the AMR data is no longer needed for this new data structure. Instead, a much simpler hash table structure is used to maintain the AMR data, with the entry keys in the hash table obtained directly from the explicitly stored cell indices. The proposed AMR data structure simplifies the implementation and parallelization of an AMR code. Two three-dimensional test cases are used to illustrate and evaluate the computational performance of the new CSAMR data structure.

  17. Structure of 3 at.% and 9 at.% Si-doped HfO{sub 2} from combined refinement of X-ray and neutron diffraction patterns

    Zhao, Lili [Department of Materials Science and Engineering, North Carolina State University, NC 27695 (United States); School of Information Science and Technology, Northwest University, Xi' an 710127 (China); Hou, Dong; Usher, Tedi-Marie; Iamsasri, Thanakorn; Fancher, Chris M.; Forrester, Jennifer S. [Department of Materials Science and Engineering, North Carolina State University, NC 27695 (United States); Nishida, Toshikazu [Department of Electrical and Computer Engineering, University of Florida, FL 32611 (United States); Moghaddam, Saeed [Department of Mechanical and Aerospace Engineering, University of Florida, FL 32611 (United States); Jones, Jacob L., E-mail: jacobjones@ncsu.edu [Department of Materials Science and Engineering, North Carolina State University, NC 27695 (United States)

    2015-10-15

    The crystal structure of 3 at.% and 9 at.% Si-doped HfO{sub 2} powder was determined through refinements using X-ray and neutron diffraction patterns. The lattice parameters, atomic positions, dopant occupancy, and the second phase fraction were determined with high precision using a combined full pattern fitting via the Rietveld method. The results show that both 3 at.% and 9 at.% Si-doped HfO{sub 2} powder exhibit the monoclinic crystal structure with P 1 2{sub 1}/c 1 space group. Through the combined refinement, the crystal structure parameters, especially for the positions and occupancies of the lighter atoms, were more precisely determined compared to independent X-ray diffraction refinement. Although the ionic radius of Si{sup 4+} is smaller than Hf{sup 4+}, with increasing Si occupancy, the unit cell volume slightly increases; possible mechanisms for this effect are discussed. Moreover, the refined results provide evidence of the existence of a non-equilibrium phase of Hf{sub x}Si{sub 1−x}O{sub 2}. The second phase (SiO{sub 2}) fraction is determined as 0.17 at.% for 3 at.% Si-doped HfO{sub 2} powders and 1.7 at.% for 9 at.% Si-doped HfO{sub 2} powders. - Highlights: • X-ray and neutron diffraction patterns were used to determine crystal structure. • Results from independent refinements and a combined refinement were compared. • Highly precise structural parameters were obtained by the combined refinement. • Structural data of 3 at.% and 9 at.% Si-doped HfO{sub 2} are provided. • The unit cell volume slightly increases with Si concentration from 3 to 9 at.%.

  18. Adaptive local refinement and multi-level methods for simulating multiphasic flows

    Minjeaud, Sebastian

    2010-01-01

    This thesis describes some numerical and mathematical aspects of incompressible multiphase flows simulations with a diffuse interface Cahn-Hilliard / Navier-Stokes model (interfaces have a small but a positive thickness). The space discretization is performed thanks to a Galerkin formulation and the finite elements method. The presence of different scales in the system (interfaces have a very small thickness compared to the characteristic lengths of the domain) suggests the use of a local adaptive refinement method. The algorithm that is introduced allows to implicitly handle the non-conformities of the generated meshes to produce conformal finite elements approximation spaces. It consists in refining basis functions instead of cells. The refinement of a basis function is made possible by the conceptual existence of a nested sequence of uniformly refined grids from which 'parent-child' relationships are deduced, linking the basis functions of two consecutive refinement levels. Moreover, it is shown how this method can be exploited to build multigrid pre-conditioners. From a composite finite elements approximation space, it is indeed possible to rebuild, by 'coarsening', a sequence of auxiliary nested spaces which allows to enter in the abstract multigrid framework. Concerning the time discretization, it begins with the study of the Cahn-Hilliard system. A semi-implicit scheme is proposed to remedy to convergence failures of the Newton method used to solve this (non linear) system. It guarantees the decrease of the discrete free energy ensuring the stability of the scheme. The existence and convergence of discrete solutions towards the weak solution of the system are shown. The study continues with providing an unconditionally stable time discretization of the complete Cahn-Hilliard / Navier-Stokes model. An important point is that this discretization does not strongly couple the Cahn-Hilliard and Navier-Stokes systems allowing to independently solve the two systems

  19. A compressed sensing based method with support refinement for impulse noise cancelation in DSL

    Quadeer, Ahmed Abdul

    2013-06-01

    This paper presents a compressed sensing based method to suppress impulse noise in digital subscriber line (DSL). The proposed algorithm exploits the sparse nature of the impulse noise and utilizes the carriers, already available in all practical DSL systems, for its estimation and cancelation. Specifically, compressed sensing is used for a coarse estimate of the impulse position, an a priori information based maximum aposteriori probability (MAP) metric for its refinement, followed by least squares (LS) or minimum mean square error (MMSE) estimation for estimating the impulse amplitudes. Simulation results show that the proposed scheme achieves higher rate as compared to other known sparse estimation algorithms in literature. The paper also demonstrates the superior performance of the proposed scheme compared to the ITU-T G992.3 standard that utilizes RS-coding for impulse noise refinement in DSL signals. © 2013 IEEE.

  20. Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D

    Forneris, Federico; Burnley, B. Tom; Gros, Piet

    2014-01-01

    Ensemble-refinement analysis of native and mutant factor D (FD) crystal structures indicates a dynamical transition in FD from a self-inhibited inactive conformation to a substrate-bound active conformation that is reminiscent of the allostery in thrombin. Comparison with previously observed dynamics in thrombin using NMR data supports the crystallographic ensembles. Human factor D (FD) is a self-inhibited thrombin-like serine proteinase that is critical for amplification of the complement immune response. FD is activated by its substrate through interactions outside the active site. The substrate-binding, or ‘exosite’, region displays a well defined and rigid conformation in FD. In contrast, remarkable flexibility is observed in thrombin and related proteinases, in which Na + and ligand binding is implied in allosteric regulation of enzymatic activity through protein dynamics. Here, ensemble refinement (ER) of FD and thrombin crystal structures is used to evaluate structure and dynamics simultaneously. A comparison with previously published NMR data for thrombin supports the ER analysis. The R202A FD variant has enhanced activity towards artificial peptides and simultaneously displays active and inactive conformations of the active site. ER revealed pronounced disorder in the exosite loops for this FD variant, reminiscent of thrombin in the absence of the stabilizing Na + ion. These data indicate that FD exhibits conformational dynamics like thrombin, but unlike in thrombin a mechanism has evolved in FD that locks the unbound native state into an ordered inactive conformation via the self-inhibitory loop. Thus, ensemble refinement of X-ray crystal structures may represent an approach alternative to spectroscopy to explore protein dynamics in atomic detail

  1. Magnesium substitution in carbonated hydroxyapatite: Structural and microstructural characterization by Rietveld's refinement

    Lala, S. [Materials Science Division, Department of Physics, The University of Burdwan, Golapbag, Burdwan 713104, West Bengal (India); Ghosh, M.; Das, P.K. [Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032 (India); Das, D. [UGC-DAE Consortium for Scientific Research, Kolkata 700098 (India); Kar, T. [Department of Materials Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India); Pradhan, S.K., E-mail: skpradhan@phys.buruniv.ac.in [Materials Science Division, Department of Physics, The University of Burdwan, Golapbag, Burdwan 713104, West Bengal (India)

    2016-02-15

    Four stoichiometric compositions of nanocrystalline Mg doped carbonated hydroxyapatite (cHAp) powders are synthesized by mechanical alloying (ball milling) the powder mixtures of CaCO{sub 3}, CaHPO{sub 4}.2H{sub 2}O and MgO in open air at room temperature. FTIR analysis confirms the A-type carbonation in all milled HAp powder samples (A-cHAp). Microstructure characterization in terms of lattice imperfections and phase quantification of ball milled samples are made by analyzing XRD patterns employing Rietveld's structure refinement method. Transmission electron microscopy (TEM) study of 15 mol % Mg doped A-cHAp sample reveals microstructure similar to that obtained from XRD pattern analysis. Cumulative effect of Mg substitution and mechanical alloying results in amorphization of a major part of crystalline A-cHAp, analogous to native bone mineral. Rietveld analysis reveals that the Ca2 vacancy site is energetically more favorable for occupation of Mg substitution. MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay test reveals sufficiently high percentage cell viability confirming the cytocompatibility of the sample. - Graphical abstract: Mg substitution for Ca2 site. - Highlights: • Single phase Mg doped A-cHAp synthesized by mechanical alloying (MA). • FTIR analysis confirms A-type carbonation in HAp. • Amorphization of a part of crystalline A-cHAp due to MA and Mg insertion. • Mg{sup 2+} ions substitute the Ca2 vacancy site. • High cell viability under MTT assay.

  2. Continuous method for refining sodium. [for use in LMFBR type reactors

    Batoux, B; Laurent-Atthalin, A; Salmon, M

    1973-11-16

    The invention relates to a refining method according to which commercial sodium provides a high purity sodium with, in particular, a very small calcium content. The method consists in continuously feeding a predetermined amount of sodium peroxide into a sodium stream, mixing and causing said sodium peroxide to reach with sodium at an appropriate temperature, and, finally, separating the reaction products from sodium by decanting and filtering same. The thus obtained high purity sodium meets the requirements of atomic industries in particular, in view of its possible use as coolant in nuclear reactors of the ''breeder'' type.

  3. Lanthanum hexaboride as advanced structural refiner/getter in TiAl-based refractory intermetallics

    Kartavykh, A.V., E-mail: karta@korolev-net.ru [Technological Institute for Superhard and Novel Carbon Materials (TISNCM), 7a Centralnaya str., 142190 Troitsk, Moscow (Russian Federation); National University of Science and Technology “MISIS”, Leninsky pr. 4, 119049 Moscow (Russian Federation); Asnis, E.A.; Piskun, N.V.; Statkevich, I.I. [The E.O. Paton Electric Welding Institute, 11 Bozhenko str., 03680 Kyiv (Ukraine); Gorshenkov, M.V.; Tcherdyntsev, V.V. [National University of Science and Technology “MISIS”, Leninsky pr. 4, 119049 Moscow (Russian Federation)

    2014-03-05

    Highlights: • Fist application of LaB{sub 6} additive in TiAl-based intermetallics casting. • Pilot synthesis/casting and study of selected TiAl(Nb,Cr,Zr)B,La alloys set. • Dual effect observed: phase structure refinement and oxygen impurity removal. • Co-precipitation of TiB and La{sub 2}O{sub 3} in melt: 2LaB{sub 6} + 12Ti + 3O → 12TiB↓ + La{sub 2}O{sub 3}↓. • Features of structure refinement and oxygen gettering mechanisms reported. -- Abstract: The work is aimed at the study of the formation and refinement of microstructure appearing in the solidifying refractory TiAl-based intermetallics being inoculated with precise boron addition. The novelty of research consists in test application of lanthanum hexaboride (LaB{sub 6}) ligature within semi-continuous electron beam casting process of selected alloys. Two ingots with nominal compositions Ti–44Al–5Nb–2Cr–1.5Zr–0.4B–0.07La and Ti–44Al–5Nb–1Cr–1.5Zr–1B–0.17La (at.%) have been synthesized and cast along with the reference alloy Ti–44Al–5Nb–3Cr–1.5Zr. Their comparative examination suggests (i) essential microstructural phase refinement effect coupled with (ii) threefold/fourfold decrease of background content of undesirable residual oxygen impurity in both alloys containing LaB{sub 6}. This advanced dual activity (i–ii) of LaB{sub 6} is explained by its complete dissolution, dissociation and following re-precipitation of effective Ti-based monoboride nucleants of orthorhombic B27 structure, those being accompanied by strong internal gettering of dissolved oxygen from the melt and from boride-inoculated solid α{sub 2}-Ti{sub 3}Al phase with liberated elemental lanthanum. The phase composition and structure of cast alloys; state and characterization of newly precipitated TiB boride; features of La{sub 2}O{sub 3} micro/nano-dimensional precipitation and oxygen gettering mechanism are reported and discussed.

  4. Role of grain refinement in hardening of structural steels at preliminary thermomechanical treatment

    Bukhvalov, A.B.; Grigor'eva, E.V.; Davydova, L.S.; Degtyarev, M.V.; Levit, V.I.; Smirnova, N.A.; Smirnov, L.V.

    1981-01-01

    The hardening mechanism during preliminary thermomechanical treatment with deformation by cold rolling or hydroextrusion is studied on structural 37KhN3M1 and 38KhN3MFA steels. Specimens have been tested on static tension, impact strength and fracture toughness. It is shown that hydroextrusion application instead of rolling does not change the hardening effect of preliminary thermomechanical treatment (PTMT). It is established that the increase of preliminary deformation degree and the use of accelerated short term hardening heating provides a bett er grain refinement and the increase of PTMT hardening effect [ru

  5. Structure refinement using precession electron diffraction tomography and dynamical diffraction: tests on experimental data

    Palatinus, Lukáš; Correa, Cinthia Antunes; Steciuk, G.; Jacob, D.; Roussel, P.; Boullay, P.; Klementová, Mariana; Gemmi, M.; Kopeček, Jaromír; Domeneghetti, C.; Cámara, F.; Petříček, Václav

    2015-01-01

    Roč. 71, č. 6 (2015), 740-751 ISSN 2052-5206 R&D Projects: GA MŠk(CZ) LM2011029; GA ČR GA13-25747S; GA MŠk LO1409 Grant - others:SAFMAT(XE) CZ.2.16/3.1.00/22132; FUNBIO(XE) CZ.2.16/3.1.00/21568 Keywords : XRD * structure refinement * precession electron diffraction Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.892, year: 2015

  6. Rietveld refinement of the crystal structures of Rb2XSi5O12 (X = Ni, Mn

    Anthony M. T. Bell

    2016-02-01

    Full Text Available The synthetic leucite silicate framework mineral analogues Rb2XSi5O12 {X = Ni [dirubidium nickel(II pentasilicate] and Mn [dirubidium manganese(II pentasilicate]} have been prepared by high-temperature solid-state synthesis. The results of Rietveld refinements, using X-ray powder diffraction data collected using Cu Kα X-rays, show that the title compounds crystallize in the space group Pbca and adopt the cation-ordered structure of Cs2CdSi5O12 and other leucites. The structures consist of tetrahedral SiO4 and XO4 units sharing corners to form a partially substituted silicate framework. Extraframework Rb+ cations sit in channels in the framework. All atoms occupy the 8c general position for this space group. In these refined structures, silicon and X atoms are ordered onto separate tetrahedrally coordinated sites (T-sites. However, the Ni displacement parameter and the Ni—O bond lengths suggest that for the X = Ni sample, there may actually be some T-site cation disorder.

  7. Grain Refinement by Authigenic Inoculation Inherited from the Medium-Range Order Structure of Ni-Cr-W Superalloy

    Gao, Zhongtang; Hu, Rui; Guo, Wei; Zhang, Chuanwei

    2018-05-01

    The combination of liquidus casting and thermal control solidification furnace was applied to obtain a fine-grained ingot. A rapid quenching method and x-ray diffraction measurement were used to investigate the effect of authigenic inoculation on grain refinement. The structure factor S( Q) of liquid Ni -Cr-W superalloy at 1400 °C (Liquidus temperature) and bright-field image of the microstructures quenched from 1400 °C have been measured by the high-temperature x-ray diffractometer and the transmission electron microscopy (TEM), respectively. The results show that a pre-peak exists on a S( Q) curve at the liquidus temperature. The clusters of atom in rapidly quenched microstructures obtained by isothermal heat treatment at 1400 °C were studied using TEM. Meanwhile, the effect of isothermal different temperatures on rapidly quenched microstructures was studied. The results also show that there are only the globular, equiaxed grains distributed in the solidification structure. These particles are inherited from the medium-range order structure, which is beneficial for grain refinement. The normalized work-hardening rate-strain curve indicates the work-hardening rate of fine grain is higher than that of conventional grain at the same temperature and the same deformation.

  8. A Refined Model for the Structure of Acireductone Dioxygenase from Klebsiella ATCC 8724 Incorporating Residual Dipolar Couplings

    Pochapsky, Thomas C., E-mail: pochapsk@brandeis.edu; Pochapsky, Susan S.; Ju Tingting [Brandeis University, Department of Chemistry (United States); Hoefler, Chris [Brandeis University, Department of Biochemistry (United States); Liang Jue [Brandeis University, Department of Chemistry (United States)

    2006-02-15

    Acireductone dioxygenase (ARD) from Klebsiella ATCC 8724 is a metalloenzyme that is capable of catalyzing different reactions with the same substrates (acireductone and O{sub 2}) depending upon the metal bound in the active site. A model for the solution structure of the paramagnetic Ni{sup 2+}-containing ARD has been refined using residual dipolar couplings (RDCs) measured in two media. Additional dihedral restraints based on chemical shift (TALOS) were included in the refinement, and backbone structure in the vicinity of the active site was modeled from a crystallographic structure of the mouse homolog of ARD. The incorporation of residual dipolar couplings into the structural refinement alters the relative orientations of several structural features significantly, and improves local secondary structure determination. Comparisons between the solution structures obtained with and without RDCs are made, and structural similarities and differences between mouse and bacterial enzymes are described. Finally, the biological significance of these differences is considered.

  9. Refinement of the crystal structures of biomimetic weddellites produced by microscopic fungus Aspergillus niger

    Rusakov, A. V.; Frank-Kamenetskaya, O. V.; Gurzhiy, V. V.; Zelenskaya, M. S.; Izatulina, A. R.; Sazanova, K. V.

    2014-05-01

    The single-crystal structures of four biomimetic weddellites CaC2O4 · (2 + x)H2O with different contents of zeolitic water ( x = 0.10-0.24 formula units) produced by the microscopic fungus Aspergillus niger were refined from X-ray diffraction data ( R = 0.029-0.038). The effect of zeolitic water content on the structural stability of weddellite was analyzed. The parameter a was shown to increase with increasing x due to the increase in the distance between water molecules along this direction. The water content and structural parameters of the synthesized weddellites are similar to those of weddellites from biofilms and kidney stones.

  10. Automatic mesh refinement and local multigrid methods for contact problems: application to the Pellet-Cladding mechanical Interaction

    Liu, Hao

    2016-01-01

    This Ph.D. work takes place within the framework of studies on Pellet-Cladding mechanical Interaction (PCI) which occurs in the fuel rods of pressurized water reactor. This manuscript focuses on automatic mesh refinement to simulate more accurately this phenomena while maintaining acceptable computational time and memory space for industrial calculations. An automatic mesh refinement strategy based on the combination of the Local Defect Correction multigrid method (LDC) with the Zienkiewicz and Zhu a posteriori error estimator is proposed. The estimated error is used to detect the zones to be refined, where the local sub-grids of the LDC method are generated. Several stopping criteria are studied to end the refinement process when the solution is accurate enough or when the refinement does not improve the global solution accuracy anymore. Numerical results for elastic 2D test cases with pressure discontinuity show the efficiency of the proposed strategy. The automatic mesh refinement in case of unilateral contact problems is then considered. The strategy previously introduced can be easily adapted to the multi-body refinement by estimating solution error on each body separately. Post-processing is often necessary to ensure the conformity of the refined areas regarding the contact boundaries. A variety of numerical experiments with elastic contact (with or without friction, with or without an initial gap) confirms the efficiency and adaptability of the proposed strategy. (author) [fr

  11. Structure refinement of commensurately modulated bismuth tungstate, Bi2WO6

    Rae, A.D.; Thompson, J.G.; Withers, R.L.

    1991-01-01

    The displacive ferroelectric Bi 2 WO 6 [M r = 697.81, a = 5.4559 (4), b = 5.4360 (4), c = 16.4298 (17) A, Z = 4, D x = 9.512 g cm -3 , MoKα, λ = 0sun7107 A, μ = 958.6 cm -1 , F(000) = 1151.73], is described at room temperature as a commensurate modulation of an idealized Fmmm parent structure derived from an I4/mmm structure. Transmission electron microscopy clearly showed that there are coherent intergrowths of two distinct modulated variants in Bi 2 WO 6 crystals. Displacive models of inherent F2mm and Bmab symmetry are substantial and coherent over a large volume. They reduce the space-group symmetry to B2ab. A further substantial displacive mode corresponds to rotation of corner-connected WO 6 octahedra about axes parallel to c and has either of two inherent symmetries, Abam or Bbam, the difference being associated with the way this mode reduces the space-group symmetry to P2 1 ab, while the existence of the Bbam mode reduces the intensity of h + l = 2n + 1 data and acts like a stacking fault. Group theoretical analysis of the problem details how the X-ray data can be classified so as to monitor the refinement. Anomalous dispersion selects the overall sign of the F2mm mode and determines the polarity. The overall signs chosen for the Bmab and Abam symmetry components of atom displacements select between equivalent origins. The overall signs of induced modes of inherent Amam, Bbab and Ccma symmetry had to be determined by comparative refinement since the assumption that calculated phases are best estimates can retain the initial overall sign choice for these modes during least-squares refinement. Correlations between the dominant modes and the induced modes allowed a meaningful choice of signs to resolve the pseudo homometry. Only the sign of the Bbab mode was capable of self-correction during refinement. (orig./BHO)

  12. AN AUTOMATIC OPTICAL AND SAR IMAGE REGISTRATION METHOD USING ITERATIVE MULTI-LEVEL AND REFINEMENT MODEL

    C. Xu

    2016-06-01

    Full Text Available Automatic image registration is a vital yet challenging task, particularly for multi-sensor remote sensing images. Given the diversity of the data, it is unlikely that a single registration algorithm or a single image feature will work satisfactorily for all applications. Focusing on this issue, the mainly contribution of this paper is to propose an automatic optical-to-SAR image registration method using –level and refinement model: Firstly, a multi-level strategy of coarse-to-fine registration is presented, the visual saliency features is used to acquire coarse registration, and then specific area and line features are used to refine the registration result, after that, sub-pixel matching is applied using KNN Graph. Secondly, an iterative strategy that involves adaptive parameter adjustment for re-extracting and re-matching features is presented. Considering the fact that almost all feature-based registration methods rely on feature extraction results, the iterative strategy improve the robustness of feature matching. And all parameters can be automatically and adaptively adjusted in the iterative procedure. Thirdly, a uniform level set segmentation model for optical and SAR images is presented to segment conjugate features, and Voronoi diagram is introduced into Spectral Point Matching (VSPM to further enhance the matching accuracy between two sets of matching points. Experimental results show that the proposed method can effectively and robustly generate sufficient, reliable point pairs and provide accurate registration.

  13. An angularly refineable phase space finite element method with approximate sweeping procedure

    Kophazi, J.; Lathouwers, D.

    2013-01-01

    An angularly refineable phase space finite element method is proposed to solve the neutron transport equation. The method combines the advantages of two recently published schemes. The angular domain is discretized into small patches and patch-wise discontinuous angular basis functions are restricted to these patches, i.e. there is no overlap between basis functions corresponding to different patches. This approach yields block diagonal Jacobians with small block size and retains the possibility for S n -like approximate sweeping of the spatially discontinuous elements in order to provide efficient preconditioners for the solution procedure. On the other hand, the preservation of the full FEM framework (as opposed to collocation into a high-order S n scheme) retains the possibility of the Galerkin interpolated connection between phase space elements at arbitrary levels of discretization. Since the basis vectors are not orthonormal, a generalization of the Riemann procedure is introduced to separate the incoming and outgoing contributions in case of unstructured meshes. However, due to the properties of the angular discretization, the Riemann procedure can be avoided at a large fraction of the faces and this fraction rapidly increases as the level of refinement increases, contributing to the computational efficiency. In this paper the properties of the discretization scheme are studied with uniform refinement using an iterative solver based on the S 2 sweep order of the spatial elements. The fourth order convergence of the scalar flux is shown as anticipated from earlier schemes and the rapidly decreasing fraction of required Riemann faces is illustrated. (authors)

  14. Refinement of the crystal structure of malachite, Cu2(OH)2CO3, by neutron diffraction

    Zigan, F.; Joswig, W.; Schuster, H.D.; Mason, S.A.

    1977-01-01

    The crystal structure of malachite is refined (R = 0,021) with the intensity values of 635 independent neutron reflexions from a single crystal, rather free from absorption and extinction. Concerning the structural geometry, no essential deviations occur from the known results of x-ray diffraction. The thermal elongations are generally largest about the normal to the (201) layers, between which the bonding is relatively weak. In both of the (medium, bent) OH...O hydrogen bonds, the anisotropic thermal parameters, converted according to the riding model, are - with certain restrictions - in agreement with the measured infrared spectrum as well as with frequencies and directions of the proton vibration calculated from the bonding geometry on the basis of a theoretical model. (orig.) [de

  15. Refinement-Animation for Event-B - Towards a Method of Validation

    Hallerstede, Stefan; Leuschel, Michael; Plagge, Daniel

    2010-01-01

    We provide a detailed description of refinement in Event-B, both as a contribution in itself and as a foundation for the approach to simultaneous animation of multiple levels of refinement that we propose. We present an algorithm for simultaneous multi-level animation of refinement, and show how ...

  16. Synthesis and refinement of ferroelectric ceramic BaBi4Ti4O15 (BBT) using Rietveld Methods

    Silva, P.M.O.; Sales, A.J.M.; Carneiro, J.C.S.; Sancho, E.O.; Sales, J.C.; Sombra, A.S.B.

    2012-01-01

    The lead zirconate titanate (PZT) has potential application in nonvolatile ferroelectric memory and capacitors, however this material is linked to environmental pollution. In order to remedy this problem, we propose the synthesis of the compound, BaBi 4 TI 4 O 15 (BBT) because of similarity to PZT. The phase of the BBT has been prepared by the method of solid state. Reagents (BaCO 3 , Bi 2 O 3 and TiO 2 ) were ground for 6 hours at 360 rpm in a planetary ball mill and suffered high energy heat treatment for 2 hours at temperatures of 850, 900, 950 and 1000 ° C. The calcined powder was characterized by X-ray diffraction (XRD) and refined by the program DBWSTools 2.3 Beta based on the Rietveld method. The results obtained confirmed the refinement of the single-phase with tetragonal structure BaBi 4 TI 4 O 15 for all samples. The sample calcined at 950 °C presented the best densification (7.508 g/cm³). (author)

  17. Structural Reliability Methods

    Ditlevsen, Ove Dalager; Madsen, H. O.

    The structural reliability methods quantitatively treat the uncertainty of predicting the behaviour and properties of a structure given the uncertain properties of its geometry, materials, and the actions it is supposed to withstand. This book addresses the probabilistic methods for evaluation...... of structural reliability, including the theoretical basis for these methods. Partial safety factor codes under current practice are briefly introduced and discussed. A probabilistic code format for obtaining a formal reliability evaluation system that catches the most essential features of the nature...... of the uncertainties and their interplay is the developed, step-by-step. The concepts presented are illustrated by numerous examples throughout the text....

  18. 1H and 15N NMR assignment and solution structure of the SH3 domain of spectrin: Comparison of unrefined and refined structure sets with the crystal structure

    Blanco, Francisco J.; Ortiz, Angel R.; Serrano, Luis

    1997-01-01

    The assignment of the 1 H and 15 Nnuclear magnetic resonance spectra of the Src-homology region 3 domain of chicken brain α-spectrin has been obtained. A set of solution structures has been determined from distance and dihedral angle restraints,which provide a reasonable representation of the protein structure in solution, as evaluated by a principal component analysis of the global pairwise root-mean-square deviation (rmsd) in a large set of structures consisting of the refined and unrefined solution structures and the crystal structure. The solution structure is well defined, with a lower degree of convergence between the structures in the loop regions than in the secondary structure elements. The average pairwise rmsd between the 15 refined solution structures is 0.71 ± 0.13 A for the backbone atoms and 1.43 ± 0.14 A for all heavy atoms. The solution structure is basically the same as the crystal structure. The average rmsd between the 15 refined solution structures and the crystal structure is 0.76 A for the backbone atoms and 1.45 ± 0.09 A for all heavy atoms. There are, however, small differences probably caused by intermolecular contacts in the crystal structure

  19. New Ghost-node method for linking different models with varied grid refinement

    Mehl, Steffen W.; Hill, Mary Catherine; James, Scott Carlton; Leake, Stanley A.; Zyvoloski, George A.; Dickinson, Jesse E.; Eddebbarh, Al A.

    2006-01-01

    A flexible, robust method for linking grids of locally refined models constructed with different numerical methods is needed to address a variety of hydrologic problems. This work outlines and tests a new ghost-node model-linking method for a refined 'child' model that is contained within a larger and coarser 'parent' model that is based on the iterative method of Mehl and Hill (2002, 2004). The method is applicable to steady-state solutions for ground-water flow. Tests are presented for a homogeneous two-dimensional system that has either matching grids (parent cells border an integer number of child cells; Figure 2a) or non-matching grids (parent cells border a non-integer number of child cells; Figure 2b). The coupled grids are simulated using the finite-difference and finite-element models MODFLOW and FEHM, respectively. The simulations require no alteration of the MODFLOW or FEHM models and are executed using a batch file on Windows operating systems. Results indicate that when the grids are matched spatially so that nodes and child cell boundaries are aligned, the new coupling technique has error nearly equal to that when coupling two MODFLOW models (Mehl and Hill, 2002). When the grids are non-matching, model accuracy is slightly increased over matching-grid cases. Overall, results indicate that the ghost-node technique is a viable means to accurately couple distinct models because the overall error is less than if only the regional model was used to simulate flow in the child model's domain

  20. New ghost-node method for linking different models with varied grid refinement

    James, S.C.; Dickinson, J.E.; Mehl, S.W.; Hill, M.C.; Leake, S.A.; Zyvoloski, G.A.; Eddebbarh, A.-A.

    2006-01-01

    A flexible, robust method for linking grids of locally refined ground-water flow models constructed with different numerical methods is needed to address a variety of hydrologic problems. This work outlines and tests a new ghost-node model-linking method for a refined "child" model that is contained within a larger and coarser "parent" model that is based on the iterative method of Steffen W. Mehl and Mary C. Hill (2002, Advances in Water Res., 25, p. 497-511; 2004, Advances in Water Res., 27, p. 899-912). The method is applicable to steady-state solutions for ground-water flow. Tests are presented for a homogeneous two-dimensional system that has matching grids (parent cells border an integer number of child cells) or nonmatching grids. The coupled grids are simulated by using the finite-difference and finite-element models MODFLOW and FEHM, respectively. The simulations require no alteration of the MODFLOW or FEHM models and are executed using a batch file on Windows operating systems. Results indicate that when the grids are matched spatially so that nodes and child-cell boundaries are aligned, the new coupling technique has error nearly equal to that when coupling two MODFLOW models. When the grids are nonmatching, model accuracy is slightly increased compared to that for matching-grid cases. Overall, results indicate that the ghost-node technique is a viable means to couple distinct models because the overall head and flow errors relative to the analytical solution are less than if only the regional coarse-grid model was used to simulate flow in the child model's domain.

  1. Structure refinement of flexible proteins using dipolar couplings: Application to the protein p8MTCP1

    Demene, Helene; Ducat, Thierry; Barthe, Philippe; Delsuc, Marc-Andre; Roumestand, Christian

    2002-01-01

    The present study deals with the relevance of using mobility-averaged dipolar couplings for the structure refinement of flexible proteins. The 68-residue protein p8 MTCP1 has been chosen as model for this study. Its solution state consists mainly of three α-helices. The two N-terminal helices are strapped in a well-determined α-hairpin, whereas, due to an intrinsic mobility, the position of the third helix is less well defined in the NMR structure. To further characterize the degrees of freedom of this helix, we have measured the dipolar coupling constants in the backbone of p8 MTCP1 in a bicellar medium. We show here that including D HN dip dipolar couplings in the structure calculation protocol improves the structure of the α-hairpin but not the positioning of the third helix. This is due to the motional averaging of the dipolar couplings measured in the last helix. Performing two calculations with different force constants for the dipolar restraints highlights the inconstancy of these mobility-averaged dipolar couplings. Alternatively, prior to any structure calculations, comparing the values of the dipolar couplings measured in helix III to values back-calculated from an ideal helix demonstrates that they are atypical for a helix. This can be partly attributed to mobility effects since the inclusion of the 15 N relaxation derived order parameter allows for a better fit

  2. A refined element-based Lagrangian shell element for geometrically nonlinear analysis of shell structures

    Woo-Young Jung

    2015-04-01

    Full Text Available For the solution of geometrically nonlinear analysis of plates and shells, the formulation of a nonlinear nine-node refined first-order shear deformable element-based Lagrangian shell element is presented. Natural co-ordinate-based higher order transverse shear strains are used in present shell element. Using the assumed natural strain method with proper interpolation functions, the present shell element generates neither membrane nor shear locking behavior even when full integration is used in the formulation. Furthermore, a refined first-order shear deformation theory for thin and thick shells, which results in parabolic through-thickness distribution of the transverse shear strains from the formulation based on the third-order shear deformation theory, is proposed. This formulation eliminates the need for shear correction factors in the first-order theory. To avoid difficulties resulting from large increments of the rotations, a scheme of attached reference system is used for the expression of rotations of shell normal. Numerical examples demonstrate that the present element behaves reasonably satisfactorily either for the linear or for geometrically nonlinear analysis of thin and thick plates and shells with large displacement but small strain. Especially, the nonlinear results of slit annular plates with various loads provided the benchmark to test the accuracy of related numerical solutions.

  3. 1H CSA parameters by ultrafast MAS NMR: Measurement and applications to structure refinement.

    Miah, Habeeba K; Cresswell, Rosalie; Iuga, Dinu; Titman, Jeremy J

    2017-10-01

    A 1 H anisotropic-isotropic chemical shift correlation experiment which employs symmetry-based recoupling sequences to reintroduce the chemical shift anisotropy in ν 1 and ultrafast MAS to resolve 1 H sites in ν 2 is described. This experiment is used to measure 1 H shift parameters for L-ascorbic acid, a compound with a relatively complex hydrogen-bonding network in the solid. The 1 H CSAs of hydrogen-bonded sites with resolved isotropic shifts can be extracted directly from the recoupled lineshapes. In combination with DFT calculations, hydrogen positions in crystal structures obtained from X-ray and neutron diffraction are refined by comparison with simulations of the full two-dimensional NMR spectrum. The improved resolution afforded by the second dimension allows even unresolved hydrogen-bonded sites 1 H to be assigned and their shift parameters to be obtained. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Structure refinement and membrane positioning of selectively labeled OmpX in phospholipid nanodiscs

    Hagn, Franz, E-mail: franz.hagn@tum.de; Wagner, Gerhard, E-mail: gerhard-wagner@hms.harvard.edu [Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (United States)

    2015-04-15

    NMR structural studies on membrane proteins are often complicated by their large size, taking into account the contribution of the membrane mimetic. Therefore, classical resonance assignment approaches often fail. The large size of phospholipid nanodiscs, a detergent-free phospholipid bilayer mimetic, prevented their use in high-resolution solution-state NMR spectroscopy so far. We recently introduced smaller nanodiscs that are suitable for NMR structure determination. However, side-chain assignments of a membrane protein in nanodiscs still remain elusive. Here, we utilized a NOE-based approach to assign (stereo-) specifically labeled Ile, Leu, Val and Ala methyl labeled and uniformly {sup 15}N-Phe and {sup 15}N-Tyr labeled OmpX and calculated a refined high-resolution structure. In addition, we were able to obtain residual dipolar couplings (RDCs) of OmpX in nanodiscs using Pf1 phage medium for the induction of weak alignment. Back-calculated NOESY spectra of the obtained NMR structures were compared to experimental NOESYs in order to validate the quality of these structures. We further used NOE information between protonated lipid head groups and side-chain methyls to determine the position of OmpX in the phospholipid bilayer. These data were verified by paramagnetic relaxation enhancement (PRE) experiments obtained with Gd{sup 3+}-modified lipids. Taken together, this study emphasizes the need for the (stereo-) specific labeling of membrane proteins in a highly deuterated background for high-resolution structure determination, particularly in large membrane mimicking systems like phospholipid nanodiscs. Structure validation by NOESY back-calculation will be helpful for the structure determination and validation of membrane proteins where NOE assignment is often difficult. The use of protein to lipid NOEs will be beneficial for the positioning of a membrane protein in the lipid bilayer without the need for preparing multiple protein samples.

  5. A refined Frequency Domain Decomposition tool for structural modal monitoring in earthquake engineering

    Pioldi, Fabio; Rizzi, Egidio

    2017-07-01

    Output-only structural identification is developed by a refined Frequency Domain Decomposition ( rFDD) approach, towards assessing current modal properties of heavy-damped buildings (in terms of identification challenge), under strong ground motions. Structural responses from earthquake excitations are taken as input signals for the identification algorithm. A new dedicated computational procedure, based on coupled Chebyshev Type II bandpass filters, is outlined for the effective estimation of natural frequencies, mode shapes and modal damping ratios. The identification technique is also coupled with a Gabor Wavelet Transform, resulting in an effective and self-contained time-frequency analysis framework. Simulated response signals generated by shear-type frames (with variable structural features) are used as a necessary validation condition. In this context use is made of a complete set of seismic records taken from the FEMA P695 database, i.e. all 44 "Far-Field" (22 NS, 22 WE) earthquake signals. The modal estimates are statistically compared to their target values, proving the accuracy of the developed algorithm in providing prompt and accurate estimates of all current strong ground motion modal parameters. At this stage, such analysis tool may be employed for convenient application in the realm of Earthquake Engineering, towards potential Structural Health Monitoring and damage detection purposes.

  6. Effects of grain refinement on cast structure and tensile properties of superalloy K4169 at high pouring temperature

    Zi-qi Jie

    2016-03-01

    Full Text Available In order to improve the filling ability of large complex thin wall castings, the pouring temperature should be increased, but this will result in the grain coarsening. To overcome this problem, two kinds of grain refiners of Co-Fe-Nb and Cr-Fe-Nb ternary alloys, which contain high stability compound particles, were prepared. The effects of the refiners on the as-cast structures and tensile properties of the K4169 superalloy with different casting conditions were studied by analyzing specimens 110 mm long and 20 mm in diameter. Results showed that the mixture addition of the two refiners in the melt of K4169 can reduce the columnar grain region and decrease the equiaxed grain size greatly. After refinement, the amount of Laves phase decreases and its morphology changes from island to blocky structure. The carbides in the fine grain samples are fine and dispersive. Meanwhile, the porosity in specimens is decreased due to grain refinement. As a result, the yield strength, ultimate strength and the elongation of the specimens are increased. The grain refinement mechanisms are also discussed.

  7. Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data

    Gorelik, Tatiana E; van de Streek, Jacco; Kilbinger, Andreas F M

    2012-01-01

    Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal stru...

  8. As-cast structure refinement of Ti-46Al alloy by hafnium and boron additions

    Zhang Li

    2009-05-01

    Full Text Available The infl uence of Hf and B on the solidifi cation structure of cast Ti-46Al alloys was investigated. The results show that the coupling effect of Hf and B changes the solidifi cation structure morphology and strongly refi nes the grain size. When the Hf+B contents were increased from 0 + 0.0 to 3 + 0.2, 5 + 0.6 and 7 + 1.0 (in at. %, the solidification structure morphology changed from coarse columnar dendrite to fine columnar dendrite, then to equiaxed dendrite, and further to fi ne near granular grain whilst the average grain size decreased to 20 μm. It is concluded that the columnar dendrite refinement is due to the effect of Hf and B on the decrease of Al diffusion coeffi cient in the melt. The fi ne near granular grain formation is attributed to the combined constitutional supercooling formed by Al and B segregation that is strengthened by Hf and B additions at the solid/liquid interface during solidifi cation, and the TiB2 precipitates acting as heterogeneous nuclei

  9. NMR structural refinement of a tandem G·A mismatched decamer d(CCAAGATTGG)2 via the hybrid matrix procedure

    Nikonowicz, E.P.; Meadows, R.P.; Fagan, P.; Gorenstein, D.G.

    1991-01-01

    A complete relaxation matrix approach employing a matrix eigenvalue/eigenvector solution to the Bloch equations is used to evaluate the NMR solution structure of a tandemly positioned G·A double mismatch decamer oligodeoxyribonucleotide duplex, d(CCAAGATTGG) 2 . An iterative refinement method using a hybrid relaxation matrix combined with restrained molecular dynamics calculations is shown to provide structures having good agreement with the experimentally derived structures. Distances incorporated into the MD simulations have been calculated from the relaxation rate matrix evaluated from a hybrid NOESY volume matrix whose elements are obtained from the merging of experimental and calculated NOESY intensities. Starting from both A- and B-DNA and mismatch syn and anti models, it is possible to calculate structures that are in good atomic RMS agreement with each other ( 3.6 angstrom). Importantly, the hybrid matrix derived structures are in excellent agreement with the experimental solution conformation as determined by comparison of the 200-ms simulated and experimental NOESY spectra, while the crystallographic data provide spectra that are grossly different

  10. Prediction of proton chemical shifts in RNA - Their use in structure refinement and validation

    Cromsigt, Jenny A.M.T.C.; Hilbers, Cees W.; Wijmenga, Sybren S.

    2001-01-01

    An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct.,76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1 H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn χ-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1 H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings

  11. Stabilized Conservative Level Set Method with Adaptive Wavelet-based Mesh Refinement

    Shervani-Tabar, Navid; Vasilyev, Oleg V.

    2016-11-01

    This paper addresses one of the main challenges of the conservative level set method, namely the ill-conditioned behavior of the normal vector away from the interface. An alternative formulation for reconstruction of the interface is proposed. Unlike the commonly used methods which rely on the unit normal vector, Stabilized Conservative Level Set (SCLS) uses a modified renormalization vector with diminishing magnitude away from the interface. With the new formulation, in the vicinity of the interface the reinitialization procedure utilizes compressive flux and diffusive terms only in the normal direction to the interface, thus, preserving the conservative level set properties, while away from the interfaces the directional diffusion mechanism automatically switches to homogeneous diffusion. The proposed formulation is robust and general. It is especially well suited for use with adaptive mesh refinement (AMR) approaches due to need for a finer resolution in the vicinity of the interface in comparison with the rest of the domain. All of the results were obtained using the Adaptive Wavelet Collocation Method, a general AMR-type method, which utilizes wavelet decomposition to adapt on steep gradients in the solution while retaining a predetermined order of accuracy.

  12. Structure refinement of Ag-free heyrovskýite from Vulcano (Aeolian Islands, Italy)

    Pinto, Daniella; Balic Zunic, Tonci; Garavelli, Anna

    2011-01-01

    The first single-crystal structure refinement of Ag- and Cu-free heyrovskýite was performed in this study. Crystals investigated were sampled from the high-temperature fumaroles of La Fossa crater of Vulcano, Aeolian Islands, Italy. Electron microprobe analyses gave the average chemical formula (Pb...... with Fo > 4s(Fo). In Ag-free heyrovskýite from Vulcano, as well as in the synthetic Pb6Bi2S9, the trigonal prismatic coordinated position Me1, as well as the octahedrally coordinated position Me3 are occupied only by Pb. Me2, also octahedrally coordinated, is dominated by Pb, whereas the octahedra...... the ideal composition, Pb6Bi2S9. Selenium is preferentially ordered at the fivefold-coordinated anionic sites. Taking into account vacancies, as well as Se for S substitutions the structural formula of Ag-free heyrovskýite from Vulcano is Pb5.82Bi2.12¿0.06S8.70Se0.30. Comparison with the Ag...

  13. Refined energetic ordering for sulphate-water (n = 3-6) clusters using high-level electronic structure calculations

    Lambrecht, Daniel S.; McCaslin, Laura; Xantheas, Sotiris S.; Epifanovsky, Evgeny; Head-Gordon, Martin

    2012-10-01

    This work reports refinements of the energetic ordering of the known low-energy structures of sulphate-water clusters ? (n = 3-6) using high-level electronic structure methods. Coupled cluster singles and doubles with perturbative triples (CCSD(T)) is used in combination with an estimate of basis set effects up to the complete basis set limit using second-order Møller-Plesset theory. Harmonic zero-point energy (ZPE), included at the B3LYP/6-311 + + G(3df,3pd) level, was found to have a significant effect on the energetic ordering. In fact, we show that the energetic ordering is a result of a delicate balance between the electronic and vibrational energies. Limitations of the ZPE calculations, both due to electronic structure errors, and use of the harmonic approximation, probably constitute the largest remaining errors. Due to the often small energy differences between cluster isomers, and the significant role of ZPE, deuteration can alter the relative energies of low-lying structures, and, when it is applied in conjunction with calculated harmonic ZPEs, even alters the global minimum for n = 5. Experiments on deuterated clusters, as well as more sophisticated vibrational calculations, may therefore be quite interesting.

  14. Acquiring and refining CBT skills and competencies: which training methods are perceived to be most effective?

    Bennett-Levy, James; McManus, Freda; Westling, Bengt E; Fennell, Melanie

    2009-10-01

    A theoretical and empirical base for CBT training and supervision has started to emerge. Increasingly sophisticated maps of CBT therapist competencies have recently been developed, and there is evidence that CBT training and supervision can produce enhancement of CBT skills. However, the evidence base suggesting which specific training techniques are most effective for the development of CBT competencies is lacking. This paper addresses the question: What training or supervision methods are perceived by experienced therapists to be most effective for training CBT competencies? 120 experienced CBT therapists rated which training or supervision methods in their experience had been most effective in enhancing different types of therapy-relevant knowledge or skills. In line with the main prediction, it was found that different training methods were perceived to be differentially effective. For instance, reading, lectures/talks and modelling were perceived to be most useful for the acquisition of declarative knowledge, while enactive learning strategies (role-play, self-experiential work), together with modelling and reflective practice, were perceived to be most effective in enhancing procedural skills. Self-experiential work and reflective practice were seen as particularly helpful in improving reflective capability and interpersonal skills. The study provides a framework for thinking about the acquisition and refinement of therapist skills that may help trainers, supervisors and clinicians target their learning objectives with the most effective training strategies.

  15. Analysis of a HP-refinement method for solving the neutron transport equation using two error estimators

    Fournier, D.; Le Tellier, R.; Suteau, C.; Herbin, R.

    2011-01-01

    The solution of the time-independent neutron transport equation in a deterministic way invariably consists in the successive discretization of the three variables: energy, angle and space. In the SNATCH solver used in this study, the energy and the angle are respectively discretized with a multigroup approach and the discrete ordinate method. A set of spatial coupled transport equations is obtained and solved using the Discontinuous Galerkin Finite Element Method (DGFEM). Within this method, the spatial domain is decomposed into elements and the solution is approximated by a hierarchical polynomial basis in each one. This approach is time and memory consuming when the mesh becomes fine or the basis order high. To improve the computational time and the memory footprint, adaptive algorithms are proposed. These algorithms are based on an error estimation in each cell. If the error is important in a given region, the mesh has to be refined (h−refinement) or the polynomial basis order increased (p−refinement). This paper is related to the choice between the two types of refinement. Two ways to estimate the error are compared on different benchmarks. Analyzing the differences, a hp−refinement method is proposed and tested. (author)

  16. A new method for grain refinement in magnesium alloy: High speed extrusion machining

    Liu, Yao, E-mail: liuyao@ustb.edu.cn [School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083 (China); Cai, Songlin [China Electric Power Research Institute, State Grid Corporation of China, Beijing 100192 (China); Dai, Lanhong [State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Science, Beijing 100190 (China)

    2016-01-10

    Magnesium alloys have received broad attentions in industry due to their competitive strength to density ratio, but the poor ductility and strength limit their wide range of applications as engineering materials. A novel severe plastic deformation (SPD) technique of high speed extrusion machining (HSEM) was used here. This method could improve the aforementioned disadvantages of magnesium alloys by one single processing step. In this work, systematic HSEM experiments with different chip thickness ratios were conducted for magnesium alloy AZ31B. The microstructure of the chips reveals that HSEM is an effective SPD method for attaining magnesium alloys with different grain sizes and textures. The magnesium alloy with bimodal grain size distribution has increased mechanical properties than initial sample. The electron backscatter diffraction (EBSD) analysis shows that the dynamic recrystallization (DRX) affects the grain refinement and resulting hardness in AZ31B. Based on the experimental observations, a new theoretical model is put forward to describe the effect of DRX on materials during HSEM. Compared with the experimental measurements, the theoretical model is effective to predict the mechanical property of materials after HSEM.

  17. Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.

    Potrzebowski, Wojciech; André, Ingemar

    2015-07-01

    For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints.

  18. Refined Diebold-Mariano Test Methods for the Evaluation of Wind Power Forecasting Models

    Hao Chen

    2014-07-01

    Full Text Available The scientific evaluation methodology for the forecast accuracy of wind power forecasting models is an important issue in the domain of wind power forecasting. However, traditional forecast evaluation criteria, such as Mean Squared Error (MSE and Mean Absolute Error (MAE, have limitations in application to some degree. In this paper, a modern evaluation criterion, the Diebold-Mariano (DM test, is introduced. The DM test can discriminate the significant differences of forecasting accuracy between different models based on the scheme of quantitative analysis. Furthermore, the augmented DM test with rolling windows approach is proposed to give a more strict forecasting evaluation. By extending the loss function to an asymmetric structure, the asymmetric DM test is proposed. Case study indicates that the evaluation criteria based on DM test can relieve the influence of random sample disturbance. Moreover, the proposed augmented DM test can provide more evidence when the cost of changing models is expensive, and the proposed asymmetric DM test can add in the asymmetric factor, and provide practical evaluation of wind power forecasting models. It is concluded that the two refined DM tests can provide reference to the comprehensive evaluation for wind power forecasting models.

  19. Analyses of magnetic structures and nuclear-density distribution by the structure-refinement and three-dimensional visualization systems RIETAN-FP-VENUS

    Izumi, Fujio; Momma, Koichi

    2010-01-01

    We have been developing a multi-purpose pattern-fitting system RIETAN-FP and a three-dimensional visualization system VENUS, which have been extensively used for structure refinements of various metal and inorganic materials from neutron powder diffraction data. At first, their outlines and the history of their developments are shortly looked back. The second part describes procedures for analyzing collinear magnetic structures with the combination of VESTA in the VENUS system and RIETAN-FP by taking BiCoO 3 for instance. Finally, a new C++ program, Dysnomia, for the maximum entropy method is introduced with emphasis on its new features. Dysnomia excels its predecessor, PRIMA, in computation speed, memory efficiency, scalability, and reliability. In particular, addition of a normal-distribution constraint is effective in obtaining nuclear-density distribution that is physically and chemically reasonable. (author)

  20. Rietveld refinement and electronic structure studies for the Sm2FeMnO6 new complex perovskite

    Landinez Tellez, D.A.; Munevar, J.A.; Arbey Rodriguez, J.M.; Fajardo, F.; Roa-Rojas, J.

    2008-01-01

    We report synthesis and crystalline structure study of the Sm 2 FeMnO 6 new complex perovskite, by X-ray diffraction experiments and through the application of Rietveld refinement. Results revealed the crystallization of system in a structure given by Pmn21 (no. 31) space group and lattice parameters a=7.621(1) A, b=5.675(3) A and c=5.378(3) A. Ab initio calculations of density of states (DOS) and electronic structure were carried out for this perovskite-like system by the density functional theory (DFT) and using the full-potential linearized augmented plane waves (FP-LAPW) method. All calculations were carried out using spin polarization. Material evidences a conductor-like character, predominantly due to d-xy Fe orbital of the spin down channel. Magnetic response of system has contributions of Fe and Mn spin up orientation. The calculated magnetic moment in cell was 34.48 μ B and the magnetic moment in interstitial was 1.54 μ B

  1. An efficient Adaptive Mesh Refinement (AMR) algorithm for the Discontinuous Galerkin method: Applications for the computation of compressible two-phase flows

    Papoutsakis, Andreas; Sazhin, Sergei S.; Begg, Steven; Danaila, Ionut; Luddens, Francky

    2018-06-01

    We present an Adaptive Mesh Refinement (AMR) method suitable for hybrid unstructured meshes that allows for local refinement and de-refinement of the computational grid during the evolution of the flow. The adaptive implementation of the Discontinuous Galerkin (DG) method introduced in this work (ForestDG) is based on a topological representation of the computational mesh by a hierarchical structure consisting of oct- quad- and binary trees. Adaptive mesh refinement (h-refinement) enables us to increase the spatial resolution of the computational mesh in the vicinity of the points of interest such as interfaces, geometrical features, or flow discontinuities. The local increase in the expansion order (p-refinement) at areas of high strain rates or vorticity magnitude results in an increase of the order of accuracy in the region of shear layers and vortices. A graph of unitarian-trees, representing hexahedral, prismatic and tetrahedral elements is used for the representation of the initial domain. The ancestral elements of the mesh can be split into self-similar elements allowing each tree to grow branches to an arbitrary level of refinement. The connectivity of the elements, their genealogy and their partitioning are described by linked lists of pointers. An explicit calculation of these relations, presented in this paper, facilitates the on-the-fly splitting, merging and repartitioning of the computational mesh by rearranging the links of each node of the tree with a minimal computational overhead. The modal basis used in the DG implementation facilitates the mapping of the fluxes across the non conformal faces. The AMR methodology is presented and assessed using a series of inviscid and viscous test cases. Also, the AMR methodology is used for the modelling of the interaction between droplets and the carrier phase in a two-phase flow. This approach is applied to the analysis of a spray injected into a chamber of quiescent air, using the Eulerian

  2. Weldability of thermally grain-refined Fe-12Ni-0.25Ti for cryogenic structural applications

    Williams, D.E.

    1980-02-01

    The weldability of a research alloy designed for structural use in liquid helium temperature, cryogenic environments was investigated. Plates of iron-12 weight percent nickel-0.25 weight percent titanium were grain refined by the four-step, grain refining thermal treatment developed for this alloy and welded with Inconel Number 92 weld wire using the Gas Metal Arc (GMA) welding process with argon-15% helium gas shielding. Both a single pass and a double-sided, 2 pass electron beam (EB) weld were also made without filler metal addition. Weldments were radiographed and sectioned and the charpy V-notch specimens removed were tested at liquid nitrogen and helium temperatures

  3. Determination of Cation Distributions in Mineral Structures by use of the Rietveld Full-Profile Refinement Technique

    Nord, A.G.

    1986-01-01

    Use of the Rietveld full-profile refinement technique with X-ray or neutron powder diffraction data for the determination of divalent-metal cation distributions in three mineral structure types (farringtonite, grafonite, sarcopside) is demonstrated. The accuracy of the conventional cation distribution coefficient Ksub(D) is about 5-10 percent with 24-46 parameters to be refined, and the averaged metal-oxygen distances are reliable and well correlated to the observed cation distribution pattern. In particular the usefulness of the Rietveld technique in combination with Moessbauer spectroscopy is stressed. Some concluding remarks are also given

  4. An assessment of the contributing factors to the nanoscale structural refinement of advanced bainitic steels

    Cornide, J.; Garcia-Mateo, C.; Capdevila, C.; Caballero, F.G.

    2013-01-01

    A new generation of steels has been designed, which on transformation at low temperature (200–350 °C), leads to a nano-scale microstructure, known as NANOBAIN. The microstructure consists of slender crystals of ferrite, whose controlling scale compares well with that of carbon nanotubes (20–40 nm). These advanced steels present the highest strength/toughness combinations ever recorded in bainitic steels. Their properties are mainly a consequence of the formation of nanoscale bainitic ferrite plates at very low temperatures. Transmission electron microscopy observations have shown that plastic relaxation in the austenite adjacent to the bainite plates may control the final size of the bainitic ferrite plates. The dislocation debris generated in this process resists the advance of the bainitic ferrite–austenite interface, the resistance being greatest for strong austenite. The yield strength of the austenite must then feature in any assessment of plate size. In this scenario, the plates are expected to become thicker at high temperatures because the yield strength of the austenite will then be lower. The goal of this study is to evaluate the influence of yield strength of austenite to the nanoscale structural refinement of advanced bainitic steels. In this sense, in situ measurements of austenite strength before bainite formation using a deformation dilatometer Bähr 805D have been performed in a medium carbon high silicon steel transforming at intermediate temperatures (325–400 °C) to a submicron structure of bainite and in a high carbon high silicon steel transforming at low temperatures (200–350 °C) to nanostructured bainite. The role of the transformation driving force on the bainite plate thickness will be also discussed

  5. An assessment of the contributing factors to the nanoscale structural refinement of advanced bainitic steels

    Cornide, J., E-mail: jca@cenim.csic.es [Centro Nacional de Investigaciones Metalúrgicas (CENIM-CSIC), Avda Gregorio del Amo 8, Madrid E-28040 (Spain); Garcia-Mateo, C., E-mail: cgm@cenim.csic.es [Centro Nacional de Investigaciones Metalúrgicas (CENIM-CSIC), Avda Gregorio del Amo 8, Madrid E-28040 (Spain); Capdevila, C., E-mail: ccm@cenim.csic.es [Centro Nacional de Investigaciones Metalúrgicas (CENIM-CSIC), Avda Gregorio del Amo 8, Madrid E-28040 (Spain); Caballero, F.G., E-mail: fgc@cenim.csic.es [Centro Nacional de Investigaciones Metalúrgicas (CENIM-CSIC), Avda Gregorio del Amo 8, Madrid E-28040 (Spain)

    2013-11-15

    A new generation of steels has been designed, which on transformation at low temperature (200–350 °C), leads to a nano-scale microstructure, known as NANOBAIN. The microstructure consists of slender crystals of ferrite, whose controlling scale compares well with that of carbon nanotubes (20–40 nm). These advanced steels present the highest strength/toughness combinations ever recorded in bainitic steels. Their properties are mainly a consequence of the formation of nanoscale bainitic ferrite plates at very low temperatures. Transmission electron microscopy observations have shown that plastic relaxation in the austenite adjacent to the bainite plates may control the final size of the bainitic ferrite plates. The dislocation debris generated in this process resists the advance of the bainitic ferrite–austenite interface, the resistance being greatest for strong austenite. The yield strength of the austenite must then feature in any assessment of plate size. In this scenario, the plates are expected to become thicker at high temperatures because the yield strength of the austenite will then be lower. The goal of this study is to evaluate the influence of yield strength of austenite to the nanoscale structural refinement of advanced bainitic steels. In this sense, in situ measurements of austenite strength before bainite formation using a deformation dilatometer Bähr 805D have been performed in a medium carbon high silicon steel transforming at intermediate temperatures (325–400 °C) to a submicron structure of bainite and in a high carbon high silicon steel transforming at low temperatures (200–350 °C) to nanostructured bainite. The role of the transformation driving force on the bainite plate thickness will be also discussed.

  6. Refinement and fracture mechanisms of as-cast QT700-6 alloy by alloying method

    Min-qiang Gao

    2017-01-01

    Full Text Available The as-cast QT700-6 alloy was synthesized with addition of a certain amount of copper, nickel, niobium and stannum elements by alloying method in a medium frequency induction furnace, aiming at improving its strength and toughness. Microstructures of the as-cast QT700-6 alloy were observed using a scanning-electron microscope (SEM and the mechanical properties were investigated using a universal tensile test machine. Results indicate that the ratio of pearlite/ferrite is about 9:1 and the graphite size is less than 40 μm in diameter in the as-cast QT700-6 alloy. The predominant refinement mechanism is attributed to the formation of niobium carbides, which increases the heterogeneous nucleus and hinders the growth of graphite. Meanwhile, niobium carbides also exist around the grain boundaries, which improve the strength of the ductile iron. The tensile strength and elongation of the as-cast QT700-6 alloy reach over 700 MPa and 6%, respectively, when the addition amount of niobium is 0.8%. The addition of copper and nickel elements contributed to the decrease of eutectoid transformation temperature, resulting in the decrease of pearlite lamellar spacing (about 248 nm, which is also beneficial to enhancing the tensile strength. The main fracture mechanism is cleavage fracture with the appearance of a small amount of dimples.

  7. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis.

    Lindahl, Erik; Azuara, Cyril; Koehl, Patrice; Delarue, Marc

    2006-07-01

    Normal mode analysis (NMA) is an efficient way to study collective motions in biomolecules that bypasses the computational costs and many limitations associated with full dynamics simulations. The NOMAD-Ref web server presented here provides tools for online calculation of the normal modes of large molecules (up to 100,000 atoms) maintaining a full all-atom representation of their structures, as well as access to a number of programs that utilize these collective motions for deformation and refinement of biomolecular structures. Applications include the generation of sets of decoys with correct stereochemistry but arbitrary large amplitude movements, the quantification of the overlap between alternative conformations of a molecule, refinement of structures against experimental data, such as X-ray diffraction structure factors or Cryo-EM maps and optimization of docked complexes by modeling receptor/ligand flexibility through normal mode motions. The server can be accessed at the URL http://lorentz.immstr.pasteur.fr/nomad-ref.php.

  8. Study of the crystallite size of nitrosylpentacyanoferrate through refinement of structures; Estudio del tamano de cristalita de nitrosilpentacianoferratos mediante refinamiento de estructuras

    Jimenez G, J.A.; Yee M, H.T. [ESFM-IPN, 07738 Mexico D.F. (Mexico); Balmaceda E, J. [IIM-UNAM, 04510 Mexico D.F. (Mexico); Reguera R, E. [CICATA-IPN, Av. Legaria 694, 11500 Mexico D.F. (Mexico)

    2006-07-01

    The development reached in the instrumentation and in the computer science of the diffraction of rays X, it has enlarged the reach of the method of powders considerably, in the resolution of crystalline structures of polycrystalline material converting it in a potent tool that, attended by spectroscopic techniques, it allows the fine characterization to atomic scale of having been accustomed to crystalline. In the thesis it is developed an effective methodology of determination of the crystallite size and structural refinement starting from data of diffraction of powders, based on the use of the equation of Sherrer for the estimate of the crystallite size and the method of Rietveld for the structural refinement; supplemented with the employment of the spectroscopic methods (IR and Moessbauer). The combined use of these techniques in the structural study of having been accustomed to crystalline lens of high complexity provides a novel and advanced work. The estimate of the crystallite size, it has been little explored to study accustomed to crystalline such as the pentacyanonitrosyl ferrates. One of the reasons for the which have intended to study the glass size in these structures it is due to that the molecular materials have attracted the attention of the international scientific community for their promissory properties in fields so diverse as: the absorption, desorption and separation of gases among others. Of the entreated information by means of databases and articles of scientific popularization were refined the structures of two compounds (NPCo and NPNi) obtained by powders diffraction; offering the possibility to develop a titled work: 'Physical description of the desorption of the water in nano structured material of nitrosyl penta cyano ferrates' which is carried out in parallel way to this thesis. This tools supplemented with the spectroscopic methods, potent the reach of the methods of diffraction of powders for the structural study of having

  9. A highly efficient sharp-interface immersed boundary method with adaptive mesh refinement for bio-inspired flow simulations

    Deng, Xiaolong; Dong, Haibo

    2017-11-01

    Developing a high-fidelity, high-efficiency numerical method for bio-inspired flow problems with flow-structure interaction is important for understanding related physics and developing many bio-inspired technologies. To simulate a fast-swimming big fish with multiple finlets or fish schooling, we need fine grids and/or a big computational domain, which are big challenges for 3-D simulations. In current work, based on the 3-D finite-difference sharp-interface immersed boundary method for incompressible flows (Mittal et al., JCP 2008), we developed an octree-like Adaptive Mesh Refinement (AMR) technique to enhance the computational ability and increase the computational efficiency. The AMR is coupled with a multigrid acceleration technique and a MPI +OpenMP hybrid parallelization. In this work, different AMR layers are treated separately and the synchronization is performed in the buffer regions and iterations are performed for the convergence of solution. Each big region is calculated by a MPI process which then uses multiple OpenMP threads for further acceleration, so that the communication cost is reduced. With these acceleration techniques, various canonical and bio-inspired flow problems with complex boundaries can be simulated accurately and efficiently. This work is supported by the MURI Grant Number N00014-14-1-0533 and NSF Grant CBET-1605434.

  10. Method of preparing an Al-Ti-B grain refiner for aluminium-comprising products, and a method of casting aluminium products

    Brinkman, H.J.; Duszczyk, J.; Katgerman, L.

    1999-01-01

    The invention relates to a method of preparing an Al-Ti-B grain refiner for cast aluminium-comprising products. According to the invention the preparation is realized by mixing powders selected from the group comprising aluminium, titanium, boron, and alloys and intermetallic compounds thereof, compressing, heating in an inert environment until an exothermic reaction is initiated and cooling. It has been shown that when the grain refiner thus prepared is applied, the quality of cast products ...

  11. Vibration-based health monitoring and model refinement of civil engineering structures

    Farrar, C.R.; Doebling, S.W.

    1997-10-01

    Damage or fault detection, as determined by changes in the dynamic properties of structures, is a subject that has received considerable attention in the technical literature beginning approximately 30 years ago. The basic idea is that changes in the structure`s properties, primarily stiffness, will alter the dynamic properties of the structure such as resonant frequencies and mode shapes, and properties derived from these quantities such as modal-based flexibility. Recently, this technology has been investigated for applications to health monitoring of large civil engineering structures. This presentation will discuss such a study undertaken by engineers from New Mexico Sate University, Sandia National Laboratory and Los Alamos National Laboratory. Experimental modal analyses were performed in an undamaged interstate highway bridge and immediately after four successively more severe damage cases were inflicted in the main girder of the structure. Results of these tests provide insight into the abilities of modal-based damage ID methods to identify damage and the current limitations of this technology. Closely related topics that will be discussed are the use of modal properties to validate computer models of the structure, the use of these computer models in the damage detection process, and the general lack of experimental investigation of large civil engineering structures.

  12. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...

  13. 2010 Diffraction Methods in Structural Biology

    Dr. Ana Gonzalez

    2011-03-10

    Advances in basic methodologies have played a major role in the dramatic progress in macromolecular crystallography over the past decade, both in terms of overall productivity and in the increasing complexity of the systems being successfully tackled. The 2010 Gordon Research Conference on Diffraction Methods in Structural Biology will, as in the past, focus on the most recent developments in methodology, covering all aspects of the process from crystallization to model building and refinement, complemented by examples of structural highlights and complementary methods. Extensive discussion will be encouraged and it is hoped that all attendees will participate by giving oral or poster presentations, the latter using the excellent poster display area available at Bates College. The relatively small size and informal atmosphere of the meeting provides an excellent opportunity for all participants, especially younger scientists, to meet and exchange ideas with leading methods developers.

  14. Method of cleansing and refining of liquid hydrocarbons and derivatives of hydrocarbons

    Hahn, C A; Nielsen, H

    1934-10-11

    A process is described for cleaning and refining liquid hydrocarbons and derivatives by utilization of acids, followed by washing partly with a basic solution, partly with clean water. The process is characterized by using, in connection with the acid solutions mentioned, a strong solution of a mixture of sulfuric acid and phosphoric acid.

  15. Unambiguous Determination of Intermolecular Hydrogen Bond of NMR Structure by Molecular Dynamics Refinement Using All-Atom Force Field and Implicit Solvent Model

    Jee, Jun Goo

    2010-01-01

    It has been shown that AMD refinement is very useful for defining an intermolecular hydrogen bond in NMR structure calculation. The refined structure also provides a clue for explaining the pH dependence in Ub and UIM complexes. As reported by Choi et al., serine-mediated hydrogen bonds are the third most populated hydrogen bonds found in protein-protein intermolecular interactions, after the backbone-backbone and backbone-aspartate ones. The abundance imposes the requirement of an method to determine the interface of protein-protein complexes. The precise geometry is particularly important in the complex structures between Ub and UBDs. Ub recognizes various targets with the same surface, where both hydrophobic and hydrophobic interactions are involved. Hence, the details of the hydrophilic interactions are necessary to find the common binding modes. The structure determination of a biomolecule by NMR depends heavily on the distance restraints derived by the NOE cross peaks that are observed between two protons within 6 A through space. Therefore, the existence of the NOE peaks and their correct assignments to two corresponding protons are essential for an accurate and precise structure determination. Recent developments of NOE assignment and calculation algorithms have enabled the determination of protein 3D structures without any manual interpretation, provided chemical shifts are assigned in most atoms and sufficient NOE peaks exist. Along with these advances, the necessity of determining complicated structures such as complexes is increasing

  16. Solution structure of tRNA{sup Val} from refinement of homology model against residual dipolar coupling and SAXS data

    Grishaev, Alexander, E-mail: AlexanderG@intra.niddk.nih.gov; Ying, Jinfa [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Canny, Marella D.; Pardi, Arthur [University of Colorado, Boulder, Department of Chemistry and Biochemistry, 215 UCB (United States)], E-mail: Arthur.Pardi@Colorado.edu; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

    2008-10-15

    A procedure is presented for refinement of a homology model of E. coli tRNA{sup Val}, originally based on the X-ray structure of yeast tRNA{sup Phe}, using experimental residual dipolar coupling (RDC) and small angle X-ray scattering (SAXS) data. A spherical sampling algorithm is described for refinement against SAXS data that does not require a globbic approximation, which is particularly important for nucleic acids where such approximations are less appropriate. Substantially higher speed of the algorithm also makes its application favorable for proteins. In addition to the SAXS data, the structure refinement employed a sparse set of NMR data consisting of 24 imino N-H{sup N} RDCs measured with Pf1 phage alignment, and 20 imino N-H{sup N} RDCs obtained from magnetic field dependent alignment of tRNA{sup Val}. The refinement strategy aims to largely retain the local geometry of the 58% identical tRNA{sup Phe} by ensuring that the atomic coordinates for short, overlapping segments of the ribose-phosphate backbone and the conserved base pairs remain close to those of the starting model. Local coordinate restraints are enforced using the non-crystallographic symmetry (NCS) term in the XPLOR-NIH or CNS software package, while still permitting modest movements of adjacent segments. The RDCs mainly drive the relative orientation of the helical arms, whereas the SAXS restraints ensure an overall molecular shape compatible with experimental scattering data. The resulting structure exhibits good cross-validation statistics (jack-knifed Q{sub free} = 14% for the Pf1 RDCs, compared to 25% for the starting model) and exhibits a larger angle between the two helical arms than observed in the X-ray structure of tRNA{sup Phe}, in agreement with previous NMR-based tRNA{sup Val} models.

  17. Grain refinement by cold deformation and recrystallization of bainite and acicular ferrite structures of C-Mn steels

    Hossein Nedjad, S.; Zahedi Moghaddam, Y.; Mamdouh Vazirabadi, A.; Shirazi, H.; Nili Ahmadabadi, M.

    2011-01-01

    Research highlights: → Bainite showed weak property improvement after rolling and annealing. → Additions of titanium and titanium oxide stimulated acicular ferrite. → Acicular ferrite obtained by nanoparticles exhibited very high strength. → Rolling and annealing of acicular ferrite gave substantial property improvement. - Abstract: The propensity of bainite and acicular ferrite structures of experimental C-Mn steels for enhanced grain refinement by combining phase transformation and plastic deformation has been investigated. Formation of acicular ferrite structures were stimulated with a small amount of titanium and titanium oxide nanoparticles added into the molten steels of high Mn concentrations. Isothermal transformations into the bainite and acicular ferrite structures were performed for 1.8 ks at 823 K after preliminary austenitization for 1.8 ks at 1523 K. Cold rolling for 50% thickness reduction was conducted on the isothermally transformed structures. Subsequent annealing of the deformed structures was conducted for 3.6 ks at 773, 873 and 973 K. Optical microscopy, scanning electron microscopy and tensile test were used for characterization of the studied steels. Cold rolling and annealing of the transformed structures at 873 K resulted in strengthening at the expense of ductility where an initial stage of recrystallization is realized. Acicular ferrite obtained by the addition of titanium into the molten steel exhibited the remarkable improvement of tensile properties. Discontinuous recrystallization of the deformed structures at 973 K leads to the formation of fine grains wherein acicular structures represented more enhanced grain refinement than bainite.

  18. Adaptive Mesh Refinement and High Order Geometrical Moment Method for the Simulation of Polydisperse Evaporating Sprays

    Essadki Mohamed

    2016-09-01

    Full Text Available Predictive simulation of liquid fuel injection in automotive engines has become a major challenge for science and applications. The key issue in order to properly predict various combustion regimes and pollutant formation is to accurately describe the interaction between the carrier gaseous phase and the polydisperse evaporating spray produced through atomization. For this purpose, we rely on the EMSM (Eulerian Multi-Size Moment Eulerian polydisperse model. It is based on a high order moment method in size, with a maximization of entropy technique in order to provide a smooth reconstruction of the distribution, derived from a Williams-Boltzmann mesoscopic model under the monokinetic assumption [O. Emre (2014 PhD Thesis, École Centrale Paris; O. Emre, R.O. Fox, M. Massot, S. Chaisemartin, S. Jay, F. Laurent (2014 Flow, Turbulence and Combustion 93, 689-722; O. Emre, D. Kah, S. Jay, Q.-H. Tran, A. Velghe, S. de Chaisemartin, F. Laurent, M. Massot (2015 Atomization Sprays 25, 189-254; D. Kah, F. Laurent, M. Massot, S. Jay (2012 J. Comput. Phys. 231, 394-422; D. Kah, O. Emre, Q.-H. Tran, S. de Chaisemartin, S. Jay, F. Laurent, M. Massot (2015 Int. J. Multiphase Flows 71, 38-65; A. Vié, F. Laurent, M. Massot (2013 J. Comp. Phys. 237, 277-310]. The present contribution relies on a major extension of this model [M. Essadki, S. de Chaisemartin, F. Laurent, A. Larat, M. Massot (2016 Submitted to SIAM J. Appl. Math.], with the aim of building a unified approach and coupling with a separated phases model describing the dynamics and atomization of the interface near the injector. The novelty is to be found in terms of modeling, numerical schemes and implementation. A new high order moment approach is introduced using fractional moments in surface, which can be related to geometrical quantities of the gas-liquid interface. We also provide a novel algorithm for an accurate resolution of the evaporation. Adaptive mesh refinement properly scaling on massively

  19. A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions

    Sala, Davide; Giachetti, Andrea; Luchinat, Claudio, E-mail: luchinat@cerm.unifi.it; Rosato, Antonio, E-mail: rosato@cerm.unifi.it [University of Florence, Magnetic Resonance Center (CERM) (Italy)

    2016-11-15

    The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions. By preparing multiple samples in each of which a different ion of the lanthanide series is introduced, it is possible to obtain multiple independent PCS datasets that can be used synergistically to generate protein structure ensembles (typically called bundles). For typical NMR-based determination of protein structure, it is necessary to perform an energetic refinement of such initial bundles to obtain final structures whose geometric quality is suitable for deposition in the PDB. This can be conveniently done by using restrained molecular dynamics simulations (rMD) in explicit solvent. However, there are no available protocols for rMD using multiple PCS datasets as part of the restraints. In this work, we extended the PCS module of the AMBER MD package to handle multiple datasets and tuned a previously developed protocol for NMR structure refinement to achieve consistent convergence with PCS restraints. Test calculations with real experimental data show that this new implementation delivers the expected improvement of protein geometry, resulting in final structures that are of suitable quality for deposition. Furthermore, we observe that also initial structures generated only with traditional restraints can be successfully refined using traditional and PCS restraints simultaneously.

  20. Dynamics of the European refining and petrochemical industry. Strategies, structure and change

    Steenbakkers, K.

    1997-01-01

    The changes in the market position of producers engaged in the oil refining and basic petrochemical industry on the Western European market are the central theme of this book. Analysis of this reshuffling process among these actors is conducted on three levels. First, research is carried out at the level of world regions. In order to understand the reorganization of oil refining and basic petrochemical production in Western Europe, it is necessary to explore the recent aggregate dynamics of these activities on a global scale. Second, the differences in strategic behaviour are exanuned at the level of groups of market participants, namely the major oil companies, the chemical companies, the state-owned companies from both consumer and producer countries, and the independents. Finally, the investment/disinvestment decisions in the Western European oil refining and basic petrochemical industry are investigated at the level of the individual firm. Particular emphasis is placed upon explaining why companies active in the sectors under study have followed different strategies, although they have been confronted with similar adverse market conditions in Western Europe during the last decades. 341 refs

  1. Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure

    Henriksen, Niel M.; Davis, Darrell R.; Cheatham, Thomas E. III

    2012-01-01

    Restrained molecular dynamics simulations are a robust, though perhaps underused, tool for the end-stage refinement of biomolecular structures. We demonstrate their utility—using modern simulation protocols, optimized force fields, and inclusion of explicit solvent and mobile counterions—by re-investigating the solution structures of two RNA hairpins that had previously been refined using conventional techniques. The structures, both domain 5 group II intron ribozymes from yeast ai5γ and Pylaiella littoralis, share a nearly identical primary sequence yet the published 3D structures appear quite different. Relatively long restrained MD simulations using the original NMR restraint data identified the presence of a small set of violated distance restraints in one structure and a possibly incorrect trapped bulge nucleotide conformation in the other structure. The removal of problematic distance restraints and the addition of a heating step yielded representative ensembles with very similar 3D structures and much lower pairwise RMSD values. Analysis of ion density during the restrained simulations helped to explain chemical shift perturbation data published previously. These results suggest that restrained MD simulations, with proper caution, can be used to “update” older structures or aid in the refinement of new structures that lack sufficient experimental data to produce a high quality result. Notable cautions include the need for sufficient sampling, awareness of potential force field bias (such as small angle deviations with the current AMBER force fields), and a proper balance between the various restraint weights.

  2. Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure

    Henriksen, Niel M.; Davis, Darrell R.; Cheatham, Thomas E. III, E-mail: tec3@utah.edu [College of Pharmacy, University of Utah, Department of Medicinal Chemistry (United States)

    2012-08-15

    Restrained molecular dynamics simulations are a robust, though perhaps underused, tool for the end-stage refinement of biomolecular structures. We demonstrate their utility-using modern simulation protocols, optimized force fields, and inclusion of explicit solvent and mobile counterions-by re-investigating the solution structures of two RNA hairpins that had previously been refined using conventional techniques. The structures, both domain 5 group II intron ribozymes from yeast ai5{gamma} and Pylaiella littoralis, share a nearly identical primary sequence yet the published 3D structures appear quite different. Relatively long restrained MD simulations using the original NMR restraint data identified the presence of a small set of violated distance restraints in one structure and a possibly incorrect trapped bulge nucleotide conformation in the other structure. The removal of problematic distance restraints and the addition of a heating step yielded representative ensembles with very similar 3D structures and much lower pairwise RMSD values. Analysis of ion density during the restrained simulations helped to explain chemical shift perturbation data published previously. These results suggest that restrained MD simulations, with proper caution, can be used to 'update' older structures or aid in the refinement of new structures that lack sufficient experimental data to produce a high quality result. Notable cautions include the need for sufficient sampling, awareness of potential force field bias (such as small angle deviations with the current AMBER force fields), and a proper balance between the various restraint weights.

  3. An efficient and target-oriented sample enrichment method for preparative separation of minor alkaloids by pH-zone-refining counter-current chromatography.

    Feng, Rui-Hong; Hou, Jin-Jun; Zhang, Yi-Bei; Pan, Hui-Qin; Yang, Wenzhi; Qi, Peng; Yao, Shuai; Cai, Lu-Ying; Yang, Min; Jiang, Bao-Hong; Liu, Xuan; Wu, Wan-Ying; Guo, De-An

    2015-08-28

    An efficient and target-oriented sample enrichment method was established to increase the content of the minor alkaloids in crude extract by using the corresponding two-phase solvent system applied in pH-zone-refining counter-current chromatography. The enrichment and separation of seven minor indole alkaloids from Uncaria rhynchophylla (Miq.) Miq. ex Havil(UR) were selected as an example to show the advantage of this method. An optimized two-phase solvent system composed of n-hexane-ethyl acetate-methanol-water (3:7:1:9, v/v) was used in this study, where triethylamine (TEA) as the retainer and hydrochloric acid (HCl) as the eluter were added at the equimolar of 10mM. Crude alkaloids of UR dissolved in the corresponding upper phase (containing 10mM TEA) were extracted twice with lower phase (containing 10mM TEA) and lower phase (containing 10mM HCl), respectively, the second lower phase extract was subjected to pH-zone-refining CCC separation after alkalization and desalination. Finally, from 10g of crude alkaloids, 4g of refined alkaloids was obtained and the total content of seven target indole alkaloids was increased from 4.64% to 15.78%. Seven indole alkaloids, including 54mg isocorynoxeine, 21mg corynoxeine, 46mg isorhynchophylline, 35mg rhynchophylline, 65mg hirsutine, 51mg hirsuteine and 27mg geissoschizine methylether were all simultaneously separated from 2.5g of refined alkaloids, with the purity of 86.4%, 97.5%, 90.3%, 92.1%, 98.5%, 92.3%, and 92.8%, respectively. The total content and purities of the seven minor indole alkaloids were tested by HPLC and their chemical structures were elucidated by ESI-HRMS and (1)H NMR. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. A novel high-temperature commensurate superstructure in a natural bariopyrochlore: A structural study by means of a multiphase crystal structure refinement

    Bindi, L.; Petříček, Václav; Withers, R. L.; Zoppi, M.; Bonazzi, P.

    2006-01-01

    Roč. 179, - (2006), s. 716-725 ISSN 0022-4596 R&D Projects: GA ČR(CZ) GA202/03/0430 Institutional research plan: CEZ:AV0Z10100521 Keywords : pyrochlore * superstructure * X-ray data * multiphase structure refinement * TEM study Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.107, year: 2006

  5. Patched based methods for adaptive mesh refinement solutions of partial differential equations

    Saltzman, J.

    1997-09-02

    This manuscript contains the lecture notes for a course taught from July 7th through July 11th at the 1997 Numerical Analysis Summer School sponsored by C.E.A., I.N.R.I.A., and E.D.F. The subject area was chosen to support the general theme of that year`s school which is ``Multiscale Methods and Wavelets in Numerical Simulation.`` The first topic covered in these notes is a description of the problem domain. This coverage is limited to classical PDEs with a heavier emphasis on hyperbolic systems and constrained hyperbolic systems. The next topic is difference schemes. These schemes are the foundation for the adaptive methods. After the background material is covered, attention is focused on a simple patched based adaptive algorithm and its associated data structures for square grids and hyperbolic conservation laws. Embellishments include curvilinear meshes, embedded boundary and overset meshes. Next, several strategies for parallel implementations are examined. The remainder of the notes contains descriptions of elliptic solutions on the mesh hierarchy, elliptically constrained flow solution methods and elliptically constrained flow solution methods with diffusion.

  6. Determination of the populations and structures of multiple conformers in an ensemble from NMR data: Multiple-copy refinement of nucleic acid structures using floating weights

    Goerler, Adrian; Ulyanov, Nikolai B.; James, Thomas L.

    2000-01-01

    A new algorithm is presented for determination of structural conformers and their populations based on NMR data. Restrained Metropolis Monte Carlo simulations or restrained energy minimizations are performed for several copies of a molecule simultaneously. The calculations are restrained with dipolar relaxation rates derived from measured NOE intensities via complete relaxation matrix analysis. The novel feature of the algorithm is that the weights of individual conformers are determined in every refinement step, by the quadratic programming algorithm, in such a way that the restraint energy is minimized. Its design ensures that the calculated populations of the individual conformers are based only on experimental restraints. Presence of internally inconsistent restraints is the driving force for determination of distinct multiple conformers. The method is applied to various simulated test systems. Conformational calculations on nucleic acids are carried out using generalized helical parameters with the program DNAminiCarlo. From different mixtures of A- and B-DNA, minor fractions as low as 10% could be determined with restrained energy minimization. For B-DNA with three local conformers (C2'-endo, O4'-exo, C3'-endo), the minor O4'-exo conformer could not be reliably determined using NOE data typically measured for DNA. The other two conformers, C2'-endo and C3'-endo, could be reproduced by Metropolis Monte Carlo simulated annealing. The behavior of the algorithm in various situations is analyzed, and a number of refinement protocols are discussed. Prior to application of this algorithm to each experimental system, it is suggested that the presence of internal inconsistencies in experimental data be ascertained. In addition, because the performance of the algorithm depends on the type of conformers involved and experimental data available, it is advisable to carry out test calculations with simulated data modeling each experimental system studied

  7. Refining revolution

    Fesharaki, F.; Isaak, D.

    1984-01-01

    A review of changes in the oil refining industry since 1973 examines the drop in capacity use and its effect on profits of the Organization of Economic Cooperation and Development (OECD) countries compared to world refining. OPEC countries used their new oil revenues to expand Gulf refineries, which put additional pressure on OECD refiners. OPEC involvement in global marketing, however, could help to secure supplies. Scrapping some older OECD refineries could improve the percentage of capacity in use if new construction is kept to a minimum. Other issues facing refiners are the changes in oil demand patterns and government responses to the market. 2 tables.

  8. Hirshfeld atom refinement.

    Capelli, Silvia C; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan

    2014-09-01

    Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

  9. Creating value in refining

    Cobb, C.B.

    2001-01-01

    This article focuses on recent developments in the US refining industry and presents a model for improving the performance of refineries based on the analysis of the refining industry by Cap Gemini Ernst and Young. The identification of refineries in risk of failing, the construction of pipelines for refinery products from Gulf State refineries, mergers and acquisitions, and poor financial performance are discussed. Current challenges concerning the stagnant demand for refinery products, environmental regulations, and shareholder value are highlighted. The structure of the industry, the creation of value in refining, and the search for business models are examined. The top 25 US companies and US refining business groups are listed

  10. A rich solution spray as a refining method in a small capacity, single effect, solar assisted absorption machine with the pair NH3/H2O: Experimental results

    Mendes, L.F.; Collares-Pereira, M.; Ziegler, F.

    2007-01-01

    Ammonia vapour refining is a common procedure in ammonia-water absorption machines. A solar assisted single effect absorption machine that uses the pair ammonia-water was developed and tested. Its desorber has a built-in adiabatic refining column constituted by a rich solution spray. The refining method proved its feasibility. The spray provided a more or less constant ammonia vapour enrichment of about 1% which is enough for the working temperature ranges of this type of machine. It was also verified that the refining effect of the spray is almost independent of the refrigerant vapour and solution mass flow rates

  11. Computational methods and modeling. 3. Adaptive Mesh Refinement for the Nodal Integral Method and Application to the Convection-Diffusion Equation

    Torej, Allen J.; Rizwan-Uddin

    2001-01-01

    The nodal integral method (NIM) has been developed for several problems, including the Navier-Stokes equations, the convection-diffusion equation, and the multigroup neutron diffusion equations. The coarse-mesh efficiency of the NIM is not fully realized in problems characterized by a wide range of spatial scales. However, the combination of adaptive mesh refinement (AMR) capability with the NIM can recover the coarse mesh efficiency by allowing high degrees of resolution in specific localized areas where it is needed and by using a lower resolution everywhere else. Furthermore, certain features of the NIM can be fruitfully exploited in the application of the AMR process. In this paper, we outline a general approach to couple nodal schemes with AMR and then apply it to the convection-diffusion (energy) equation. The development of the NIM with AMR capability (NIMAMR) is based on the well-known Berger-Oliger method for structured AMR. In general, the main components of all AMR schemes are 1. the solver; 2. the level-grid hierarchy; 3. the selection algorithm; 4. the communication procedures; 5. the governing algorithm. The first component, the solver, consists of the numerical scheme for the governing partial differential equations and the algorithm used to solve the resulting system of discrete algebraic equations. In the case of the NIM-AMR, the solver is the iterative approach to the solution of the set of discrete equations obtained by applying the NIM. Furthermore, in the NIM-AMR, the level-grid hierarchy (the second component) is based on the Hierarchical Adaptive Mesh Refinement (HAMR) system,6 and hence, the details of the hierarchy are omitted here. In the selection algorithm, regions of the domain that require mesh refinement are identified. The criterion to select regions for mesh refinement can be based on the magnitude of the gradient or on the Richardson truncation error estimate. Although an excellent choice for the selection criterion, the Richardson

  12. Structure of Insulin: Results of joint neutron and X-ray refinement

    Wlodawer, A; Savage, H; Dodson, G

    1989-02-01

    Neutron diffraction data for porcine 2Zn insulin were collected to 2.2 A resolution from a single crystal deuterated by slow exchange of mother liquor. A joint neutron/X-ray restrained-least-squares refinement was undertaken using the neutron data, as well as the 1.5 A resolution X-ray data collected previously. The final R factors were 0.182 for the X-ray data and 0.191 for the neutron data. Resulting atomic coordinates were compared with the initial X-ray model, showing a total r.m.s. shift of 0.36 A for the protein and 0.6 A for the solvent. Protonation of a number of individual amino acids was investigated by analysis of the neutron maps. No D atoms were found between the carboxylates of Glu B13 which make an intermolecular contact, suggesting nonbonded interaction rather than the predicted hydrogen bond. Amide hydrogen exchange was investigated in a refinement of their atomic occupancies. Regions of unexchanged amide groups were found in the center of the B helices. The results of this study emphasize the limited amount of information available in neutron diffraction studies of proteins at resolution lower than 2 A.

  13. Method of preparing an Al-Ti-B grain refiner for aluminium-comprising products, and a method of casting aluminium products

    Brinkman, H.J.; Duszczyk, J.; Katgerman, L.

    1999-01-01

    The invention relates to a method of preparing an Al-Ti-B grain refiner for cast aluminium-comprising products. According to the invention the preparation is realized by mixing powders selected from the group comprising aluminium, titanium, boron, and alloys and intermetallic compounds thereof,

  14. Application of the heat-balance and refined integral methods to the Korteweg-de Vries equation

    Myers Timothy G.

    2009-01-01

    Full Text Available In this paper we consider approximate travelling wave solutions to the Korteweg-de Vries equation. The heat-balance integral method is first applied to the problem, using two different quartic approximating functions, and then the refined integral method is investigated. We examine two types of solution, chosen by matching the wave speed to that of the exact solution and by imposing the same area. The first set of solutions is generally better with an error that is fixed in time. The second set of solutions has an error that grows with time. This is shown to be due to slight discrepancies in the wave speed.

  15. Synthesis of hydroxyapatite and structural refinement by X-ray diffraction

    Araujo, Jorge Correa de

    2007-01-01

    A sample of hydroxyapatite was synthesized and its crystalline structure was analyzed by X-ray diffraction by means of the Rietveld method. Two functions were used to fit the peak profiles, modified Voigt (TCHZ) and Pearson VII. The occupational factors and lattice parameters obtained by both models show that the sample does not contain relevant cationic substitutions. The interatomic distances from Ca1 to oxygens O1, O2 and O3 were adequate for a pure hydroxyapatite without defect at site Ca1. Besides, the use of multiple lines in planes (300) and (002) associated with the model Pearson VII resulted in good agreement with the TCHZ model with respect to the size-strain effects with an ellipsoidal shape of crystallites. In conclusion, the procedures adopted in the synthesis of hydroxyapatite produced a pure and crystalline material. The experimental results of transmission electron microscopy confirmed the predicted shape of crystals. (author)

  16. Refined Modeling of Flexural Deformation of Layered Plates with a Regular Structure Made from Nonlinear Hereditary Materials

    Yankovskii, A. P.

    2018-01-01

    On the basis of constitutive equations of the Rabotnov nonlinear hereditary theory of creep, the problem on the rheonomic flexural behavior of layered plates with a regular structure is formu-lated. Equations allowing one to describe, with different degrees of accuracy, the stress-strain state of such plates with account of their weakened resistance to transverse shear were ob-tained. From them, the relations of the nonclassical Reissner- and Reddytype theories can be found. For axially loaded annular plates clamped at one edge and loaded quasistatically on the other edge, a simplified version of the refined theory, whose complexity is comparable to that of the Reissner and Reddy theories, is developed. The flexural strains of such metal-composite annular plates in shortterm and long-term loadings at different levels of heat action are calcu-lated. It is shown that, for plates with a relative thickness of order of 1/10, neither the classical theory, nor the traditional nonclassical Reissner and Reddy theories guarantee reliable results for deflections even with the rough 10% accuracy. The accuracy of these theories decreases at elevated temperatures and with time under long-term loadings of structures. On the basic of relations of the refined theory, it is revealed that, in bending of layered metal-composite heat-sensitive plates under elevated temperatures, marked edge effects arise in the neighborhood of the supported edge, which characterize the shear of these structures in the transverse direction

  17. A high-order finite-volume method for hyperbolic conservation laws on locally-refined grids

    McCorquodale, Peter; Colella, Phillip

    2011-01-28

    We present a fourth-order accurate finite-volume method for solving time-dependent hyperbolic systems of conservation laws on Cartesian grids with multiple levels of refinement. The underlying method is a generalization of that in [5] to nonlinear systems, and is based on using fourth-order accurate quadratures for computing fluxes on faces, combined with fourth-order accurate Runge?Kutta discretization in time. To interpolate boundary conditions at refinement boundaries, we interpolate in time in a manner consistent with the individual stages of the Runge-Kutta method, and interpolate in space by solving a least-squares problem over a neighborhood of each target cell for the coefficients of a cubic polynomial. The method also uses a variation on the extremum-preserving limiter in [8], as well as slope flattening and a fourth-order accurate artificial viscosity for strong shocks. We show that the resulting method is fourth-order accurate for smooth solutions, and is robust in the presence of complex combinations of shocks and smooth flows.

  18. An Isogeometric Design-through-analysis Methodology based on Adaptive Hierarchical Refinement of NURBS, Immersed Boundary Methods, and T-spline CAD Surfaces

    2012-01-22

    Bungartz HJ, Rank E, Niggl A, Romberg R. Extending the p-Version of Finite Elements by an Octree-Based Hierarchy. In: Widlund OB, Keyes DE (eds...generalization to higher dimensions. We test hierarchical refinement of NURBS for some elementary fluid and structural analysis problems in two and three...with straightforward implementation in tree data structures and simple generalization to higher dimensions. We test hierarchical refinement of NURBS

  19. Liver segmentation in contrast enhanced CT data using graph cuts and interactive 3D segmentation refinement methods

    Beichel, Reinhard; Bornik, Alexander; Bauer, Christian; Sorantin, Erich

    2012-01-01

    Purpose: Liver segmentation is an important prerequisite for the assessment of liver cancer treatment options like tumor resection, image-guided radiation therapy (IGRT), radiofrequency ablation, etc. The purpose of this work was to evaluate a new approach for liver segmentation. Methods: A graph cuts segmentation method was combined with a three-dimensional virtual reality based segmentation refinement approach. The developed interactive segmentation system allowed the user to manipulate volume chunks and/or surfaces instead of 2D contours in cross-sectional images (i.e, slice-by-slice). The method was evaluated on twenty routinely acquired portal-phase contrast enhanced multislice computed tomography (CT) data sets. An independent reference was generated by utilizing a currently clinically utilized slice-by-slice segmentation method. After 1 h of introduction to the developed segmentation system, three experts were asked to segment all twenty data sets with the proposed method. Results: Compared to the independent standard, the relative volumetric segmentation overlap error averaged over all three experts and all twenty data sets was 3.74%. Liver segmentation required on average 16 min of user interaction per case. The calculated relative volumetric overlap errors were not found to be significantly different [analysis of variance (ANOVA) test, p = 0.82] between experts who utilized the proposed 3D system. In contrast, the time required by each expert for segmentation was found to be significantly different (ANOVA test, p = 0.0009). Major differences between generated segmentations and independent references were observed in areas were vessels enter or leave the liver and no accepted criteria for defining liver boundaries exist. In comparison, slice-by-slice based generation of the independent standard utilizing a live wire tool took 70.1 min on average. A standard 2D segmentation refinement approach applied to all twenty data sets required on average 38.2 min of

  20. Liver segmentation in contrast enhanced CT data using graph cuts and interactive 3D segmentation refinement methods

    Beichel, Reinhard; Bornik, Alexander; Bauer, Christian; Sorantin, Erich [Departments of Electrical and Computer Engineering and Internal Medicine, Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, Iowa 52242 (United States); Institute for Computer Graphics and Vision, Graz University of Technology, Inffeldgasse 16, A-8010 Graz (Austria); Department of Electrical and Computer Engineering, Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, Iowa 52242 (United States); Department of Radiology, Medical University Graz, Auenbruggerplatz 34, A-8010 Graz (Austria)

    2012-03-15

    Purpose: Liver segmentation is an important prerequisite for the assessment of liver cancer treatment options like tumor resection, image-guided radiation therapy (IGRT), radiofrequency ablation, etc. The purpose of this work was to evaluate a new approach for liver segmentation. Methods: A graph cuts segmentation method was combined with a three-dimensional virtual reality based segmentation refinement approach. The developed interactive segmentation system allowed the user to manipulate volume chunks and/or surfaces instead of 2D contours in cross-sectional images (i.e, slice-by-slice). The method was evaluated on twenty routinely acquired portal-phase contrast enhanced multislice computed tomography (CT) data sets. An independent reference was generated by utilizing a currently clinically utilized slice-by-slice segmentation method. After 1 h of introduction to the developed segmentation system, three experts were asked to segment all twenty data sets with the proposed method. Results: Compared to the independent standard, the relative volumetric segmentation overlap error averaged over all three experts and all twenty data sets was 3.74%. Liver segmentation required on average 16 min of user interaction per case. The calculated relative volumetric overlap errors were not found to be significantly different [analysis of variance (ANOVA) test, p = 0.82] between experts who utilized the proposed 3D system. In contrast, the time required by each expert for segmentation was found to be significantly different (ANOVA test, p = 0.0009). Major differences between generated segmentations and independent references were observed in areas were vessels enter or leave the liver and no accepted criteria for defining liver boundaries exist. In comparison, slice-by-slice based generation of the independent standard utilizing a live wire tool took 70.1 min on average. A standard 2D segmentation refinement approach applied to all twenty data sets required on average 38.2 min of

  1. Development of an object oriented nodal code using the refined AFEN derived from the method of component decomposition

    Noh, J. M.; Yoo, J. W.; Joo, H. K.

    2004-01-01

    In this study, we invented a method of component decomposition to derive the systematic inter-nodal coupled equations of the refined AFEN method and developed an object oriented nodal code to solve the derived coupled equations. The method of component decomposition decomposes the intra-nodal flux expansion of a nodal method into even and odd components in three dimensions to reduce the large coupled linear system equation into several small single equations. This method requires no additional technique to accelerate the iteration process to solve the inter-nodal coupled equations, since the derived equations can automatically act as the coarse mesh re-balance equations. By utilizing the object oriented programming concepts such as abstraction, encapsulation, inheritance and polymorphism, dynamic memory allocation, and operator overloading, we developed an object oriented nodal code that can facilitate the input/output and the dynamic control of the memories, and can make the maintenance easy. (authors)

  2. Liver segmentation in contrast enhanced CT data using graph cuts and interactive 3D segmentation refinement methods.

    Beichel, Reinhard; Bornik, Alexander; Bauer, Christian; Sorantin, Erich

    2012-03-01

    Liver segmentation is an important prerequisite for the assessment of liver cancer treatment options like tumor resection, image-guided radiation therapy (IGRT), radiofrequency ablation, etc. The purpose of this work was to evaluate a new approach for liver segmentation. A graph cuts segmentation method was combined with a three-dimensional virtual reality based segmentation refinement approach. The developed interactive segmentation system allowed the user to manipulate volume chunks and∕or surfaces instead of 2D contours in cross-sectional images (i.e, slice-by-slice). The method was evaluated on twenty routinely acquired portal-phase contrast enhanced multislice computed tomography (CT) data sets. An independent reference was generated by utilizing a currently clinically utilized slice-by-slice segmentation method. After 1 h of introduction to the developed segmentation system, three experts were asked to segment all twenty data sets with the proposed method. Compared to the independent standard, the relative volumetric segmentation overlap error averaged over all three experts and all twenty data sets was 3.74%. Liver segmentation required on average 16 min of user interaction per case. The calculated relative volumetric overlap errors were not found to be significantly different [analysis of variance (ANOVA) test, p = 0.82] between experts who utilized the proposed 3D system. In contrast, the time required by each expert for segmentation was found to be significantly different (ANOVA test, p = 0.0009). Major differences between generated segmentations and independent references were observed in areas were vessels enter or leave the liver and no accepted criteria for defining liver boundaries exist. In comparison, slice-by-slice based generation of the independent standard utilizing a live wire tool took 70.1 min on average. A standard 2D segmentation refinement approach applied to all twenty data sets required on average 38.2 min of user interaction

  3. Mechanical Properties of Al-Si-Mg Alloy Castings as a Function of Structure Refinement and Porosity Fraction

    Hajkowski M.

    2012-12-01

    Full Text Available During design of the casting products technology, an important issue is a possibility of prediction of mechanical properties resulting from the course of the casting solidification process. Frequently there is a need for relations describing mechanical properties of silumin alloys as a function of phase refinement in a structure and a porosity fraction, and relations describing phase refinement in the structure and the porosity fraction as a function of solidification conditions. The study was conducted on castings of a 22 mm thick plate, made of EN AC-AlSi7Mg0,3 alloy in moulds: of quartz sand, of quartz sand with chill and in permanent moulds. On the basis of cooling curves, values of cooling rate in various casting parts were calculated. The paper also presents results of examination of distance between arms in dendrites of a solid solution α (DASL, precipitations length of silicon in an eutectic (DlSi and gas-shrinkage porosity (Por as a function of cooling rate. Statistical relations of DASL, DlSi, Por as a function of cooling rate and statistical multiparameter dependencies describing mechanical properties (tensile strength, yield strength, elongation of alloy as a function of DASL, DlSi and Por are also presented in the paper.

  4. Modeling of the inhomogeneity of grain refinement during combined metal forming process by finite element and cellular automata methods

    Majta, Janusz; Madej, Łukasz; Svyetlichnyy, Dmytro S.; Perzyński, Konrad; Kwiecień, Marcin, E-mail: mkwiecie@agh.edu.pl; Muszka, Krzysztof

    2016-08-01

    The potential of discrete cellular automata technique to predict the grain refinement in wires produced using combined metal forming process is presented and discussed within the paper. The developed combined metal forming process can be treated as one of the Severe Plastic Deformation (SPD) techniques that consists of three different modes of deformation: asymmetric drawing with bending, namely accumulated angular drawing (AAD), wire drawing (WD) and wire flattening (WF). To accurately replicate complex stress state both at macro and micro scales during subsequent deformations two stage modeling approach was used. First, the Finite Element Method (FEM), implemented in commercial ABAQUS software, was applied to simulate entire combined forming process at the macro scale level. Then, based on FEM results, the Cellular Automata (CA) method was applied for simulation of grain refinement at the microstructure level. Data transferred between FEM and CA methods included set of files with strain tensor components obtained from selected integration points in the macro scale model. As a result of CA simulation, detailed information on microstructure evolution during severe plastic deformation conditions was obtained, namely: changes of shape and sizes of modeled representative volume with imposed microstructure, changes of the number of grains, subgrains and dislocation cells, development of grain boundaries angle distribution as well as changes in the pole figures. To evaluate CA model predictive capabilities, results of computer simulation were compared with scanning electron microscopy and electron back scattered diffraction images (SEM/EBSD) studies of samples after AAD+WD+WF process.

  5. Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of an oligodeoxyribonucleotide duplex refined via a hybrid relaxation matrix procedure

    Powers, R.; Jones, C.R.; Gorenstein, D.G.

    1990-01-01

    Assignment of the 1H and 31P resonances of a decamer DNA duplex, d(CGCTTAAGCG)2 was determined by two-dimensional COSY, NOESY and 1H-31P Pure Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. The solution structure of the decamer was calculated by an iterative hybrid relaxation matrix method combined with NOESY-distance restrained molecular dynamics. The distances from the 2D NOESY spectra were calculated from the relaxation rate matrix which were evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix-derived distances were then used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure was then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete. JH3'-P coupling constants for each of the phosphates of the decamer were obtained from 1H-31P J-resolved selective proton flip 2D spectra. By using a modified Karplus relationship the C4'-C3'-O3'-P torsional angles were obtained. Comparison of the 31P chemical shifts and JH3'-P coupling constants of this sequence has allowed a greater insight into the various factors responsible for 31P chemical shift variations in oligonucleotides. It also provides an important probe of the sequence-dependent structural variation of the deoxyribose phosphate backbone of DNA in solution. These correlations are consistent with the hypothesis that changes in local helical structure perturb the deoxyribose phosphate backbone. The variation of the 31P chemical shift, and the degree of this variation from one base step to the next is proposed as a potential probe of local helical conformation within the DNA double helix

  6. Structure of the Yersinia pestis tip protein LcrV refined to 1.65 Å resolution

    Chaudhury, Sukanya; Battaile, Kevin P.; Lovell, Scott; Plano, Gregory V.; De Guzman, Roberto N.

    2013-01-01

    Here, the crystal structure of Yersinia pestis tip protein LcrV is reported at a resolution of 1.65 Å. The human pathogen Yersinia pestis requires the assembly of the type III secretion system (T3SS) for virulence. The structural component of the T3SS contains an external needle and a tip complex, which is formed by LcrV in Y. pestis. The structure of an LcrV triple mutant (K40A/D41A/K42A) in a C273S background has previously been reported to 2.2 Å resolution. Here, the crystal structure of LcrV without the triple mutation in a C273S background is reported at a higher resolution of 1.65 Å. Overall the two structures are similar, but there are also notable differences, particularly near the site of the triple mutation. The refined structure revealed a slight shift in the backbone positions of residues Gly28–Asn43 and displayed electron density in the loop region consisting of residues Ile46–Val63, which was disordered in the original structure. In addition, the helical turn region spanning residues Tyr77–Gln95 adopts a different orientation

  7. Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures

    Genshaft, Alexander; Moser, Joe-Ann S.; D'Antonio, Edward L.; Bowman, Christine M.; Christianson, David W.

    2013-01-01

    The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular “switch” for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly-accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations. PMID:23401043

  8. X-ray refinement of the structure of (N,N'-(3-Aza-1,5-pentanediyl)-bos(salicylideneiminato))dioxouranium(VI)

    Benetollo, F; Bombieri, G [Consiglio Nazionale delle Ricerche, Padua (Italy). Lab. di Chimica e Tecnologia dei Radioelementi; Smith, A J [Sheffield Univ. (UK)

    1979-12-15

    C/sub 18/H/sub 19/N/sub 3/O/sub 4/U, (U(C/sub 18/H/sub 19/N/sub 3/O/sub 2/)O/sub 2/), orthorhombic, Pnma, a=10.473 (3), b=21.803 (10), c=8.024 (2) A, V=1832.2 A/sup 3/, Z=4, Dsub(c)=2.10 Mg m/sup -3/, ..mu..(Mo K..cap alpha..)=8.48 mm/sup -1/, lambda(Mo K..cap alpha..)=0.7107 A. The structure has been refined by full-matrix least-squares methods to an R of 0.036 for 1272 observed reflections. The results confirm those of an earlier structure determination but give interatomic distances and angles with greater accuracy. Anisotropic temperature factors are introduced for all non-hydrogen atoms.

  9. A mass-conserving lattice Boltzmann method with dynamic grid refinement for immiscible two-phase flows

    Fakhari, Abbas; Geier, Martin; Lee, Taehun

    2016-01-01

    A mass-conserving lattice Boltzmann method (LBM) for multiphase flows is presented in this paper. The proposed LBM improves a previous model (Lee and Liu, 2010 [21]) in terms of mass conservation, speed-up, and efficiency, and also extends its capabilities for implementation on non-uniform grids. The presented model consists of a phase-field lattice Boltzmann equation (LBE) for tracking the interface between different fluids and a pressure-evolution LBM for recovering the hydrodynamic properties. In addition to the mass conservation property and the simplicity of the algorithm, the advantages of the current phase-field LBE are that it is an order of magnitude faster than the previous interface tracking LBE proposed by Lee and Liu (2010) [21] and it requires less memory resources for data storage. Meanwhile, the pressure-evolution LBM is equipped with a multi-relaxation-time (MRT) collision operator to facilitate attainability of small relaxation rates thereby allowing simulation of multiphase flows at higher Reynolds numbers. Additionally, we reformulate the presented MRT-LBM on nonuniform grids within an adaptive mesh refinement (AMR) framework. Various benchmark studies such as a rising bubble and a falling drop under buoyancy, droplet splashing on a wet surface, and droplet coalescence onto a fluid interface are conducted to examine the accuracy and versatility of the proposed AMR-LBM. The proposed model is further validated by comparing the results with other LB models on uniform grids. A factor of about 20 in savings of computational resources is achieved by using the proposed AMR-LBM. As a more demanding application, the Kelvin–Helmholtz instability (KHI) of a shear-layer flow is investigated for both density-matched and density-stratified binary fluids. The KHI results of the density-matched fluids are shown to be in good agreement with the benchmark AMR results based on the sharp-interface approach. When a density contrast between the two fluids exists, a

  10. A mass-conserving lattice Boltzmann method with dynamic grid refinement for immiscible two-phase flows

    Fakhari, Abbas, E-mail: afakhari@nd.edu [Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556 (United States); Geier, Martin [TU Braunschweig, Institute for Computational Modeling in Civil Engineering (iRMB), TU-Braunschweig, Pockelsstr. 3, 38106 Braunschweig (Germany); Lee, Taehun [Department of Mechanical Engineering, The City College of the City University of New York, New York, NY 10031 (United States)

    2016-06-15

    A mass-conserving lattice Boltzmann method (LBM) for multiphase flows is presented in this paper. The proposed LBM improves a previous model (Lee and Liu, 2010 [21]) in terms of mass conservation, speed-up, and efficiency, and also extends its capabilities for implementation on non-uniform grids. The presented model consists of a phase-field lattice Boltzmann equation (LBE) for tracking the interface between different fluids and a pressure-evolution LBM for recovering the hydrodynamic properties. In addition to the mass conservation property and the simplicity of the algorithm, the advantages of the current phase-field LBE are that it is an order of magnitude faster than the previous interface tracking LBE proposed by Lee and Liu (2010) [21] and it requires less memory resources for data storage. Meanwhile, the pressure-evolution LBM is equipped with a multi-relaxation-time (MRT) collision operator to facilitate attainability of small relaxation rates thereby allowing simulation of multiphase flows at higher Reynolds numbers. Additionally, we reformulate the presented MRT-LBM on nonuniform grids within an adaptive mesh refinement (AMR) framework. Various benchmark studies such as a rising bubble and a falling drop under buoyancy, droplet splashing on a wet surface, and droplet coalescence onto a fluid interface are conducted to examine the accuracy and versatility of the proposed AMR-LBM. The proposed model is further validated by comparing the results with other LB models on uniform grids. A factor of about 20 in savings of computational resources is achieved by using the proposed AMR-LBM. As a more demanding application, the Kelvin–Helmholtz instability (KHI) of a shear-layer flow is investigated for both density-matched and density-stratified binary fluids. The KHI results of the density-matched fluids are shown to be in good agreement with the benchmark AMR results based on the sharp-interface approach. When a density contrast between the two fluids exists, a

  11. Discontinuous Galerkin finite element method with anisotropic local grid refinement for inviscid compressible flows

    van der Vegt, Jacobus J.W.; van der Ven, H.

    1998-01-01

    A new discretization method for the three-dimensional Euler equations of gas dynamics is presented, which is based on the discontinuous Galerkin finite element method. Special attention is paid to an efficient implementation of the discontinuous Galerkin method that minimizes the number of flux

  12. Fourier Collocation Approach With Mesh Refinement Method for Simulating Transit-Time Ultrasonic Flowmeters Under Multiphase Flow Conditions.

    Simurda, Matej; Duggen, Lars; Basse, Nils T; Lassen, Benny

    2018-02-01

    A numerical model for transit-time ultrasonic flowmeters operating under multiphase flow conditions previously presented by us is extended by mesh refinement and grid point redistribution. The method solves modified first-order stress-velocity equations of elastodynamics with additional terms to account for the effect of the background flow. Spatial derivatives are calculated by a Fourier collocation scheme allowing the use of the fast Fourier transform, while the time integration is realized by the explicit third-order Runge-Kutta finite-difference scheme. The method is compared against analytical solutions and experimental measurements to verify the benefit of using mapped grids. Additionally, a study of clamp-on and in-line ultrasonic flowmeters operating under multiphase flow conditions is carried out.

  13. Some refinements on the comparison of areal sampling methods via simulation

    Jeffrey Gove

    2017-01-01

    The design of forest inventories and development of new sampling methods useful in such inventories normally have a two-fold target of design unbiasedness and minimum variance in mind. Many considerations such as costs go into the choices of sampling method for operational and other levels of inventory. However, the variance in terms of meeting a specified level of...

  14. Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

    Bratholm, Lars Andersen

    to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...... mechanics / molecular mechanics (QM/MM) computations of chemical shieldings. Several improvements to the predictor is ongoing, where among other things, kernel based machine learning techniques have successfully been used to improve the quantum mechanical level of theory used in the predictions....

  15. Crystallographic computing system Jana2006: solution and refinement of twinned structures

    Petříček, Václav; Dušek, Michal; Plášil, Jakub

    2016-01-01

    Roč. 231, č. 10 (2016), s. 583-599 ISSN 2194-4946 R&D Projects: GA ČR GA15-12653S; GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : crystal structure analysis * Jana2006 * twinning Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.179, year: 2016

  16. Measurements of Residual Stresses In Cold-Rolled 304 Stainless Steel Plates Using X-Ray Diffraction with Rietveld Refinement Method

    Parikin; Killen, P; Rafterry, A.

    2009-01-01

    The determination of the residual stresses using X-ray powder diffraction in a series of cold-rolled 304 stainless steel plates, deforming 0, 34, 84, 152, 158, 175 and 196 % reduction in thickness has been carried out. The diffraction data were analyzed using the Rietveld structure refinement method. The analysis shows that for all specimens, the martensite particles are closely in compression and the austenite matrix is in tension. Both the martensite and austenite, for a sample reducing 34% in thickness (containing of about 1% martensite phase) the average lattice strains are anisotropic and decrease approximately exponential with an increase in the corresponding percent reduction (essentially phase content). It is shown that this feature can be qualitatively understood by taking into consideration the thermal expansion mismatch between the martensite and austenite grains. Also, for all cold-rolled stainless steel specimens, the diffraction peaks are broader than the unrolled one (instrumental resolution), indicating that the strains in these specimens are inhomogeneous. From an analysis of the refined peak shape parameters, the average root-mean square strain, which describes the distribution of the inhomogeneous strain field, was predicted. The average residual stresses in cold-rolled 304 stainless steel plates showed a combination effect of hydrostatic stresses of the martensite particles and the austenite matrix. (author)

  17. Single crystal growth and structure refinements of CsMxTe2-xO6 (M = Al, Ga, Ge, In) pyrochlores

    Siritanon, Theeranun; Sleight, A.W.; Subramanian, M.A.

    2011-01-01

    Graphical abstract: Single crystals of CsM x Te 2-x O 6 pyrochlores with M = Al, Ga, Ge, and In have been grown and structure refinements indicate deviations from ideal stoichiometry presumably related to mixed valency of tellurium. Highlights: → Single crystals of CsM x Te 2-x O 6 pyrochlores with M = Al, Ga, Ge, and In have been grown. → Structure refinements from single crystal X-ray diffraction data confirm e structure. → Deviations from ideal stoichiometry suggest mixed valency of tellurium and hence conductivity. -- Abstract: Single crystals of CsM x Te 2-x O 6 pyrochlores with M = Al, Ga, Ge, and In have been grown from a TeO 2 flux. Structure refinements from single crystal X-ray diffraction data are reported. These results are used to discuss deviations from ideal stoichiometry that result in electronic conductivity presumably related to mixed valency of tellurium.

  18. Conservative multi-implicit integral deferred correction methods with adaptive mesh refinement

    Layton, A.T.

    2004-01-01

    In most models of reacting gas dynamics, the characteristic time scales of chemical reactions are much shorter than the hydrodynamic and diffusive time scales, rendering the reaction part of the model equations stiff. Moreover, nonlinear forcings may introduce into the solutions sharp gradients or shocks, the robust behavior and correct propagation of which require the use of specialized spatial discretization procedures. This study presents high-order conservative methods for the temporal integration of model equations of reacting flows. By means of a method of lines discretization on the flux difference form of the equations, these methods compute approximations to the cell-averaged or finite-volume solution. The temporal discretization is based on a multi-implicit generalization of integral deferred correction methods. The advection term is integrated explicitly, and the diffusion and reaction terms are treated implicitly but independently, with the splitting errors present in traditional operator splitting methods reduced via the integral deferred correction procedure. To reduce computational cost, time steps used to integrate processes with widely-differing time scales may differ in size. (author)

  19. Antibodies: From novel repertoires to defining and refining the structure of biologically important targets.

    Conroy, Paul J; Law, Ruby H P; Caradoc-Davies, Tom T; Whisstock, James C

    2017-03-01

    Antibodies represent a highly successful class of molecules that bind a wide-range of targets in therapeutic-, diagnostic- and research-based applications. The antibody repertoire is composed of the building blocks required to develop an effective adaptive immune response against foreign insults. A number of species have developed novel genetic and structural mechanisms from which they derive these antibody repertoires, however, traditionally antibodies are isolated from human, and rodent sources. Due to their high-value therapeutic, diagnostic, biotechnological and research applications, much innovation has resulted in techniques and approaches to isolate novel antibodies. These approaches are bolstered by advances in our understanding of species immune repertoires, next generation sequencing capacity, combinatorial antibody discovery and high-throughput screening. Structural determination of antibodies and antibody-antigen complexes has proven to be pivotal to our current understanding of the immune repertoire for a range of species leading to advances in man-made libraries and fine tuning approaches to develop antibodies from immune-repertoires. Furthermore, the isolation of antibodies directed against antigens of importance in health, disease and developmental processes, has yielded a plethora of structural and functional insights. This review highlights the significant contribution of antibody-based crystallography to our understanding of adaptive immunity and its application to providing critical information on a range of human-health related indications. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Action Refinement

    Gorrieri, R.; Rensink, Arend; Bergstra, J.A.; Ponse, A.; Smolka, S.A.

    2001-01-01

    In this chapter, we give a comprehensive overview of the research results in the field of action refinement during the past 12 years. The different approaches that have been followed are outlined in detail and contrasted to each other in a uniform framework. We use two running examples to discuss

  1. Synthesis mechanism of an Al-Ti-C grain refiner master alloy prepared by a new method

    Zhang, B. Q.; Lu, L.; Lai, M. O.; Fang, H. S.; Ma, H. T.; Li, J. G.

    2003-08-01

    The mechanisms of in-situ synthesis of an Al-Ti-C grain-refiner master alloy, prepared by adding a powder mixture of potassium titanium fluoride and carbon into an aluminum melt, have been systematically studied. It was found that vigorous reactions occurred at the initial stage of reaction and then slowed down. After about 20 minutes, the reactions, which led the formation of blocky titanium aluminides and submicron titanium carbides in the aluminum matrix, appeared to reach completion. Potassium titanium fluoride reacted with aluminum and carbon at 724 °C and 736 °C, respectively, resulting in the formation of titanium aluminides and titanium carbides in the aluminum matrix as well as in the formation of a low-melting-point slag of binary potassium aluminofluorides. The reaction between potassium titanium fluoride and carbon is believed to be the predominant mechanism in the synthesis of TiC by this method.

  2. A novel high-temperature commensurate superstructure in a natural bariopyrochlore: A structural study by means of a multiphase crystal structure refinement

    Bindi, L.; Petricek, V.; Withers, R.L.; Zoppi, M.; Bonazzi, P.

    2006-01-01

    Additional X-ray diffraction effects yielding an eightfold commensurate superstructure [a=20.974(5)A] of the ideal pyrochlore structure were observed after annealing at 873K of a thallium-doped bariopyrochlore single crystal. Electron diffraction indicated the coexistence of two cubic phases, the pyrochlore structure and a new F-centred, cubic phase. The superstructure was solved and refined in the space group F4-bar 3m. The two phases were combined together and refined as independently diffracting to R=0.0628. The resulting unit-cell content is (A,-bar ) 20 Nb 16 Ti 2 O 53 (Z=8), with A=Ba, Tl, Ce, Th. For some atomic positions of the superstructure, third- and fourth-order anharmonic ADP's were used to account for the specific density shape having a continuous character as typical for ionic conductors. There are three distinct clusters in the superstructure, leading to a new structure type no longer strictly of pyrochlore-structure type

  3. Rietveld structure refinement and elastic properties of MgAlxCrxFe2-2xO4 spinel ferrites

    Thummer, K. P.; Tanna, Ashish R.; Joshi, Hiren H.

    2017-05-01

    MgAlxCrxFe2-2xO4 (x = 0.1, 03 & 0.6) ferrites are synthesized by solid state reaction method. The Rietveld refinement of X-ray diffraction (XRD) data confirms the cubic spinel structure with Fd3m space group. The Fourier Transform Infrared Transmission Spectroscopy (FTIR) is employed to study elastic properties of present systems at 300K. The force constants for tetrahedral (A) and octahedral (B) sites of the spinel lattice are determined by infrared spectral and X-ray diffraction analysis. The elastic constants like bulk modulus, rigidity modulus, Young's modulus, Poisson's ratio and Debye temperature are determined. The vibrational frequency of both the interstitial sites increases as Al-Cr content increases hence the force constant and elastic moduli for all the samples are found to increase for the present ferrite system.

  4. Refinement of crystal structures of CaHCl, SrHCl, BaHCl, BaHBr, and BaHI

    Beck, H.P.; Limmer, A.

    1983-01-01

    The structures of CaHCl, SrHCl, BaHBr, BaHCl, and BaHI have been refined using single crystal data. The comparison of the parameters with the corresponding data of isotypic fluorohalide compounds gives a valuable insight into the bonding interactions in this structure type. (author)

  5. Refinement of crystal structures of CaHCl, SrHCl, BaHCl, BaHBr, and BaHI

    Beck, H.P.; Limmer, A. (Erlangen-Nuernberg Univ., Erlangen (Germany, F.R.). Inst. fuer Anorganische Chemie)

    1983-07-01

    The structures of CaHCl, SrHCl, BaHBr, BaHCl, and BaHI have been refined using single crystal data. The comparison of the parameters with the corresponding data of isotypic fluorohalide compounds gives a valuable insight into the bonding interactions in this structure type.

  6. A refinement of the potassium tracer method for residential wood smoke

    Calloway, C. P.; Li, S.; Buchanan, J. W.; Stevens, R. K.

    Potassium has been used as a tracer for the mass of fine particles emitted to the air from residential wood burning stoves and fireplaces. The technique involves measurement by x-ray fluorescence of the total K collected on fine particle filters. Since wind blown soil particles also contain K, a correction for this contribution is made based upon soil analysis or an assumed K/Fe ratio in local soil. K in excess of this ratio is considered to be from wood smoke. The purpose of this study is to demonstrate an alternative method for determining wood smoke K. The underlying assumption is that wood smoke K is water soluble but that K in crustal particles is in a mineralized form and only slightly water soluble. Results from analyses of particle samples indicate the two methods yield essentially the same amount of wood smoke K.

  7. Structural exploration for the refinement of anticancer matrix metalloproteinase-2 inhibitor designing approaches through robust validated multi-QSARs

    Adhikari, Nilanjan; Amin, Sk. Abdul; Saha, Achintya; Jha, Tarun

    2018-03-01

    Matrix metalloproteinase-2 (MMP-2) is a promising pharmacological target for designing potential anticancer drugs. MMP-2 plays critical functions in apoptosis by cleaving the DNA repair enzyme namely poly (ADP-ribose) polymerase (PARP). Moreover, MMP-2 expression triggers the vascular endothelial growth factor (VEGF) having a positive influence on tumor size, invasion, and angiogenesis. Therefore, it is an urgent need to develop potential MMP-2 inhibitors without any toxicity but better pharmacokinetic property. In this article, robust validated multi-quantitative structure-activity relationship (QSAR) modeling approaches were attempted on a dataset of 222 MMP-2 inhibitors to explore the important structural and pharmacophoric requirements for higher MMP-2 inhibition. Different validated regression and classification-based QSARs, pharmacophore mapping and 3D-QSAR techniques were performed. These results were challenged and subjected to further validation to explain 24 in house MMP-2 inhibitors to judge the reliability of these models further. All these models were individually validated internally as well as externally and were supported and validated by each other. These results were further justified by molecular docking analysis. Modeling techniques adopted here not only helps to explore the necessary structural and pharmacophoric requirements but also for the overall validation and refinement techniques for designing potential MMP-2 inhibitors.

  8. Dissipative structures and related methods

    Langhorst, Benjamin R; Chu, Henry S

    2013-11-05

    Dissipative structures include at least one panel and a cell structure disposed adjacent to the at least one panel having interconnected cells. A deformable material, which may comprise at least one hydrogel, is disposed within at least one interconnected cell proximate to the at least one panel. Dissipative structures may also include a cell structure having interconnected cells formed by wall elements. The wall elements may include a mesh formed by overlapping fibers having apertures formed therebetween. The apertures may form passageways between the interconnected cells. Methods of dissipating a force include disposing at least one hydrogel in a cell structure proximate to at least one panel, applying a force to the at least one panel, and forcing at least a portion of the at least one hydrogel through apertures formed in the cell structure.

  9. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB-REDO strategies

    Rimsa, Vadim; Eadsforth, Thomas C. [University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom); Joosten, Robbie P. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Hunter, William N., E-mail: w.n.hunter@dundee.ac.uk [University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom)

    2014-02-01

    The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase. A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB-REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn{sup 2+}-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn{sup 2+}, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate.

  10. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB-REDO strategies

    Rimsa, Vadim; Eadsforth, Thomas C.; Joosten, Robbie P.; Hunter, William N.

    2014-01-01

    The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase. A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB-REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn 2+ -containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn 2+ , where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate

  11. Structural refinement and prediction of potential CCR2 antagonists through validated multi-QSAR modeling studies.

    Amin, Sk Abdul; Adhikari, Nilanjan; Baidya, Sandip Kumar; Gayen, Shovanlal; Jha, Tarun

    2018-01-03

    Chemokines trigger numerous inflammatory responses and modulate the immune system. The interaction between monocyte chemoattractant protein-1 and chemokine receptor 2 (CCR2) may be the cause of atherosclerosis, obesity, and insulin resistance. However, CCR2 is also implicated in other inflammatory diseases such as rheumatoid arthritis, multiple sclerosis, asthma, and neuropathic pain. Therefore, there is a paramount importance of designing potent and selective CCR2 antagonists despite a number of drug candidates failed in clinical trials. In this article, 83 CCR2 antagonists by Jhonson and Jhonson Pharmaceuticals have been considered for robust validated multi-QSAR modeling studies to get an idea about the structural and pharmacophoric requirements for designing more potent CCR2 antagonists. All these QSAR models were validated and statistically reliable. Observations resulted from different modeling studies correlated and validated results of other ones. Finally, depending on these QSAR observations, some new molecules were proposed that may exhibit higher activity against CCR2.

  12. Linearly Refined Session Types

    Pedro Baltazar

    2012-11-01

    Full Text Available Session types capture precise protocol structure in concurrent programming, but do not specify properties of the exchanged values beyond their basic type. Refinement types are a form of dependent types that can address this limitation, combining types with logical formulae that may refer to program values and can constrain types using arbitrary predicates. We present a pi calculus with assume and assert operations, typed using a session discipline that incorporates refinement formulae written in a fragment of Multiplicative Linear Logic. Our original combination of session and refinement types, together with the well established benefits of linearity, allows very fine-grained specifications of communication protocols in which refinement formulae are treated as logical resources rather than persistent truths.

  13. Application of the crystalline structure determination method by X-ray diffraction to natural products and organic compounds

    Vencato, I.

    1984-01-01

    The structures of two natural compounds, a synthetic phosphate and a copper complexe were determined and the structure of another copper complex was refined. The reflection intensities were measured with a CAD-4 automatic diffractometer. The structures were solved by direct methods using either MULTAN-80 or the Patterson function and were refined by the least squares method, with a full matrix. (E.G.) [pt

  14. Pareto-Lognormal Modeling of Known and Unknown Metal Resources. II. Method Refinement and Further Applications

    Agterberg, Frits

    2017-01-01

    Pareto-lognormal modeling of worldwide metal deposit size–frequency distributions was proposed in an earlier paper (Agterberg in Nat Resour 26:3–20, 2017). In the current paper, the approach is applied to four metals (Cu, Zn, Au and Ag) and a number of model improvements are described and illustrated in detail for copper and gold. The new approach has become possible because of the very large inventory of worldwide metal deposit data recently published by Patiño Douce (Nat Resour 25:97–124, 2016c). Worldwide metal deposits for Cu, Zn and Ag follow basic lognormal size–frequency distributions that form straight lines on lognormal Q–Q plots. Au deposits show a departure from the straight-line model in the vicinity of their median size. Both largest and smallest deposits for the four metals taken as examples exhibit hyperbolic size–frequency relations and their Pareto coefficients are determined by fitting straight lines on log rank–log size plots. As originally pointed out by Patiño Douce (Nat Resour Res 25:365–387, 2016d), the upper Pareto tail cannot be distinguished clearly from the tail of what would be a secondary lognormal distribution. The method previously used in Agterberg (2017) for fitting the bridge function separating the largest deposit size–frequency Pareto tail from the basic lognormal is significantly improved in this paper. A new method is presented for estimating the approximate deposit size value at which the upper tail Pareto comes into effect. Although a theoretical explanation of the proposed Pareto-lognormal distribution model is not a required condition for its applicability, it is shown that existing double Pareto-lognormal models based on Brownian motion generalizations of the multiplicative central limit theorem are not applicable to worldwide metal deposits. Neither are various upper tail frequency amplification models in their present form. Although a physicochemical explanation remains possible, it is argued that

  15. Pareto-Lognormal Modeling of Known and Unknown Metal Resources. II. Method Refinement and Further Applications

    Agterberg, Frits, E-mail: agterber@nrcan.gc.ca [Geological Survey of Canada (Canada)

    2017-07-01

    Pareto-lognormal modeling of worldwide metal deposit size–frequency distributions was proposed in an earlier paper (Agterberg in Nat Resour 26:3–20, 2017). In the current paper, the approach is applied to four metals (Cu, Zn, Au and Ag) and a number of model improvements are described and illustrated in detail for copper and gold. The new approach has become possible because of the very large inventory of worldwide metal deposit data recently published by Patiño Douce (Nat Resour 25:97–124, 2016c). Worldwide metal deposits for Cu, Zn and Ag follow basic lognormal size–frequency distributions that form straight lines on lognormal Q–Q plots. Au deposits show a departure from the straight-line model in the vicinity of their median size. Both largest and smallest deposits for the four metals taken as examples exhibit hyperbolic size–frequency relations and their Pareto coefficients are determined by fitting straight lines on log rank–log size plots. As originally pointed out by Patiño Douce (Nat Resour Res 25:365–387, 2016d), the upper Pareto tail cannot be distinguished clearly from the tail of what would be a secondary lognormal distribution. The method previously used in Agterberg (2017) for fitting the bridge function separating the largest deposit size–frequency Pareto tail from the basic lognormal is significantly improved in this paper. A new method is presented for estimating the approximate deposit size value at which the upper tail Pareto comes into effect. Although a theoretical explanation of the proposed Pareto-lognormal distribution model is not a required condition for its applicability, it is shown that existing double Pareto-lognormal models based on Brownian motion generalizations of the multiplicative central limit theorem are not applicable to worldwide metal deposits. Neither are various upper tail frequency amplification models in their present form. Although a physicochemical explanation remains possible, it is argued that

  16. Optimization methods in structural design

    Rothwell, Alan

    2017-01-01

    This book offers an introduction to numerical optimization methods in structural design. Employing a readily accessible and compact format, the book presents an overview of optimization methods, and equips readers to properly set up optimization problems and interpret the results. A ‘how-to-do-it’ approach is followed throughout, with less emphasis at this stage on mathematical derivations. The book features spreadsheet programs provided in Microsoft Excel, which allow readers to experience optimization ‘hands-on.’ Examples covered include truss structures, columns, beams, reinforced shell structures, stiffened panels and composite laminates. For the last three, a review of relevant analysis methods is included. Exercises, with solutions where appropriate, are also included with each chapter. The book offers a valuable resource for engineering students at the upper undergraduate and postgraduate level, as well as others in the industry and elsewhere who are new to these highly practical techniques.Whi...

  17. Refinement of Structural Leads for Centrally Acting Oxime Reactivators of Phosphylated Cholinesterases*

    Radić, Zoran; Sit, Rakesh K.; Kovarik, Zrinka; Berend, Suzana; Garcia, Edzna; Zhang, Limin; Amitai, Gabriel; Green, Carol; Radić, Božica; Fokin, Valery V.; Sharpless, K. Barry; Taylor, Palmer

    2012-01-01

    We present a systematic structural optimization of uncharged but ionizable N-substituted 2-hydroxyiminoacetamido alkylamine reactivators of phosphylated human acetylcholinesterase (hAChE) intended to catalyze the hydrolysis of organophosphate (OP)-inhibited hAChE in the CNS. Starting with the initial lead oxime RS41A identified in our earlier study and extending to the azepine analog RS194B, reactivation rates for OP-hAChE conjugates formed by sarin, cyclosarin, VX, paraoxon, and tabun are enhanced severalfold in vitro. To analyze the mechanism of intrinsic reactivation of the OP-AChE conjugate and penetration of the blood-brain barrier, the pH dependence of the oxime and amine ionizing groups of the compounds and their nucleophilic potential were examined by UV-visible spectroscopy, 1H NMR, and oximolysis rates for acetylthiocholine and phosphoester hydrolysis. Oximolysis rates were compared in solution and on AChE conjugates and analyzed in terms of the ionization states for reactivation of the OP-conjugated AChE. In addition, toxicity and pharmacokinetic studies in mice show significantly improved CNS penetration and retention for RS194B when compared with RS41A. The enhanced intrinsic reactivity against the OP-AChE target combined with favorable pharmacokinetic properties resulted in great improvement of antidotal properties of RS194B compared with RS41A and the standard peripherally active oxime, 2-pyridinealdoxime methiodide. Improvement was particularly noticeable when pretreatment of mice with RS194B before OP exposure was combined with RS194B reactivation therapy after the OP insult. PMID:22343626

  18. Impacts of Modification of Alloying Method on Inclusion Evolution in RH Refining of Silicon Steel

    Fangjie Li

    2017-10-01

    Full Text Available This study explores the effect of introducing additional alloy elements not only in a different order but also at different stages of the Ruhrstahl-Heraeus (RH process of low-carbon silicon steel production. A more economical method, described as “pre-alloying”, has been introduced. The evolution of MnO-FeO inclusions produced by pre-alloying was investigated. Results show that spherical 3FeO·MnO inclusions form first, then shelled FeO·zMnO (z = 0.7–4 inclusions nucleate on the surface of pre-existing 3FeO·MnO. Spherical FeO·zMnO (z = 3–5 is further evolved from shelled 3FeO·MnO by diffusion. Because these MnO-FeO inclusions float up into the slag before degassing, the pre-alloying process does not affect the quality of the melt in the end. Both carbon content and inclusion size conform to industry standards.

  19. Impacts of Modification of Alloying Method on Inclusion Evolution in RH Refining of Silicon Steel.

    Li, Fangjie; Li, Huigai; Zheng, Shaobo; You, Jinglin; Han, Ke; Zhai, Qijie

    2017-10-19

    This study explores the effect of introducing additional alloy elements not only in a different order but also at different stages of the Ruhrstahl-Heraeus (RH) process of low-carbon silicon steel production. A more economical method, described as "pre-alloying", has been introduced. The evolution of MnO-FeO inclusions produced by pre-alloying was investigated. Results show that spherical 3FeO·MnO inclusions form first, then shelled FeO·zMnO (z = 0.7-4) inclusions nucleate on the surface of pre-existing 3FeO·MnO. Spherical FeO·zMnO (z = 3-5) is further evolved from shelled 3FeO·MnO by diffusion. Because these MnO-FeO inclusions float up into the slag before degassing, the pre-alloying process does not affect the quality of the melt in the end. Both carbon content and inclusion size conform to industry standards.

  20. Spanish Refining

    Lores, F.R.

    2001-01-01

    An overview of petroleum refining in Spain is presented (by Repsol YPF) and some views on future trends are discussed. Spain depends heavily on imports. Sub-headings in the article cover: sources of crude imports, investments and logistics and marketing, -detailed data for each are shown diagrammatically. Tables show: (1) economic indicators (e.g. total GDP, vehicle numbers and inflation) for 1998-200; (2) crude oil imports for 1995-2000; (3) oil products balance for 1995-2000; (4) commodities demand, by product; (5) refining in Spain in terms of capacity per region; (6) outlets in Spain and other European countries in 2002 and (7) sales distribution channel by product

  1. Glycidyl fatty acid esters in refined edible oils: A review on formation, occurrence, analysis, and elimination methods

    Glycidyl fatty acid esters (GEs), one of the main contaminants in processed oil, are mainly formed during the deodorization step in the oil refining process of edible oils and therefore occur in almost all refined edible oils. GEs are potential carcinogens, due to the fact that they hydrolyze into t...

  2. Refinement of a Method for Identifying Probable Archaeological Sites from Remotely Sensed Data

    Tilton, James C.; Comer, Douglas C.; Priebe, Carey E.; Sussman, Daniel; Chen, Li

    2012-01-01

    To facilitate locating archaeological sites before they are compromised or destroyed, we are developing approaches for generating maps of probable archaeological sites, through detecting subtle anomalies in vegetative cover, soil chemistry, and soil moisture by analyzing remotely sensed data from multiple sources. We previously reported some success in this effort with a statistical analysis of slope, radar, and Ikonos data (including tasseled cap and NDVI transforms) with Student's t-test. We report here on new developments in our work, performing an analysis of 8-band multispectral Worldview-2 data. The Worldview-2 analysis begins by computing medians and median absolute deviations for the pixels in various annuli around each site of interest on the 28 band difference ratios. We then use principle components analysis followed by linear discriminant analysis to train a classifier which assigns a posterior probability that a location is an archaeological site. We tested the procedure using leave-one-out cross validation with a second leave-one-out step to choose parameters on a 9,859x23,000 subset of the WorldView-2 data over the western portion of Ft. Irwin, CA, USA. We used 100 known non-sites and trained one classifier for lithic sites (n=33) and one classifier for habitation sites (n=16). We then analyzed convex combinations of scores from the Archaeological Predictive Model (APM) and our scores. We found that that the combined scores had a higher area under the ROC curve than either individual method, indicating that including WorldView-2 data in analysis improved the predictive power of the provided APM.

  3. PyCPR - a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures.

    Gisdon, Florian J; Culka, Martin; Ullmann, G Matthias

    2016-10-01

    Conjugate peak refinement (CPR) is a powerful and robust method to search transition states on a molecular potential energy surface. Nevertheless, the method was to the best of our knowledge so far only implemented in CHARMM. In this paper, we present PyCPR, a new Python-based implementation of the CPR algorithm within the pDynamo framework. We provide a detailed description of the theory underlying our implementation and discuss the different parts of the implementation. The method is applied to two different problems. First, we illustrate the method by analyzing the gauche to anti-periplanar transition of butane using a semiempirical QM method. Second, we reanalyze the mechanism of a glycyl-radical enzyme, namely of 4-hydroxyphenylacetate decarboxylase (HPD) using QM/MM calculations. In the end, we suggest a strategy how to use our implementation of the CPR algorithm. The integration of PyCPR into the framework pDynamo allows the combination of CPR with the large variety of methods implemented in pDynamo. PyCPR can be used in combination with quantum mechanical and molecular mechanical methods (and hybrid methods) implemented directly in pDynamo, but also in combination with external programs such as ORCA using pDynamo as interface. PyCPR is distributed as free, open source software and can be downloaded from http://www.bisb.uni-bayreuth.de/index.php?page=downloads . Graphical Abstract PyCPR is a search tool for finding saddle points on the potential energy landscape of a molecular system.

  4. Creation and Delphi-method refinement of pediatric disaster triage simulations.

    Cicero, Mark X; Brown, Linda; Overly, Frank; Yarzebski, Jorge; Meckler, Garth; Fuchs, Susan; Tomassoni, Anthony; Aghababian, Richard; Chung, Sarita; Garrett, Andrew; Fagbuyi, Daniel; Adelgais, Kathleen; Goldman, Ran; Parker, James; Auerbach, Marc; Riera, Antonio; Cone, David; Baum, Carl R

    2014-01-01

    There is a need for rigorously designed pediatric disaster triage (PDT) training simulations for paramedics. First, we sought to design three multiple patient incidents for EMS provider training simulations. Our second objective was to determine the appropriate interventions and triage level for each victim in each of the simulations and develop evaluation instruments for each simulation. The final objective was to ensure that each simulation and evaluation tool was free of bias toward any specific PDT strategy. We created mixed-methods disaster simulation scenarios with pediatric victims: a school shooting, a school bus crash, and a multiple-victim house fire. Standardized patients, high-fidelity manikins, and low-fidelity manikins were used to portray the victims. Each simulation had similar acuity of injuries and 10 victims. Examples include children with special health-care needs, gunshot wounds, and smoke inhalation. Checklist-based evaluation tools and behaviorally anchored global assessments of function were created for each simulation. Eight physicians and paramedics from areas with differing PDT strategies were recruited as Subject Matter Experts (SMEs) for a modified Delphi iterative critique of the simulations and evaluation tools. The modified Delphi was managed with an online survey tool. The SMEs provided an expected triage category for each patient. The target for modified Delphi consensus was ≥85%. Using Likert scales and free text, the SMEs assessed the validity of the simulations, including instances of bias toward a specific PDT strategy, clarity of learning objectives, and the correlation of the evaluation tools to the learning objectives and scenarios. After two rounds of the modified Delphi, consensus for expected triage level was >85% for 28 of 30 victims, with the remaining two achieving >85% consensus after three Delphi iterations. To achieve consensus, we amended 11 instances of bias toward a specific PDT strategy and corrected 10

  5. Surface Protonation at the Rutile (110) Interface: Explicit Incorporation of Solvation Structure within the Refined MUSIC Model Framework

    Machesky, Michael L. [Illinois State Water Survey, Champaign, IL; Predota, M. [University of South Bohemia, Czech Republic; Wesolowski, David J [ORNL

    2008-01-01

    The detailed solvation structure at the (110) surface of rutile ({alpha}-TiO{sub 2}) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 {angstrom} of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 C that agrees quantitatively with the experimentally determined value (5.4 {+-} 0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pH{sub znpc} values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pH{sub znpc} value of the rutile (110) surface at 25 C into quantitative agreement with the experimental value (4.8 {+-} 0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic

  6. Surface Protonation at the Rutile (110) Interface: Explicit Incorporation of Solvation Structure within the Refined MUSIC Model Framework

    Machesky, Michael L.; Predota, M.; Wesolowski, David J.

    2008-01-01

    The detailed solvation structure at the (110) surface of rutile (α-TiO 2 ) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 (angstrom) of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 C that agrees quantitatively with the experimentally determined value (5.4 ± 0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pH znpc values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pH znpc value of the rutile (110) surface at 25 C into quantitative agreement with the experimental value (4.8 ± 0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic strength. Additionally, the H

  7. Strengthening method of concrete structure

    Inge, Wewin; Audrey; Nugroho, Sofie; Njo, Helen

    2018-03-01

    Building extension in Indonesia is not favored, and not many people know the advantages of the method because architects and engineers tend to lack the knowledge and experience. The aim of this paper is to explain a method on how to strengthen a concrete building structure that people can use/learn as a better way to cut potential cost and save time. The strengthening method explained in this paper is steel jacketing, providing a case study of this method in the extension of a restaurant located in Medan, Indonesia. In this study, engineers calculated that the tensile stress of the existing RC column and beam is not strong enough to reinforce the building extension applied load. Therefore, the steel jacketing method can be applied to improve the column and beam strength and ductility. The result of the case study proves that this is one of the best methods for building extension applied in Indonesia.

  8. Solution of free-boundary problems using finite-element/Newton methods and locally refined grids - Application to analysis of solidification microstructure

    Tsiveriotis, K.; Brown, R. A.

    1993-01-01

    A new method is presented for the solution of free-boundary problems using Lagrangian finite element approximations defined on locally refined grids. The formulation allows for direct transition from coarse to fine grids without introducing non-conforming basis functions. The calculation of elemental stiffness matrices and residual vectors are unaffected by changes in the refinement level, which are accounted for in the loading of elemental data to the global stiffness matrix and residual vector. This technique for local mesh refinement is combined with recently developed mapping methods and Newton's method to form an efficient algorithm for the solution of free-boundary problems, as demonstrated here by sample calculations of cellular interfacial microstructure during directional solidification of a binary alloy.

  9. Refinement of Parallel and Reactive Programs

    Back, R. J. R.

    1992-01-01

    We show how to apply the refinement calculus to stepwise refinement of parallel and reactive programs. We use action systems as our basic program model. Action systems are sequential programs which can be implemented in a parallel fashion. Hence refinement calculus methods, originally developed for sequential programs, carry over to the derivation of parallel programs. Refinement of reactive programs is handled by data refinement techniques originally developed for the sequential refinement c...

  10. Method for mercury refinement

    Grossman, M.W.; Speer, R.; George, W.A.

    1991-04-09

    The effluent from mercury collected during the photochemical separation of the [sup 196]Hg isotope is often contaminated with particulate mercurous chloride, Hg[sub 2]Cl[sub 2]. The use of mechanical filtering via thin glass tubes, ultrasonic rinsing with acetone (dimethyl ketone) and a specially designed cold trap have been found effective in removing the particulate (i.e., solid) Hg[sub 2]Cl[sub 2] contaminant. The present invention is particularly directed to such filtering. 5 figures.

  11. Method for mercury refinement

    Grossman, M.W.; Speer, R.; George, W.A.

    1991-01-01

    The effluent from mercury collected during the photochemical separation of the 196 Hg isotope is often contaminated with particulate mercurous chloride, Hg 2 Cl 2 . The use of mechanical filtering via thin glass tubes, ultrasonic rinsing with acetone (dimethyl ketone) and a specially designed cold trap have been found effective in removing the particulate (i.e., solid) Hg 2 Cl 2 contaminant. The present invention is particularly directed to such filtering. 5 figures

  12. Haplotype analysis and a novel allele-sharing method refines a chromosome 4p locus linked to bipolar affective disorder.

    Le Hellard, Stephanie; Lee, Andrew J; Underwood, Sarah; Thomson, Pippa A; Morris, Stewart W; Torrance, Helen S; Anderson, Susan M; Adams, Richard R; Navarro, Pau; Christoforou, Andrea; Houlihan, Lorna M; Detera-Wadleigh, Sevilla; Owen, Michael J; Asherson, Philip; Muir, Walter J; Blackwood, Douglas H R; Wray, Naomi R; Porteous, David J; Evans, Kathryn L

    2007-03-15

    Bipolar affective disorder (BPAD) and schizophrenia (SCZ) are common conditions. Their causes are unknown, but they include a substantial genetic component. Previously, we described significant linkage of BPAD to a chromosome 4p locus within a large pedigree (F22). Others subsequently have found evidence for linkage of BPAD and SCZ to this region. We constructed high-resolution haplotypes for four linked families, calculated logarithm of the odds (LOD) scores, and developed a novel method to assess the extent of allele sharing within genes between the families. We describe an increase in the F22 LOD score for this region. Definition and comparison of the linked haplotypes allowed us to prioritize two subregions of 3.8 and 4.4 Mb. Analysis of the extent of allele sharing within these subregions identified 200 kb that shows increased allele sharing between families. Linkage of BPAD to chromosome 4p has been strengthened. Haplotype analysis in the additional linked families refined the 20-Mb linkage region. Development of a novel allele-sharing method allowed us to bridge the gap between conventional linkage and association studies. Description of a 200-kb region of increased allele sharing prioritizes this region, which contains two functional candidate genes for BPAD, SLC2A9, and WDR1, for subsequent studies.

  13. Adaptive mesh refinement for a finite volume method for flow and transport of radionuclides in heterogeneous porous media

    Amaziane, Brahim; Bourgeois, Marc; El Fatini, Mohamed

    2014-01-01

    In this paper, we consider adaptive numerical simulation of miscible displacement problems in porous media, which are modeled by single phase flow equations. A vertex-centred finite volume method is employed to discretize the coupled system: the Darcy flow equation and the diffusion-convection concentration equation. The convection term is approximated with a Godunov scheme over the dual finite volume mesh, whereas the diffusion-dispersion term is discretized by piecewise linear conforming finite elements. We introduce two kinds of indicators, both of them of residual type. The first one is related to time discretization and is local with respect to the time discretization: thus, at each time, it provides an appropriate information for the choice of the next time step. The second is related to space discretization and is local with respect to both the time and space variable and the idea is that at each time it is an efficient tool for mesh adaptivity. An error estimation procedure evaluates where additional refinement is needed and grid generation procedures dynamically create or remove fine-grid patches as resolution requirements change. The method was implemented in the software MELODIE, developed by the French Institute for Radiological Protection and Nuclear Safety (IRSN, Institut de Radioprotection et de Surete Nucleaire). The algorithm is then used to simulate the evolution of radionuclide migration from the waste packages through a heterogeneous disposal, demonstrating its capability to capture complex behavior of the resulting flow. (authors)

  14. Software abstractions and computational issues in parallel structure adaptive mesh methods for electronic structure calculations

    Kohn, S.; Weare, J.; Ong, E.; Baden, S.

    1997-05-01

    We have applied structured adaptive mesh refinement techniques to the solution of the LDA equations for electronic structure calculations. Local spatial refinement concentrates memory resources and numerical effort where it is most needed, near the atomic centers and in regions of rapidly varying charge density. The structured grid representation enables us to employ efficient iterative solver techniques such as conjugate gradient with FAC multigrid preconditioning. We have parallelized our solver using an object- oriented adaptive mesh refinement framework.

  15. Effect of Grain Refinement on Structure Evolution, “Floating” Grains, and Centerline Macrosegregation in Direct-Chill Cast AA2024 Alloy Billets

    Nadella, R.; Eskin, D.G.; Katgerman, L.

    2007-01-01

    Direct-chill (DC) cast billets 192 mm in diameter of an Al-Cu-Mg alloy were examined in detail with the aim to reveal the effects of grain refining (GR) and casting speed on structure, “floating” grains, and centerline macrosegregation. Experimental results show that grain size and dendrite arm

  16. Refined shape model fitting methods for detecting various types of phenological information on major U.S. crops

    Sakamoto, Toshihiro

    2018-04-01

    Crop phenological information is a critical variable in evaluating the influence of environmental stress on the final crop yield in spatio-temporal dimensions. Although the MODIS (Moderate Resolution Imaging Spectroradiometer) Land Cover Dynamics product (MCD12Q2) is widely used in place of crop phenological information, the definitions of MCD12Q2-derived phenological events (e.g. green-up date, dormancy date) were not completely consistent with those of crop development stages used in statistical surveys (e.g. emerged date, harvested date). It has been necessary to devise an alternative method focused on detecting continental-scale crop developmental stages using a different approach. Therefore, this study aimed to refine the Shape Model Fitting (SMF) method to improve its applicability to multiple major U.S. crops. The newly-refined SMF methods could estimate the timing of 36 crop-development stages of major U.S. crops, including corn, soybeans, winter wheat, spring wheat, barley, sorghum, rice, and cotton. The newly-developed calibration process did not require any long-term field observation data, and could calibrate crop-specific phenological parameters, which were used as coefficients in estimated equation, by using only freely accessible public data. The calibration of phenological parameters was conducted in two steps. In the first step, the national common phenological parameters, referred to as X0[base], were calibrated by using the statistical data of 2008. The SMF method coupled using X0[base] was named the rSMF[base] method. The second step was a further calibration to gain regionally-adjusted phenological parameters for each state, referred to as X0[local], by using additional statistical data of 2015 and 2016. The rSMF method using the X0[local] was named the rSMF[local] method. This second calibration process improved the estimation accuracy for all tested crops. When applying the rSMF[base] method to the validation data set (2009-2014), the root

  17. The Factors Affecting the Adoption of Enviromental Management Accounting in the Oil Refining and Petrochemical Companies with Structural Equation Modeling Aprpoach

    Zohre Karimi

    2017-07-01

    Full Text Available Introduction: Today, businesses must focus on profits on the one hand and social and environmental issues on the other hand to make balance between them. Conservation and sustainability are increasingly dependent on observance of corporate social responsibilities. For this reason, business units report on their sustainability and environmental accounting. The aim of this study was to examine and model the factors influencing the use of environmental management accounting tools from the points of view of financial managers and assistants who are in the oil refining and petrochemical companies. Method: The method used in this study was based on a descriptive survey and its design was quasi-experimental. For the field of study, a questionnaire including 5 general and 31 specific questions was used. The population consisted of financial administrators and assistants in oil refining and petrochemical companies, a subsidiary of the national oil company. There was no sampling method used and we tested the whole society including 182 people. To evaluate the reliability of the questionnaire, Cronbach’s Alpha and spilit-half were used. The measurement tools used in the study were reliable and none of the questions was removed. One sample t-test, Pearson correlation, confirmatory factor analysis, path analysis, structural equation modeling, two sample T-test and analysis of variance were performed by using LISREL and SPSS software. Results: The result of this test by using confirmatory factor analysis and structural equation test showed that the significance level of all the factors were larger than 1/96 and all the routes specified in the model were significant. Culture of the society in dealing with environmental issues, with a significance level of 5/54, had the greatest impact among the factors influencing the use of environmental management accounting tools. Conclusion: According to the results of the study, it is recommended that, by using

  18. Role and distribution of strontium during the dissolving and grain refining process of AlSi7Mg alloy's structure

    Moldovan, P.; Popescu, G.; Zsigmond, M.; Apostolescu, I. [Universitatea Politehnica, Bucharest (Romania)

    2002-07-01

    The aim of this paper is the study of the modification of AlSi7Mg alloy with two types of master alloys: AlSr10 wire type and AlSr10 block type, at a temperature of 750 C with different contents of strontium. Due to the applicability of the AlSr10 master alloy wire type, the study was mainly elaborated on the dissolving process of this one. Due to this fact we used a 10 mm diameter wire of AlSr10 master alloy, which was introduced in the melt. After the grain refining process we obtained a sample, which was cut at different heights for a better observation of the alloy structure. We can notice that the grain refining degree is not uniform along the sample. Strontium as a grain refiner equalize the qualities of sodium but is much more efficient and keeps its grain refining properties for a longer period of time. The efficiency of the two types of master alloys was compared by the grain refinement degree of AlSi7Mg alloy function of the distance till the lower part of the casting mould and by determination of the grain refinement degree function of strontium content added. We made a micrographic study of the pieces of the sample and we used an optical microscope (OLYMPUS BX 60M) and the image analyzing system was OMNIMENT EXPRESS. Analyzing the results of this study we can see that the AlSi7Mg alloy grain refining degree doesn't depend too much on the form of the master alloy (if is wire or block) but grain refining time is increased when we use block types of master alloy. Also we can see that the cooling rate has a significant influence on the grain refinement degree. The industrial application of the AlSr master alloys are mainly for the light alloys ingots producers and light alloys casting plant for the obtaining of high quality components required by automotive and aeronautical industry. (orig.)

  19. Refinement of the experimental dynamic structure factor for liquid para-hydrogen and ortho-deuterium using semi-classical quantum simulation

    Smith, Kyle K. G.; Rossky, Peter J.; Poulsen, Jens Aage; Cunsolo, A.

    2014-01-01

    The dynamic structure factor of liquid para-hydrogen and ortho-deuterium in corresponding thermodynamic states (T = 20.0 K, n = 21.24 nm −3 ) and (T = 23.0 K, n = 24.61 nm −3 ), respectively, has been computed by both the Feynman-Kleinert linearized path-integral (FK-LPI) and Ring-Polymer Molecular Dynamics (RPMD) methods and compared with Inelastic X Ray Scattering spectra. The combined use of computational and experimental methods enabled us to reduce experimental uncertainties in the determination of the true sample spectrum. Furthermore, the refined experimental spectrum of para-hydrogen and ortho-deuterium is consistently reproduced by both FK-LPI and RPMD results at momentum transfers lower than 12.8 nm −1 . At larger momentum transfers the FK-LPI results agree with experiment much better for ortho-deuterium than for para-hydrogen. More specifically we found that for k ∼ 20.0 nm −1 para-hydrogen provides a test case for improved approximations to quantum dynamics

  20. Refinement by Rietveld method of a rolled sheet Al-Mg-Si 6063 alloy with preferential orientation

    Carrio, J.A.G.; Hattori, C.S.; Miranda, L.F.; Domingues Junior, N.I.; Lima, N.B.; Couto, A.A.; Aguiar, A.A.

    2010-01-01

    The Rietveld refinement of a sample with preferential orientation was accomplished using data of X ray diffraction of a rolled 6063 aluminum alloy. The refinement of the preferential orientation by spherical harmonic was accomplished using a symmetry of sample mmm (rolling) until the order of 8 and was compared with experimental pole figures. The four pole figures presented indicate a sharp texture of the planes (111), (200), (220) and (311). The calculated pole figures obtained from the refinement of the X ray diffraction spectrum can incur in mistakes of preferential orientation. This happens because the measure is restricted to the planes parallel to the surface without inference to the symmetry of the sample. (author)

  1. Global/local methods for probabilistic structural analysis

    Millwater, H. R.; Wu, Y.-T.

    1993-04-01

    A probabilistic global/local method is proposed to reduce the computational requirements of probabilistic structural analysis. A coarser global model is used for most of the computations with a local more refined model used only at key probabilistic conditions. The global model is used to establish the cumulative distribution function (cdf) and the Most Probable Point (MPP). The local model then uses the predicted MPP to adjust the cdf value. The global/local method is used within the advanced mean value probabilistic algorithm. The local model can be more refined with respect to the g1obal model in terms of finer mesh, smaller time step, tighter tolerances, etc. and can be used with linear or nonlinear models. The basis for this approach is described in terms of the correlation between the global and local models which can be estimated from the global and local MPPs. A numerical example is presented using the NESSUS probabilistic structural analysis program with the finite element method used for the structural modeling. The results clearly indicate a significant computer savings with minimal loss in accuracy.

  2. Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of Mn K-edge XANES data

    Monesi, C.; Meneghini, C.; Bardelli, F.; Benfatto, M.; Mobilio, S.; Manju, U.; Sarma, D.D.

    2005-01-01

    Hole-doped perovskites such as La 1-x Ca x MnO 3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K-edge XANES of LaMnO 3 and CaMnO 3 compounds; they are the end compounds of the doped manganite series La x Ca 1-x MnO 3 . The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K-edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds

  3. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

    Rinaldelli, Mauro; Ravera, Enrico; Calderone, Vito; Parigi, Giacomo [University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy); University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (Finland) (Italy); Murshudov, Garib N., E-mail: garib@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Luchinat, Claudio, E-mail: garib@mrc-lmb.cam.ac.uk [University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy); University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (Finland) (Italy)

    2014-04-01

    Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

  4. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

    Rinaldelli, Mauro; Ravera, Enrico; Calderone, Vito; Parigi, Giacomo; Murshudov, Garib N.; Luchinat, Claudio

    2014-01-01

    Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state

  5. A State Space Model for the Wood Chip Refining Model

    David Di Ruscio

    1997-07-01

    Full Text Available A detailed dynamic model of the fibre size distribution between the refiner discs, distributed along the refiner radius, is presented. Both one- and two-dimensional descriptions for the fibre or shive geometry are given. It is shown that this model may be simplified and that analytic solutions exist under non-restrictive assumptions. A direct method for the recursive estimation of unknown parameters is presented. This method is applicable to linear or linearized systems which have a triangular structure.

  6. Joint refinement model for the spin resolved one-electron reduced density matrix of YTiO3 using magnetic structure factors and magnetic Compton profiles data.

    Gueddida, Saber; Yan, Zeyin; Kibalin, Iurii; Voufack, Ariste Bolivard; Claiser, Nicolas; Souhassou, Mohamed; Lecomte, Claude; Gillon, Béatrice; Gillet, Jean-Michel

    2018-04-28

    In this paper, we propose a simple cluster model with limited basis sets to reproduce the unpaired electron distributions in a YTiO 3 ferromagnetic crystal. The spin-resolved one-electron-reduced density matrix is reconstructed simultaneously from theoretical magnetic structure factors and directional magnetic Compton profiles using our joint refinement algorithm. This algorithm is guided by the rescaling of basis functions and the adjustment of the spin population matrix. The resulting spin electron density in both position and momentum spaces from the joint refinement model is in agreement with theoretical and experimental results. Benefits brought from magnetic Compton profiles to the entire spin density matrix are illustrated. We studied the magnetic properties of the YTiO 3 crystal along the Ti-O 1 -Ti bonding. We found that the basis functions are mostly rescaled by means of magnetic Compton profiles, while the molecular occupation numbers are mainly modified by the magnetic structure factors.

  7. Neutron Powder Diffraction and Constrained Refinement

    Pawley, G. S.; Mackenzie, Gordon A.; Dietrich, O. W.

    1977-01-01

    The first use of a new program, EDINP, is reported. This program allows the constrained refinement of molecules in a crystal structure with neutron diffraction powder data. The structures of p-C6F4Br2 and p-C6F4I2 are determined by packing considerations and then refined with EDINP. Refinement is...

  8. Structural modelling, refinement and possible formation mechanism of a 4M.sub.3./sub. non-MDO ferriphlogopite (Ruiz Peak volcano)

    Pignatelli, I.; Dušek, Michal; De Titta, G.; Nespolo, M.

    2011-01-01

    Roč. 23, č. 1 (2011), s. 73-84 ISSN 0935-1221 Grant - others:AV ČR(CZ) AP0701 Program:Akademická prémie - Praemium Academiae Institutional research plan: CEZ:AV0Z10100521 Keywords : mica polytypism * ferriphlogopite * non-MDO polytype * PID analysis * OD character * structural refinement * charge distribution Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.486, year: 2011

  9. Crystal structure redetermination of ε-Ni.sub.3./sub.Si.sub.2./sub. from a single nanowire by dynamical refinement of precession electron diffraction data

    Correa, Cinthia Antunes; Klementová, Mariana; Dřínek, Vladislav; Kopeček, Jaromír; Palatinus, Lukáš

    2016-01-01

    Roč. 672, Jul (2016), s. 505-509 ISSN 0925-8388 R&D Projects: GA ČR GA13-25747S Institutional support: RVO:68378271 ; RVO:67985858 Keywords : precession electron diffraction tomography * structure determination * nanowire * dynamical refinement Subject RIV: BM - Solid Matter Physics ; Magnetism; CA - Inorganic Chemistry (UCHP-M) OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.); Inorganic and nuclear chemistry (UCHP-M) Impact factor: 3.133, year: 2016

  10. Panorama 2012 - Refining 2030

    Marion, Pierre; Saint-Antonin, Valerie

    2011-11-01

    The major uncertainty characterizing the global energy landscape impacts particularly on transport, which remains the virtually-exclusive bastion of the oil industry. The industry must therefore respond to increasing demand for mobility against a background marked by the emergence of alternatives to oil-based fuels and the need to reduce emissions of pollutants and greenhouse gases (GHG). It is in this context that the 'Refining 2030' study conducted by IFP Energies Nouvelles (IFPEN) forecasts what the global supply and demand balance for oil products could be, and highlights the type and geographical location of the refinery investment required. Our study shows that the bulk of the refining investment will be concentrated in the emerging countries (mainly those in Asia), whilst the areas historically strong in refining (Europe and North America) face reductions in capacity. In this context, the drastic reduction in the sulphur specification of bunker oil emerges as a structural issue for European refining, in the same way as increasingly restrictive regulation of refinery CO 2 emissions (quotas/taxation) and the persistent imbalance between gasoline and diesel fuels. (authors)

  11. [Effects of oil-refining microbes (genus Acinetobacter) on cytogenetical structures of human lymphocytes in cell cultures].

    Il'inskikh, N N; Il'inskikh, E N; Il'inskikh, I N

    2012-01-01

    The objective of this study was to assess ability of oil-refining bacteria Acinetobacter calcoaceticus and A. valentis to induce karyopathological abnormalities and chromosomal aberrations in human lymphocyte cultures. It was found that the cultures infected with A. calcoaceticus showed significantly high frequencies of cytogenetical effects and chromosomal aberrant cells as compared to the intact cultures and cultures infected with A. valentis. The most of chromosomal aberrations, mainly chromatid aberrations, were located in 1 and 2 chromosomes. Moreover, the aberrations were detected in some specific chromosome areas. Abnormalities of mitotic cell division and nucleus morphology were determined in lymphocyte cultures infected with A. calcoaceticus. There were found significantly high frequencies of cells with micronuclei, nucleus protrusions, anaphase or metaphase chromosome and chromosomal fragments lagging as well as multipolar and C-mitoses. Thus, the oil-refining bacteria A. calcoaceticus in contrast to A. valentis demonstrated strong genotoxic effects in human lymphocyte cultures in vitro.

  12. Animal welfare and the refinement of neuroscience research methods--a case study of Huntington's disease models.

    Olsson, I Anna S; Hansen, Axel K; Sandøe, Peter

    2008-07-01

    The use of animals in biomedical and other research presents an ethical dilemma: we do not want to lose scientific benefits, nor do we want to cause laboratory animals to suffer. Scientists often refer to the potential human benefits of animal models to justify their use. However, even if this is accepted, it still needs to be argued that the same benefits could not have been achieved with a mitigated impact on animal welfare. Reducing the adverse effects of scientific protocols ('refinement') is therefore crucial in animal-based research. It is especially important that researchers share knowledge on how to avoid causing unnecessary suffering. We have previously demonstrated that even in studies in which animal use leads to spontaneous death, scientists often fail to report measures to minimize animal distress (Olsson et al. 2007). In this paper, we present the full results of a case study examining reports, published in peer-reviewed journals between 2003 and 2004, of experiments employing animal models to study the neurodegenerative disorder Huntington's disease. In 51 references, experiments in which animals were expected to develop motor deficits so severe that they would have difficulty eating and drinking normally were conducted, yet only three references were made to housing adaptation to facilitate food and water intake. Experiments including end-stages of the disease were reported in 14 papers, yet of these only six referred to the euthanasia of moribund animals. If the reference in scientific publications reflects the actual application of refinement, researchers do not follow the 3Rs (replacement, reduction, refinement) principle. While in some cases, it is clear that less-than-optimal techniques were used, we recognize that scientists may apply refinement without referring to it; however, if they do not include such information in publications, it suggests they find it less relevant. Journal publishing policy could play an important role: first, in

  13. Structural Rietveld refinement and vibrational study of MgCr{sub x}Fe{sub 2−x}O{sub 4} spinel ferrites

    Sabri, K. [Laboratoire des Sciences et technique de l’Environnement et de la Valorisation, département de Génie des Procédés, Université de Mostaganem, Mostaganem (Algeria); Rais, A., E-mail: amrais@yahoo.com [Laboratoire des Sciences et technique de l’Environnement et de la Valorisation, département de Génie des Procédés, Université de Mostaganem, Mostaganem (Algeria); Taibi, K. [Laboratoire de Science et Génie des Matériaux, USTHB, Alger, Algéria (Algeria); Moreau, M.; Ouddane, B. [Laboratory of LASIR Spectrochemistry, University of Science and Technology, 59650 Villeneuve d’Ascq (France); Addou, A. [Laboratoire des Sciences et technique de l’Environnement et de la Valorisation, département de Génie des Procédés, Université de Mostaganem, Mostaganem (Algeria)

    2016-11-15

    Spinel ferrites with the general formula MgCr{sub x}Fe{sub 2−x}O{sub 4} (0≤x≤1) were synthesized by the standard ceramic technique and characterized by X-ray diffraction. The XRD patterns confirmed that the mixed ferrite samples are in the cubic spinel structure which is further validated by Rietveld refinement in the space group Fd3m. The crystal structure and cell parameters were refined by Rietveld analysis. The vibrational study was achieved using Fourier Transform-InfraRed (FT-IR) and Raman spectroscopy. From FT-IR band frequencies, the force constants K{sub t} and K{sub o} , for tetrahedral (A) and octahedral (B) sites respectively, have been calculated and discussed with the trend of bond lengths obtained from Rietveld refinement. For all compositions, Raman spectra revealed the five active modes showing the vibration of O{sup 2−} ions at both the A-site and B-site ions. The frequencies trend with chromium content of both FT-IR and Raman spectra showed a shift toward higher values for all modes.

  14. Rietveld refinement of the structures of 1.0 C-S-H and 1.5 C-S-H

    Battocchio, Francesco

    2012-11-01

    Low-Q region Rietveld analyses were performed on C-S-H synchrotron XRD patterns, using the software MAUD. Two different crystal structures of tobermorite 11 Å were used as a starting model: monoclinic ordered Merlino tobermorite, and orthorhombic disordered Hamid tobermorite. Structural modifications were required to adapt the structures to the chemical composition and the different interlayer spacing of the C-S-H samples. Refinement of atomic positions was done by using special constraints called fragments that maintain interatomic distances and orientations within atomic polyhedra. Anisotropic crystallite size refinement showed that C-S-H has a nanocrystalline disordered structure with a preferred direction of elongation of the nanocrystallites in the plane of the Ca interlayer. The quality of the fit showed that the monoclinic structure gives a more adequate representation of C-S-H, whereas the disordered orthorhombic structure can be considered a more realistic model if the lack of long-range order of the silica chain along the c-direction is assumed. © 2012 Elsevier Ltd. All rights reserved.

  15. Bigraphical Refinement

    Perrone, Gian David; Debois, Søren; Hildebrandt, Thomas

    2012-01-01

    We propose a mechanism for the vertical refinement of bigraphical reactive systems, based upon a mechanism for limiting observations and utilising the underlying categorical structure of bigraphs. We present a motivating example to demonstrate that the proposed notion of refinement is sensible...... with respect to the theory of bigraphical reactive systems; and we propose a sufficient condition for guaranteeing the existence of a safety-preserving vertical refinement. We postulate the existence of a complimentary notion of horizontal refinement for bigraphical agents, and finally we discuss the...

  16. Structural studies of TiC1−xOx solid solution by Rietveld refinement and first-principles calculations

    Jiang, Bo; Hou, Na; Huang, Shanyan; Zhou, Gege; Hou, Jungang; Cao, Zhanmin; Zhu, Hongmin

    2013-01-01

    The lattice parameters, structural stability and electronic structure of titanium oxycarbides (TiC 1−x O x , 0≤x≤1) solid solution were investigated by Rietveld refinement and first-principles calculations. Series of TiC 1−x O x were precisely synthesized by sintering process under the vacuum. Rietveld refinement results of XRD patterns show the properties of continuous solid solution in TiC 1−x O x over the whole composition range. The lattice parameters vary from 0.4324 nm to 0.4194 nm decreasing with increasing oxygen concentration. Results of first-principles calculations reveal that the disorder C/O structure is stable than the order C/O structure. Further investigations of the vacancy in Ti 1−Va (C 1−x O x ) 1−Va solid solution present that the structure of vacancy segregated in TiO-part is more stable than the disorder C/O structure, which can be ascribed to the Ti–Ti bond across O-vacancy and the charge redistributed around Ti-vacancy via the analysis of the electron density difference plots and PDOS. - Graphical abstract: XRD of series of titanium oxycarbides (TiC 1−x O x , 0≤x≤1) solid solution prepared by adjusting the proportion of TiO in the starting material. Highlights: • Titanium oxycarbides were obtained by sintering TiO and TiC under carefully controlled conditions. • Rietveld refinement results show continuous solid solution with FCC structure in TiC 1−x O x . • The disorder C/O structure is stable than the order C/O structure. • Introduction of vacancy segregated in TiO-part is more stable than disorder C/O structure. • Ti–Ti bond across O-vacancy and the charge redistributed around Ti-vacancy enhance structural stability

  17. Cry1A(b)16 toxin from Bacillus thuringiensis: Theoretical refinement of three-dimensional structure and prediction of peptides as molecular markers for detection of genetically modified organisms.

    Plácido, Alexandra; Coelho, Andreia; Abreu Nascimento, Lucas; Gomes Vasconcelos, Andreanne; Fátima Barroso, Maria; Ramos-Jesus, Joilson; Costa, Vladimir; das Chagas Alves Lima, Francisco; Delerue-Matos, Cristina; Martins Ramos, Ricardo; Marani, Mariela M; Roberto de Souza de Almeida Leite, José

    2017-07-01

    Transgenic maize produced by the insertion of the Cry transgene into its genome became the second most cultivated crop worldwide. Cry gene from Bacillus thuringiensis kurstaki expresses protein derivatives of crystalline endotoxins which confer insect resistance onto the maize crop. Mandatory labeling of processed food containing or made by genetically modified organisms is in force in many countries, so, it is very urgent to develop fast and practical methods for GMO identification, for example, biosensors. In the absence of an available empirical structure of Cry1A(b)16 protein, a theoretical model was effectively generated, in this work, by homology modeling and molecular dynamics simulations based on two available homologous protein structures. Molecular dynamics simulations were carried out to refine the selected model, and an analysis of its global structure was performed. The refined models of Cry1A(b)16 showed a standard fold and structural characteristics similar to those seen in Bacillus thuringiensis Cry1A(a) insecticidal toxin and Bacillus thuringiensis serovar kurstaki Cry1A(c) toxin. After in silico analysis of Cry1A(b)16, two immunoreactive candidate peptides were selected and specific polyclonal antibodies were produced resulting in antibody-peptide interaction. Biosensing devices are expected to be developed for detection of the Cry1A(b) protein as a marker of transgenic maize in food. Proteins 2017; 85:1248-1257. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  18. Subdomain Precise Integration Method for Periodic Structures

    F. Wu

    2014-01-01

    Full Text Available A subdomain precise integration method is developed for the dynamical responses of periodic structures comprising many identical structural cells. The proposed method is based on the precise integration method, the subdomain scheme, and the repeatability of the periodic structures. In the proposed method, each structural cell is seen as a super element that is solved using the precise integration method, considering the repeatability of the structural cells. The computational efforts and the memory size of the proposed method are reduced, while high computational accuracy is achieved. Therefore, the proposed method is particularly suitable to solve the dynamical responses of periodic structures. Two numerical examples are presented to demonstrate the accuracy and efficiency of the proposed method through comparison with the Newmark and Runge-Kutta methods.

  19. Structures of Ta22W4O67 and Ta74W6O203. Pt. 1. Refined structural models using synchrotron radiation

    Schmid, S.

    1995-01-01

    The crystal structures of Ta 22 W 4 O 67 [M r = 5788.19, a = 6.1485 (5), b = 47.6205 (12), c = 3.8559 (3) A, γ = 90.04 (1) , space group = C112/m (non-standard setting), Z = 1, D x = 8.513 g cm -3 , F(000) = 2438] and Ta 74 W 6 O 203 [M r = 17741.06, a = 6.1664 (5), b = 29.2717 (14), c = 3.8731 (2) A, space group = Pbam (no. 55), Z = 0.2, D x = 8.428 g cm -3 , F(000) 1494] were determined using synchrotron radiation at four different wavelengths below the Ta L III edge [λ = 1.2741 (-146 eV), λ = 1.2586 (-26 eV), λ = 1.2571 (-14 eV) and λ = 1.2563 A (-8 eV)]. The collection of data immediately below the Ta L III edge at -8 eV enabled resolution of Ta and W of up to eight electrons, which assisted in the refinement of Ta/W ordering for both structures. Bond valence arguments have been used to locate oxygen vacancies required by the formulae. From the largest data set for Ta 22 W 4 O 67 (λ = 1.2741 A), a final value of 0.0481 for R 1 = Σ parallel F obs (h)vertical stroke - vertical stroke F calc (h) parallel /Σvertical stroke F obs (h)vertical stroke was obtained for 3082 unmerged reflections with I(h) > 3σ[I(h)] and for Ta 74 W 6 O 203 (λ = 1.2563 A) a final value of 0.0571 for R 1 was obtained for 5675 unmerged reflections. The two structures are described from a conventional polyhedral perspective as 13- and 8-times superstructures occurring in the solid solution (1-x)Ta 2 O 5 xWO 3 , 0 ≤ x ≤ 0.267. (orig.)

  20. Proposal of method for quantifying uranium weight in the interior of gas centrifuge, and performance evaluation of IF7 treatment reaction product separation and refinement

    Ema, Akira; Kado, Kazumi; Suzuki, Kazuhiko

    2011-01-01

    In uranium enrichment plant decommissioning, it is important to treat and dispose the gas centrifuge reasonably. At the Ningyo-Toge Environmental Engineering Center of JAEA, it has been planned to carry out IF 7 treatment for the gas centrifuge in the uranium enrichment plant for decontamination before dismantling. In order to carry out this IF 7 treatment, a nondestructive measurement technology to estimate the uranium weight in the interior of the gas centrifuge was needed. However, it was difficult to estimate exactly uranium weight using former methods. Therefore, in this study, we investigated a new nondestructive measurement. As a result, we succeeded in constructing theoretically the methodology using γ-ray intensity measured outside the gas centrifuge and MCNP code. Furthermore, the UF 6 and IF 5 mixture was recovered by IF 7 treatment. A technology to separate and refine IF 5 from this mixture was needed in order to use as a material of IF 7 gas. Therefore, in this study, we carried out IF 5 separation and refinement examination. This paper shows the investigation result of reasonable separation condition and the full-scale examination result. As a result, it could be proved that 86% of IF 5 was separated and refined from UF 6 and IF 5 mixture. (author)

  1. The combination of activated natural zeolite-bentonite to reduce Fe and Cu in refined bleached palm oil (RBPO) by using atomic absorption spectrophotometer method

    Zakwan; Raja, PM; Giyanto

    2018-02-01

    Indonesia is one of the crude palm oil (CPO) production country in the world. As many products are derivated from the CPO, the quality must be increased continuously. One of the things that influence the quality of palm oil is the Fe and Cu content. The objective of this research was to reduce Fe and Cu content in Refined Bleached Palm Oil (RBPO). In processing CPO or Refined Bleachead Palm Oil (RBPO) may be contaminated by Fe and Cu from metal tank and pipe in the factory. The zeolite and bentonite was activated by maceration method using hydrochloric acid (0,1 N). Four batch reactions consisting of refined palm oil (RPO), activated natural zeolite-bentonite (ANZB) was bleached by heating and stirring them at about 105°C and 1200 rpm for 30 minutes. The results showed that all combinations of ANZB can reduce the Fe content. Thereafter, the optimal combination of ANZB was obtained in K1, K2 and K4 with Cu content 0.02 ppm. In the future, it is needed to study on the reduction of the Fe and Cu content in palm oil with the other adsorbent.

  2. Method for fabricating beryllium structures

    Hovis, Jr., Victor M.; Northcutt, Jr., Walter G.

    1977-01-01

    Thin-walled beryllium structures are prepared by plasma spraying a mixture of beryllium powder and about 2500 to 4000 ppm silicon powder onto a suitable substrate, removing the plasma-sprayed body from the substrate and placing it in a sizing die having a coefficient of thermal expansion similar to that of the beryllium, exposing the plasma-sprayed body to a moist atmosphere, outgassing the plasma-sprayed body, and then sintering the plasma-sprayed body in an inert atmosphere to form a dense, low-porosity beryllium structure of the desired thin-wall configuration. The addition of the silicon and the exposure of the plasma-sprayed body to the moist atmosphere greatly facilitate the preparation of the beryllium structure while minimizing the heretofore deleterious problems due to grain growth and grain orientation.

  3. Niobium-base grain refiner for aluminium

    Silva Pontes, P. da; Robert, M.H.; Cupini, N.L.

    1980-01-01

    A new chemical grain refiner for aluminium has been developed, using inoculation of a niobium-base compound. When a bath of molten aluminium is inoculated whith this refiner, an intermetallic aluminium-niobium compound is formed which acts as a powerful nucleant, producing extremely fine structure comparable to those obtained by means of the traditional grain refiner based on titanium and boron. It was found that the refinement of the structure depends upon the weight percentage of the new refiner inoculated as well as the time of holding the bath after inoculation and before pouring, but mainly on the inoculating temperature. (Author) [pt

  4. Crystal structure refinement and microwave dielectric properties of new low dielectric loss AZrNb2O8 (A: Mn, Zn, Mg and Co) ceramics

    Ramarao, S.D.; Murthy, V.R.K.

    2013-01-01

    Graphical abstract: -- The effects of substituting different cations (Mn, Zn, Mg and Co) at the A-site of AZrNb 2 O 8 compounds on structural parameters such as packing fraction and B-site octahedral distortion were studied using X-ray powder diffraction in conjunction with Rietveld refinement. Variations in the dielectric constant (ε r ) were explained by the ionic polarizability of the compositions. The quality factor (Q × f) and temperature coefficient of resonant frequency (τ f ) were correlated with the packing fraction and B-site octahedral distortions (δ) in these compositions, respectively

  5. A posteriori estimator and adaptive mesh refinement for finite volume finite element method for monophasic flow and solute transport in porous media

    Amor, H.; Bourgeois, M.

    2012-01-01

    using an adaptive mesh refinement strategy was introduced in MELODIE for the simulation of groundwater flow and solute transport in saturated porous media in 2 dimensions. The selected estimator, based on the explicit residual error, is expected to allow local refinements and thus minimization of the discretization error at an optimal computational cost. Test case: a realistic heterogeneous case with fracturing. In addition to theoretical test cases a more complex case was tested. The purpose of this test case was twofold: - to move from pure theoretical work to an illustrative case within a realistic generic context; however parameter values for hydrodynamic characteristics were chosen so as to highlight the investigated phenomena; - to account for large time and space scales, representative for those required for the simulation of radioactive waste repositories. The general shape of the geological media was designed to cover main features representative of sedimentary formations. Three distinct radionuclide source locations were chosen in order to obtain a set of flow and transport configurations. The entire layer sequence was structured into three hydrogeological units intersected by three sub-vertical faults. The vertical 2D cross-section dimensions are 5 km long by 500 m thick. Two source terms are located in a 100 m-thick layer in the right part of the domain and another one is located in a larger layer in the left part. These two 'host rock' layers consist of the same sedimentary unit with a low permeability, though an offset due to the middle fault. Faults are considered as conductive features. Radionuclides are assumed to be instantaneously released from the three source term locations at t = 0. The a posteriori error estimator and the adaptive mesh algorithm were applied to this heterogeneous problem. Preliminary calculations showed that the implemented a posteriori error estimator method is efficient to solve the equations of flow and advective

  6. South Korea - oil refining overview

    Hayes, D.

    1999-01-01

    Following the economic problems of the 1990s, the petroleum refining industry of South Korea underwent much involuntary restructuring in 1999 with respect to takeovers and mergers and these are discussed. The demand for petroleum has now pretty well recovered. The reasons for fluctuating prices in the 1990s, how the new structure should be cushioned against changes in the future, and the potential for South Korea to export refined petroleum, are all discussed

  7. Resolving the detailed structure of cortical and thalamic neurons in the adult rat brain with refined biotinylated dextran amine labeling.

    Ling, Changying; Hendrickson, Michael L; Kalil, Ronald E

    2012-01-01

    Biotinylated dextran amine (BDA) has been used frequently for both anterograde and retrograde pathway tracing in the central nervous system. Typically, BDA labels axons and cell somas in sufficient detail to identify their topographical location accurately. However, BDA labeling often has proved to be inadequate to resolve the fine structural details of axon arbors or the dendrites of neurons at a distance from the site of BDA injection. To overcome this limitation, we varied several experimental parameters associated with the BDA labeling of neurons in the adult rat brain in order to improve the sensitivity of the method. Specifically, we compared the effect on labeling sensitivity of: (a) using 3,000 or 10,000 MW BDA; (b) injecting different volumes of BDA; (c) co-injecting BDA with NMDA; and (d) employing various post-injection survival times. Following the extracellular injection of BDA into the visual cortex, labeled cells and axons were observed in both cortical and thalamic areas of all animals studied. However, the detailed morphology of axon arbors and distal dendrites was evident only under optimal conditions for BDA labeling that take into account the: molecular weight of the BDA used, concentration and volume of BDA injected, post-injection survival time, and toning of the resolved BDA with gold and silver. In these instances, anterogradely labeled axons and retrogradely labeled dendrites were resolved in fine detail, approximating that which can be achieved with intracellularly injected compounds such as biocytin or fluorescent dyes.

  8. A refined method for assessing sup(99m)Tc-MDP whole body retention in prostate cancer patients

    Castronovo, F.P. Jr.; Strauss, H.W.; McKusick, K.A.

    1987-01-01

    Whole body retention (WBR) of sup(99m)Tc labeled methylene diphosphonate (MDP) significantly differentiates various clinical stages of prostate cancer. Whole body measurements, when performed at 5 min and 24 h after i.v. administration of sup(99m)Tc-MDP, allows for the calculations of percentage whole body retention (% WBR) after one day. In an attempt to better describe the clinical course of prostate cancer patients with bone metastases we have refined the % WBR calculations to include a normalization factor. The latter consists of the mean 24-h value of WBR's as obtained from 10 prostate cancer patients without bony metastases as determined by bone scintigram. The % WBR is then divided by the normalization factor of choice and expressed as (% WRN)sup(N). These data are used to better express sup(99m)Tc MDP 24-h whole body retentions when following the clinical course of patients with metastatic carcinoma of the prostate. Caution should be exercised when interpreting these data when metabolic bone pathology is present. A false negative (% WBR)sup(N) value will result if an infiltration of the sup(99m)Tc-MDP occurs during administration. (author)

  9. Filament wound structure and method

    Dritt, W.S.; Gerth, H.L.; Knight, C.E. Jr.; Pardue, R.M.

    1977-01-01

    A filament wound spherical structure is described comprising a plurality of filament band sets disposed about the surface of a mandrel with each band of each set formed of a continuous filament circumferentially wound about the mandrel a selected number of circuits and with each circuit of filament being wound parallel to and contiguous with an immediate previously wound circuit. Each filament band in each band set is wound at the same helix angle from the axis of revolution of the mandrel and all of the bands of each set are uniformly distributed about the mandrel circumference. The pole-to-equator wall thickness taper associated with each band set, as several contiguous band sets are wound about the mandrel starting at the poles, is accumulative as the band sets are nested to provide a complete filament wound sphere of essentially uniform thickness

  10. A cellular automaton - finite volume method for the simulation of dendritic and eutectic growth in binary alloys using an adaptive mesh refinement

    Dobravec, Tadej; Mavrič, Boštjan; Šarler, Božidar

    2017-11-01

    A two-dimensional model to simulate the dendritic and eutectic growth in binary alloys is developed. A cellular automaton method is adopted to track the movement of the solid-liquid interface. The diffusion equation is solved in the solid and liquid phases by using an explicit finite volume method. The computational domain is divided into square cells that can be hierarchically refined or coarsened using an adaptive mesh based on the quadtree algorithm. Such a mesh refines the regions of the domain near the solid-liquid interface, where the highest concentration gradients are observed. In the regions where the lowest concentration gradients are observed the cells are coarsened. The originality of the work is in the novel, adaptive approach to the efficient and accurate solution of the posed multiscale problem. The model is verified and assessed by comparison with the analytical results of the Lipton-Glicksman-Kurz model for the steady growth of a dendrite tip and the Jackson-Hunt model for regular eutectic growth. Several examples of typical microstructures are simulated and the features of the method as well as further developments are discussed.

  11. Structural reliability methods: Code development status

    Millwater, Harry R.; Thacker, Ben H.; Wu, Y.-T.; Cruse, T. A.

    1991-05-01

    The Probabilistic Structures Analysis Method (PSAM) program integrates state of the art probabilistic algorithms with structural analysis methods in order to quantify the behavior of Space Shuttle Main Engine structures subject to uncertain loadings, boundary conditions, material parameters, and geometric conditions. An advanced, efficient probabilistic structural analysis software program, NESSUS (Numerical Evaluation of Stochastic Structures Under Stress) was developed as a deliverable. NESSUS contains a number of integrated software components to perform probabilistic analysis of complex structures. A nonlinear finite element module NESSUS/FEM is used to model the structure and obtain structural sensitivities. Some of the capabilities of NESSUS/FEM are shown. A Fast Probability Integration module NESSUS/FPI estimates the probability given the structural sensitivities. A driver module, PFEM, couples the FEM and FPI. NESSUS, version 5.0, addresses component reliability, resistance, and risk.

  12. Refinement of the crystal structure of malachite, Cu/sub 2/(OH)/sub 2/CO/sub 3/, by neutron diffraction

    Zigan, F; Joswig, W; Schuster, H D [Frankfurt Univ. (Germany, F.R.); Mason, S A [Institut Max von Laue - Paul Langevin, 38 - Grenoble (France)

    1977-01-01

    The crystal structure of malachite is refined (R = 0,021) with the intensity values of 635 independent neutron reflexions from a single crystal, rather free from absorption and extinction. Concerning the structural geometry, no essential deviations occur from the known results of x-ray diffraction. The thermal elongations are generally largest about the normal to the (201) layers, between which the bonding is relatively weak. In both of the (medium, bent) OH...O hydrogen bonds, the anisotropic thermal parameters, converted according to the riding model, are - with certain restrictions - in agreement with the measured infrared spectrum as well as with frequencies and directions of the proton vibration calculated from the bonding geometry on the basis of a theoretical model.

  13. Structural refinement of Nd[Fe(CN)6].4H2O and study of NdFeO3 obtained by its oxidative thermal decomposition at very low temperatures

    Navarro, M. Carolina; Pannunzio-Miner, Elisa V.; Pagola, Silvina; Gomez, M. Ines; Carbonio, Raul E.

    2005-01-01

    The crystal structure of Nd[Fe(CN) 6 ].4H 2 O has been refined by Rietveld analysis using high resolution synchrotron powder X-ray diffraction data. It belonged to the orthorhombic crystal system, Cmcm space group, with cell parameters: a=7.473952(1)A, b=12.919104(2)A and c=13.800549(2)A. The change in space group from P6 3 /m which is observed in the pentahydrates (LnFe(CN) 6 .5H 2 O) to Cmcm in the tetrahydrates has been analyzed to be a consequence of the change in 9-fold coordination of Nd 3+ in the pentahydrates to 8-fold coordination in the tetrahydrates, which changes the Nd 3+ environment from tricapped trigonal prism to a distorted tricapped trigonal prism or square antiprism. Its decomposition process in air to produce NdFeO 3 has been followed by thermogravimetric and differential thermal analysis, IR spectroscopy and laboratory powder XRD. We found that it is possible to synthesize crystalline NdFeO 3 at temperatures as low as 380 o C and refine the structure of single phase crystalline NdFeO 3 synthesized by this method at 600 deg. C

  14. Multigrid methods in structural mechanics

    Raju, I. S.; Bigelow, C. A.; Taasan, S.; Hussaini, M. Y.

    1986-01-01

    Although the application of multigrid methods to the equations of elasticity has been suggested, few such applications have been reported in the literature. In the present work, multigrid techniques are applied to the finite element analysis of a simply supported Bernoulli-Euler beam, and various aspects of the multigrid algorithm are studied and explained in detail. In this study, six grid levels were used to model half the beam. With linear prolongation and sequential ordering, the multigrid algorithm yielded results which were of machine accuracy with work equivalent to 200 standard Gauss-Seidel iterations on the fine grid. Also with linear prolongation and sequential ordering, the V(1,n) cycle with n greater than 2 yielded better convergence rates than the V(n,1) cycle. The restriction and prolongation operators were derived based on energy principles. Conserving energy during the inter-grid transfers required that the prolongation operator be the transpose of the restriction operator, and led to improved convergence rates. With energy-conserving prolongation and sequential ordering, the multigrid algorithm yielded results of machine accuracy with a work equivalent to 45 Gauss-Seidel iterations on the fine grid. The red-black ordering of relaxations yielded solutions of machine accuracy in a single V(1,1) cycle, which required work equivalent to about 4 iterations on the finest grid level.

  15. Clustering methods for the optimization of atomic cluster structure

    Bagattini, Francesco; Schoen, Fabio; Tigli, Luca

    2018-04-01

    In this paper, we propose a revised global optimization method and apply it to large scale cluster conformation problems. In the 1990s, the so-called clustering methods were considered among the most efficient general purpose global optimization techniques; however, their usage has quickly declined in recent years, mainly due to the inherent difficulties of clustering approaches in large dimensional spaces. Inspired from the machine learning literature, we redesigned clustering methods in order to deal with molecular structures in a reduced feature space. Our aim is to show that by suitably choosing a good set of geometrical features coupled with a very efficient descent method, an effective optimization tool is obtained which is capable of finding, with a very high success rate, all known putative optima for medium size clusters without any prior information, both for Lennard-Jones and Morse potentials. The main result is that, beyond being a reliable approach, the proposed method, based on the idea of starting a computationally expensive deep local search only when it seems worth doing so, is capable of saving a huge amount of searches with respect to an analogous algorithm which does not employ a clustering phase. In this paper, we are not claiming the superiority of the proposed method compared to specific, refined, state-of-the-art procedures, but rather indicating a quite straightforward way to save local searches by means of a clustering scheme working in a reduced variable space, which might prove useful when included in many modern methods.

  16. A Multiscale Adaptive Mesh Refinement Approach to Architectured Steel Specification in the Design of a Frameless Stressed Skin Structure

    Nicholas, Paul; Stasiuk, David; Nørgaard, Esben

    2015-01-01

    This paper describes the development of a modelling approach for the design and fabrication of an incrementally formed, stressed skin metal structure. The term incremental forming refers to a progression of localised plastic deformation to impart 3D form onto a 2D metal sheet, directly from 3D...... design data. A brief introduction presents this fabrication concept, as well as the context of structures whose skin plays a significant structural role. Existing research into ISF privileges either the control of forming parameters to minimise geometric deviation, or the more accurate measurement...... of the impact of the forming process at the scale of the grain. But to enhance structural performance for architectural applications requires that both aspects are considered synthetically. We demonstrate a mesh-based approach that incorporates critical parameters at the scales of structure, element...

  17. The effect of Al-5Ti-1B grain refiner on the structure and tensile properties of Al-20%Mg alloy

    Fakhraei, O. [Center of Excellence for High Performance Materials, School of Metallurgy and Materials, College of Engineering, University of Tehran, Tehran (Iran, Islamic Republic of); Emamy, M., E-mail: emamy@ut.ac.ir [Center of Excellence for High Performance Materials, School of Metallurgy and Materials, College of Engineering, University of Tehran, Tehran (Iran, Islamic Republic of); Farhangi, H. [Center of Excellence for High Performance Materials, School of Metallurgy and Materials, College of Engineering, University of Tehran, Tehran (Iran, Islamic Republic of)

    2013-01-10

    In current research, the effect of Al-5Ti-1B grain refiner on the structure and tensile properties of Al-20%Mg alloy have been investigated. Scanning electron microscopy (SEM) and Energy Dispersive X-ray (EDX) analysis were utilized to study the microstructure and fracture surfaces of samples. Microstructural analysis of the cast alloy showed the dendrites of a primary {alpha}-phase solid solution within the eutectic matrix which consists of {beta}-Al{sub 3}Mg{sub 2} intermetallic and {alpha}-solid solution. The results indicated that adding Al-5Ti-1B to the alloy caused a significant rise in the ultimate tensile strength (UTS) and elongation values from 168 MPa and 1.2% to maximum 253 MPa and 2.4%, respectively. The main mechanisms for the observed enhancement were found to be due to the refinement of grains during solidification and also segregation of Ti to the tip of Al ({alpha}) dendrites. This phenomenon controls the dendritic growth and changes the morphology of this phase from interconnected coarse dendrites to a star-like morphology.

  18. A hierarchical method for structural topology design problems with local stress and displacement constraints

    Stolpe, Mathias; Stidsen, Thomas K.

    2005-01-01

    In this paper we present a hierarchical optimization method for finding feasible true 0-1 solutions to finite element based topology design problems. The topology design problems are initially modeled as non-convex mixed 0-1 programs. The hierarchical optimization method is applied to the problem...... and then successively refined as needed. At each level of design mesh refinement, a neighborhood optimization method is used to solve the problem considered. The non-convex topology design problems are equivalently reformulated as convex all-quadratic mixed 0-1 programs. This reformulation enables the use of methods...... of minimizing the weight of a structure subject to displacement and local design-dependent stress constraints. The method iteratively solves a sequence of problems of increasing size of the same type as the original problem. The problems are defined on a design mesh which is initially coarse...

  19. A hierarchical method for discrete structural topology design problems with local stress and displacement constraints

    Stolpe, Mathias; Stidsen, Thomas K.

    2007-01-01

    In this paper, we present a hierarchical optimization method for finding feasible true 0-1 solutions to finite-element-based topology design problems. The topology design problems are initially modelled as non-convex mixed 0-1 programs. The hierarchical optimization method is applied to the problem...... and then successively refined as needed. At each level of design mesh refinement, a neighbourhood optimization method is used to treat the problem considered. The non-convex topology design problems are equivalently reformulated as convex all-quadratic mixed 0-1 programs. This reformulation enables the use of methods...... of minimizing the weight of a structure subject to displacement and local design-dependent stress constraints. The method iteratively treats a sequence of problems of increasing size of the same type as the original problem. The problems are defined on a design mesh which is initially coarse...

  20. Broyden's method in nuclear structure calculations

    Baran, Andrzej; Bulgac, Aurel; Forbes, Michael McNeil; Hagen, Gaute; Nazarewicz, Witold; Schunck, Nicolas; Stoitsov, Mario V.

    2008-01-01

    Broyden's method, widely used in quantum chemistry electronic-structure calculations for the numerical solution of nonlinear equations in many variables, is applied in the context of the nuclear many-body problem. Examples include the unitary gas problem, the nuclear density functional theory with Skyrme functionals, and the nuclear coupled-cluster theory. The stability of the method, its ease of use, and its rapid convergence rates make Broyden's method a tool of choice for large-scale nuclear structure calculations

  1. On the refinement calculus

    Vickers, Trevor

    1992-01-01

    On the Refinement Calculus gives one view of the development of the refinement calculus and its attempt to bring together - among other things - Z specifications and Dijkstra's programming language. It is an excellent source of reference material for all those seeking the background and mathematical underpinnings of the refinement calculus.

  2. 77 FR 2064 - Availability of the Report on the International Workshop on Alternative Methods To Reduce, Refine...

    2012-01-13

    ... Validation of Alternative Methods, and Health Canada. The workshop was co-sponsored by the Society of... Coordinating Committee on the Validation of Alternative Methods (ICCVAM), an interagency committee of the... prioritize research, development, and validation efforts needed to address these knowledge and data gaps in...

  3. Can Morphing Methods Predict Intermediate Structures?

    Weiss, Dahlia R.; Levitt, Michael

    2009-01-01

    Movement is crucial to the biological function of many proteins, yet crystallographic structures of proteins can give us only a static snapshot. The protein dynamics that are important to biological function often happen on a timescale that is unattainable through detailed simulation methods such as molecular dynamics as they often involve crossing high-energy barriers. To address this coarse-grained motion, several methods have been implemented as web servers in which a set of coordinates is usually linearly interpolated from an initial crystallographic structure to a final crystallographic structure. We present a new morphing method that does not extrapolate linearly and can therefore go around high-energy barriers and which can produce different trajectories between the same two starting points. In this work, we evaluate our method and other established coarse-grained methods according to an objective measure: how close a coarse-grained dynamics method comes to a crystallographically determined intermediate structure when calculating a trajectory between the initial and final crystal protein structure. We test this with a set of five proteins with at least three crystallographically determined on-pathway high-resolution intermediate structures from the Protein Data Bank. For simple hinging motions involving a small conformational change, segmentation of the protein into two rigid sections outperforms other more computationally involved methods. However, large-scale conformational change is best addressed using a nonlinear approach and we suggest that there is merit in further developing such methods. PMID:18996395

  4. Modelling CEC variations versus structural iron reduction levels in dioctahedral smectites. Existing approaches, new data and model refinements.

    Hadi, Jebril; Tournassat, Christophe; Ignatiadis, Ioannis; Greneche, Jean Marc; Charlet, Laurent

    2013-10-01

    A model was developed to describe how the 2:1 layer excess negative charge induced by the reduction of Fe(III) to Fe(II) by sodium dithionite buffered with citrate-bicarbonate is balanced and applied to nontronites. This model is based on new experimental data and extends structural interpretation introduced by a former model [36-38]. The 2:1 layer negative charge increase due to Fe(III) to Fe(II) reduction is balanced by an excess adsorption of cations in the clay interlayers and a specific sorption of H(+) from solution. Prevalence of one compensating mechanism over the other is related to the growing lattice distortion induced by structural Fe(III) reduction. At low reduction levels, cation adsorption dominates and some of the incorporated protons react with structural OH groups, leading to a dehydroxylation of the structure. Starting from a moderate reduction level, other structural changes occur, leading to a reorganisation of the octahedral and tetrahedral lattice: migration or release of cations, intense dehydroxylation and bonding of protons to undersaturated oxygen atoms. Experimental data highlight some particular properties of ferruginous smectites regarding chemical reduction. Contrary to previous assumptions, the negative layer charge of nontronites does not only increase towards a plateau value upon reduction. A peak is observed in the reduction domain. After this peak, the negative layer charge decreases upon extended reduction (>30%). The decrease is so dramatic that the layer charge of highly reduced nontronites can fall below that of its fully oxidised counterpart. Furthermore, the presence of a large amount of tetrahedral Fe seems to promote intense clay structural changes and Fe reducibility. Our newly acquired data clearly show that models currently available in the literature cannot be applied to the whole reduction range of clay structural Fe. Moreover, changes in the model normalising procedure clearly demonstrate that the investigated low

  5. Comparison Study of Subspace Identification Methods Applied to Flexible Structures

    Abdelghani, M.; Verhaegen, M.; Van Overschee, P.; De Moor, B.

    1998-09-01

    In the past few years, various time domain methods for identifying dynamic models of mechanical structures from modal experimental data have appeared. Much attention has been given recently to so-called subspace methods for identifying state space models. This paper presents a detailed comparison study of these subspace identification methods: the eigensystem realisation algorithm with observer/Kalman filter Markov parameters computed from input/output data (ERA/OM), the robust version of the numerical algorithm for subspace system identification (N4SID), and a refined version of the past outputs scheme of the multiple-output error state space (MOESP) family of algorithms. The comparison is performed by simulating experimental data using the five mode reduced model of the NASA Mini-Mast structure. The general conclusion is that for the case of white noise excitations as well as coloured noise excitations, the N4SID/MOESP algorithms perform equally well but give better results (improved transfer function estimates, improved estimates of the output) compared to the ERA/OM algorithm. The key computational step in the three algorithms is the approximation of the extended observability matrix of the system to be identified, for N4SID/MOESP, or of the observer for the system to be identified, for the ERA/OM. Furthermore, the three algorithms only require the specification of one dimensioning parameter.

  6. Apocrustacyanin C(1) crystals grown in space and on earth using vapour-diffusion geometry: protein structure refinements and electron-density map comparisons.

    Habash, Jarjis; Boggon, Titus J; Raftery, James; Chayen, Naomi E; Zagalsky, Peter F; Helliwell, John R

    2003-07-01

    Models of apocrustacyanin C(1) were refined against X-ray data recorded on Bending Magnet 14 at the ESRF to resolutions of 1.85 and 2 A from a space-grown and an earth-grown crystal, respectively, both using vapour-diffusion crystal-growth geometry. The space crystals were grown in the APCF on the NASA Space Shuttle. The microgravity crystal growth showed a cyclic nature attributed to Marangoni convection, thus reducing the benefits of the microgravity environment, as reported previously [Chayen et al. (1996), Q. Rev. Biophys. 29, 227-278]. A subsequent mosaicity evaluation, also reported previously, showed only a partial improvement in the space-grown crystals over the earth-grown crystals [Snell et al. (1997), Acta Cryst. D53, 231-239], contrary to the case for lysozyme crystals grown in space with liquid-liquid diffusion, i.e. without any major motion during growth [Snell et al. (1995), Acta Cryst. D52, 1099-1102]. In this paper, apocrustacyanin C(1) electron-density maps from the two refined models are now compared. It is concluded that the electron-density maps of the protein and the bound waters are found to be better overall for the structures of apocrustacyanin C(1) studied from the space-grown crystal compared with those from the earth-grown crystal, even though both crystals were grown using vapour-diffusion crystal-growth geometry. The improved residues are on the surface of the protein, with two involved in or nearby crystal lattice-forming interactions, thus linking an improved crystal-growth mechanism to the molecular level. The structural comparison procedures developed should themselves be valuable for evaluating crystal-growth procedures in the future.

  7. Implementation of the 3Rs (refinement, reduction, and replacement): validation and regulatory acceptance considerations for alternative toxicological test methods.

    Schechtman, Leonard M

    2002-01-01

    Toxicological testing in the current regulatory environment is steeped in a history of using animals to answer questions about the safety of products to which humans are exposed. That history forms the basis for the testing strategies that have evolved to satisfy the needs of the regulatory bodies that render decisions that affect, for the most part, virtually all phases of premarket product development and evaluation and, to a lesser extent, postmarketing surveillance. Only relatively recently have the levels of awareness of, and responsiveness to, animal welfare issues reached current proportions. That paradigm shift, although sluggish, has nevertheless been progressive. New and alternative toxicological methods for hazard evaluation and risk assessment have now been adopted and are being viewed as a means to address those issues in a manner that considers humane treatment of animals yet maintains scientific credibility and preserves the goal of ensuring human safety. To facilitate this transition, regulatory agencies and regulated industry must work together toward improved approaches. They will need assurance that the methods will be reliable and the results comparable with, or better than, those derived from the current classical methods. That confidence will be a function of the scientific validation and resultant acceptance of any given method. In the United States, to fulfill this need, the Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) and its operational center, the National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), have been constituted as prescribed in federal law. Under this mandate, ICCVAM has developed a process and established criteria for the scientific validation and regulatory acceptance of new and alternative methods. The role of ICCVAM in the validation and acceptance process and the criteria instituted toward that end are described. Also

  8. Anomalies in the refinement of isoleucine

    Berntsen, Karen R. M.; Vriend, Gert, E-mail: gerrit.vriend@radboudumc.nl [Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA Nijmegen (Netherlands)

    2014-04-01

    The side-chain torsion angles of isoleucines in X-ray protein structures are a function of resolution, secondary structure and refinement software. Detailing the standard torsion angles used in refinement software can improve protein structure refinement. A study of isoleucines in protein structures solved using X-ray crystallography revealed a series of systematic trends for the two side-chain torsion angles χ{sub 1} and χ{sub 2} dependent on the resolution, secondary structure and refinement software used. The average torsion angles for the nine rotamers were similar in high-resolution structures solved using either the REFMAC, CNS or PHENIX software. However, at low resolution these programs often refine towards somewhat different χ{sub 1} and χ{sub 2} values. Small systematic differences can be observed between refinement software that uses molecular dynamics-type energy terms (for example CNS) and software that does not use these terms (for example REFMAC). Detailing the standard torsion angles used in refinement software can improve the refinement of protein structures. The target values in the molecular dynamics-type energy functions can also be improved.

  9. Anomalies in the refinement of isoleucine

    Berntsen, Karen R. M.; Vriend, Gert

    2014-01-01

    The side-chain torsion angles of isoleucines in X-ray protein structures are a function of resolution, secondary structure and refinement software. Detailing the standard torsion angles used in refinement software can improve protein structure refinement. A study of isoleucines in protein structures solved using X-ray crystallography revealed a series of systematic trends for the two side-chain torsion angles χ 1 and χ 2 dependent on the resolution, secondary structure and refinement software used. The average torsion angles for the nine rotamers were similar in high-resolution structures solved using either the REFMAC, CNS or PHENIX software. However, at low resolution these programs often refine towards somewhat different χ 1 and χ 2 values. Small systematic differences can be observed between refinement software that uses molecular dynamics-type energy terms (for example CNS) and software that does not use these terms (for example REFMAC). Detailing the standard torsion angles used in refinement software can improve the refinement of protein structures. The target values in the molecular dynamics-type energy functions can also be improved

  10. Single-crystal structure refinement of YbF{sub 2} with a remark about YbH{sub 2}

    Reckeweg, Olaf; DiSalvo, Francis J. [Cornell Univ., Ithaca, NY (United States). Dept. of Chemistry and Chemical Biology

    2017-07-01

    Transparent-yellow single crystals of YbF{sub 2} were obtained as only crystalline product from the solid-state reaction of Yb and teflon designed to yield 'Yb{sub 3}C{sub 3}F{sub 2}' in addition to some amorphous black material. The first single-crystal structure determination of YbF{sub 2} (cubic space group Fm anti 3m, CaF{sub 2}-type structure, a = 559.46(16) pm; R1 = 1.2%, wR2 = 3.2%) was the starting point to compare isostructural binary fluorides MF{sub 2} and hydrides MH{sub 2} (M = Ca, Yb, Eu, Sr and Ba) exhibiting an as-yet unexplained small volume per formula unit for YbH{sub 2}.

  11. Evaluation of structural reliability using simulation methods

    Baballëku Markel

    2015-01-01

    Full Text Available Eurocode describes the 'index of reliability' as a measure of structural reliability, related to the 'probability of failure'. This paper is focused on the assessment of this index for a reinforced concrete bridge pier. It is rare to explicitly use reliability concepts for design of structures, but the problems of structural engineering are better known through them. Some of the main methods for the estimation of the probability of failure are the exact analytical integration, numerical integration, approximate analytical methods and simulation methods. Monte Carlo Simulation is used in this paper, because it offers a very good tool for the estimation of probability in multivariate functions. Complicated probability and statistics problems are solved through computer aided simulations of a large number of tests. The procedures of structural reliability assessment for the bridge pier and the comparison with the partial factor method of the Eurocodes have been demonstrated in this paper.

  12. Advanced finite element method in structural engineering

    Long, Yu-Qiu; Long, Zhi-Fei

    2009-01-01

    This book systematically introduces the research work on the Finite Element Method completed over the past 25 years. Original theoretical achievements and their applications in the fields of structural engineering and computational mechanics are discussed.

  13. Development and refinement of new statistical methods for enhanced syndromic surveillance during the 2012 Olympic and Paralympic Games.

    Morbey, Roger A; Elliot, Alex J; Charlett, Andre; Andrews, Nick; Verlander, Neville Q; Ibbotson, Sue; Smith, Gillian E

    2015-06-01

    Prior to the 2012 London Olympic and Paralympic Games, new statistical methods had to be developed for the enhanced syndromic surveillance during the Games. Different methods were developed depending on whether or not historical data were available. Practical solutions were needed to cope with the required daily reporting and data quality issues. During the Games, nearly 4800 signals were tested on average each day, generating statistical alarms that were assessed to provide information on areas of potential public health concern and reassurance that no major adverse incident had occurred. spjhi;21/2/159/FIG41460458213517577 F1 fig4-1460458213517577. © The Author(s) 2013.

  14. Nonlinear structural analysis using integrated force method

    A new formulation termed the Integrated Force Method (IFM) was proposed by Patnaik ... nated ``Structure (nY m)'' where (nY m) are the force and displacement degrees of ..... Patnaik S N, Yadagiri S 1976 Frequency analysis of structures.

  15. A simple method for the design of tension structures combining topological mapping and nonlinear structural analysis

    Jurado-Piña, R.

    2014-12-01

    Full Text Available When designing a tension structure the shape is not known at the beginning of the process. Form-finding methods allow the designer to obtain an initial shape from given boundary conditions. Several form-finding methods for tension structures are already available in the technical literature; all of them posses certain limitations and drawbacks and no single method is optimal for all problems. The engineer may select the proper combination of methods best suited to the designer’s needs. In this paper it is proposed a combined method to achieve satisfactory equilibrium configurations for fabric tension structures. The force density method (FDM implemented with topological mapping (TM is used as a search engine for the preliminary design, and a procedure that employs nonlinear structural analysis is proposed for final refinement of the initial equilibrium configuration hence allowing the use of the same analysis tool for both refinement of the solution and analysis under loading.Al diseñar una estructura tensada la forma inicial es normalmente desconocida. Los métodos de búsqueda de forma permiten al ingeniero obtener una geometría inicial dadas unas condiciones de contorno. Existen diferentes métodos de búsqueda de formas de equilibrio, pero todos tienen limitaciones y no existe uno único óptimo para cualquier tipo de problema. El ingeniero debe elegir la combinación de métodos que mejor se adapte a sus necesidades. En este artículo se propone un método combinado para generar configuraciones de equilibrio satisfactorias en estructuras tensadas. Como motor de búsqueda para el diseño preliminar se emplea el método de las densidades de fuerza (FDM implementado con mallado en topología (TM, y se propone un procedimiento basado en análisis no lineal de estructuras para el refinamiento de la configuración inicial de equilibrio, permitiéndose así el empleo de las mismas herramientas tanto para el refinamiento de la solución inicial

  16. Nanotube structures, methods of making nanotube structures, and methods of accessing intracellular space

    VanDersarl, Jules J.; Xu, Alexander M.; Melosh, Nicholas A.; Tayebi, Noureddine

    2016-02-23

    In accordance with the purpose(s) of the present disclosure, as embodied and broadly described herein, embodiments of the present disclosure, in one aspect, relate to methods of making a structure including nanotubes, a structure including nanotubes, methods of delivering a fluid to a cell, methods of removing a fluid to a cell, methods of accessing intracellular space, and the like.

  17. Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

    Cao, Haibo [Iowa State Univ., Ames, IA (United States)

    2003-01-01

    In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

  18. Protein structure recognition: From eigenvector analysis to structural threading method

    Cao, Haibo

    In this work, we try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. We found a strong correlation between amino acid sequence and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, we give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part include discussions of interactions among amino acids residues, lattice HP model, and the designablity principle. In the second part, we try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in our eigenvector study of protein contact matrix. We believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, we discuss a threading method based on the correlation between amino acid sequence and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, we list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

  19. Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

    Haibo Cao

    2003-01-01

    In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches

  20. Investigation of RNA Structure by High-Throughput SHAPE-Based Probing Methods

    Poulsen, Line Dahl

    of highthroughput SHAPE-based approaches to investigate RNA structure based on novel SHAPE reagents that permit selection of full-length cDNAs. The SHAPE Selection (SHAPES) method is applied to the foot-and-mouth disease virus (FMDV) plus strand RNA genome, and the data is used to construct a genome-wide structural...... that they are functional. The SHAPES method is further applied to the hepatitis C virus (HCV), where the data is used to refine known and predicted structures. Over the past years, the interest of studying RNA structure in their native environment has been increased, and to allow studying RNA structure inside living cells...... using the SHAPE Selection approach, I introduce a biotinylated probing reagent. This chemical can cross cell membranes and reacts with RNA inside the cells, allowing the structural conformations to be studied in the context of physiological relevant conditions in living cells. The methods and results...

  1. Influence of the milling time in the microstructural parameters of TA2O5-Al powder refined by Rietveld method

    Brito, R.A.; Mendes, M.W.D.; Alves Junior, C.; Costa, F.A. da; Gomes, U.U.

    2009-01-01

    Mechanical alloying (MA) is a solid-state powder processing technique involving repeated welding, fracturing, and re-welding of powder particles in a high energy mill. This process is used for producing of fine powders containing unique microstructures. The process starts with mixing of the powders in the desired proportion. Then, the mixture is milled using the established time in the high-energy mill. The powder particles are submitted to repeated cycles of cold working and fracture, and the final product correspond to a composite powder, containing characteristics different of the initial constituents. Ta 2 O 5 -Al powders were milled in a planetary ball mill for different times in order to evaluate the influence of the milling time in their microstructural parameters like crystallite size and micro deformation. The microstructural parameters were obtained by the Rietveld Method. The results showed that the microstructural parameters were influenced by the increase of the milling time. (author)

  2. Method of fabricating a catalytic structure

    Rollins, Harry W [Idaho Falls, ID; Petkovic, Lucia M [Idaho Falls, ID; Ginosar, Daniel M [Idaho Falls, ID

    2009-09-22

    A precursor to a catalytic structure comprising zinc oxide and copper oxide. The zinc oxide has a sheet-like morphology or a spherical morphology and the copper oxide comprises particles of copper oxide. The copper oxide is reduced to copper, producing the catalytic structure. The catalytic structure is fabricated by a hydrothermal process. A reaction mixture comprising a zinc salt, a copper salt, a hydroxyl ion source, and a structure-directing agent is formed. The reaction mixture is heated under confined volume conditions to produce the precursor. The copper oxide in the precursor is reduced to copper. A method of hydrogenating a carbon oxide using the catalytic structure is also disclosed, as is a system that includes the catalytic structure.

  3. The use of Fourier reverse transforms in crystallographic phase refinement

    Ringrose, Sharon [Iowa State Univ., Ames, IA (United States)

    1997-10-08

    Often a crystallographer obtains an electron density map which shows only part of the structure. In such cases, the phasing of the trial model is poor enough that the electron density map may show peaks in some of the atomic positions, but other atomic positions are not visible. There may also be extraneous peaks present which are not due to atomic positions. A method for determination of crystal structures that have resisted solution through normal crystallographic methods has been developed. PHASER is a series of FORTRAN programs which aids in the structure solution of poorly phased electron density maps by refining the crystallographic phases. It facilitates the refinement of such poorly phased electron density maps for difficult structures which might otherwise not be solvable. The trial model, which serves as the starting point for the phase refinement, may be acquired by several routes such as direct methods or Patterson methods. Modifications are made to the reverse transform process based on several assumptions. First, the starting electron density map is modified based on the fact that physically the electron density map must be non-negative at all points. In practice a small positive cutoff is used. A reverse Fourier transform is computed based on the modified electron density map. Secondly, the authors assume that a better electron density map will result by using the observed magnitudes of the structure factors combined with the phases calculated in the reverse transform. After convergence has been reached, more atomic positions and less extraneous peaks are observed in the refined electron density map. The starting model need not be very large to achieve success with PHASER; successful phase refinement has been achieved with a starting model that consists of only 5% of the total scattering power of the full molecule. The second part of the thesis discusses three crystal structure determinations.

  4. Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations.

    Subbotina, Julia; Yarov-Yarovoy, Vladimir; Lees-Miller, James; Durdagi, Serdar; Guo, Jiqing; Duff, Henry J; Noskov, Sergei Yu

    2010-11-01

    The hERG1 gene (Kv11.1) encodes a voltage-gated potassium channel. Mutations in this gene lead to one form of the Long QT Syndrome (LQTS) in humans. Promiscuous binding of drugs to hERG1 is known to alter the structure/function of the channel leading to an acquired form of the LQTS. Expectably, creation and validation of reliable 3D model of the channel have been a key target in molecular cardiology and pharmacology for the last decade. Although many models were built, they all were limited to pore domain. In this work, a full model of the hERG1 channel is developed which includes all transmembrane segments. We tested a template-driven de-novo design with ROSETTA-membrane modeling using side-chain placements optimized by subsequent molecular dynamics (MD) simulations. Although backbone templates for the homology modeled parts of the pore and voltage sensors were based on the available structures of KvAP, Kv1.2 and Kv1.2-Kv2.1 chimera channels, the missing parts are modeled de-novo. The impact of several alignments on the structure of the S4 helix in the voltage-sensing domain was also tested. Herein, final models are evaluated for consistency to the reported structural elements discovered mainly on the basis of mutagenesis and electrophysiology. These structural elements include salt bridges and close contacts in the voltage-sensor domain; and the topology of the extracellular S5-pore linker compared with that established by toxin foot-printing and nuclear magnetic resonance studies. Implications of the refined hERG1 model to binding of blockers and channels activators (potent new ligands for channel activations) are discussed. © 2010 Wiley-Liss, Inc.

  5. Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

    Borbulevych, Oleg Y.; Plumley, Joshua A.; Martin, Roger I. [QuantumBio Inc., 2790 West College Avenue, State College, PA 16801 (United States); Merz, Kenneth M. Jr [University of Florida, Gainesville, Florida (United States); Westerhoff, Lance M., E-mail: lance@quantumbioinc.com [QuantumBio Inc., 2790 West College Avenue, State College, PA 16801 (United States)

    2014-05-01

    Semiempirical quantum-chemical X-ray macromolecular refinement using the program DivCon integrated with PHENIX is described. Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein–ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

  6. Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.

    Brunger, Axel T; Das, Debanu; Deacon, Ashley M; Grant, Joanna; Terwilliger, Thomas C; Read, Randy J; Adams, Paul D; Levitt, Michael; Schröder, Gunnar F

    2012-04-01

    Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence.

  7. Combustible structural composites and methods of forming combustible structural composites

    Daniels, Michael A.; Heaps, Ronald J.; Steffler, Eric D.; Swank, W. David

    2013-04-02

    Combustible structural composites and methods of forming same are disclosed. In an embodiment, a combustible structural composite includes combustible material comprising a fuel metal and a metal oxide. The fuel metal is present in the combustible material at a weight ratio from 1:9 to 1:1 of the fuel metal to the metal oxide. The fuel metal and the metal oxide are capable of exothermically reacting upon application of energy at or above a threshold value to support self-sustaining combustion of the combustible material within the combustible structural composite. Structural-reinforcing fibers are present in the composite at a weight ratio from 1:20 to 10:1 of the structural-reinforcing fibers to the combustible material. Other embodiments and aspects are disclosed.

  8. Refining the structural framework of the Khimti Khola region, east-central Nepal Himalaya, using quartz textures and c-axis fabrics

    Larson, Kyle P.

    2018-02-01

    New quartz texture and c-axis fabric data from across the Paleoproterozoic Ulleri-Phaplu-Melung orthogneiss in the Khimti Khola region of east central Nepal provide new constraints on the internal structural framework of the Himalaya that help shed light on the convergence accommodation processes active in the upper portion of the crust during orogenesis. These data outline a strain history that varies across the unit. Deformation near the base of the unit occurred at ∼605 (±50) °C with evidence of significant static recrystallization and recovery preserved in quartz, whereas deformation near the top of the unit occurred at ∼540 (±50) ˚C with quartz characterized by dynamic recrystallization mechanisms. The strength of the quartz c-axis fabrics follows a similar spatial pattern, with those from near the top of the unit recording stronger fabrics than those measured from lower in the unit. Together, these data are interpreted to indicate strain localization, possibly at progressively lower temperature, near the top of the Ulleri-Phaplu-Melung orthogneiss. This interpretation is consistent with cooling ages that indicate the upper boundary of the unit coincides with an out-of-sequence shear zone. This study not only provides a structural characterization of the shear zone, helping to refine the kinematic framework of this portion of the Himalaya, but also confirms the utility of fabric strength analysis in deciphering strain localization within pervasively deformed rocks.

  9. Synthesis, crystal structure refinement, and nonlinear-optical properties of CaB{sub 3}O{sub 5}(OH): Comparative crystal chemistry of calcium triborates

    Yamnova, N. A., E-mail: aks.crys@gmail.com; Aksenov, S. M. [Moscow State University, Faculty of Geology (Russian Federation); Stefanovich, S. Yu. [Moscow State University, Faculty of Chemistry (Russian Federation); Volkov, A. S.; Dimitrova, O. V. [Moscow State University, Faculty of Geology (Russian Federation)

    2015-09-15

    Calcium triborate CaB{sub 3}O5(OH) obtained by hydrothermal synthesis in the Ca(OH){sub 2}–H{sub 3}BO{sub 3}–Na{sub 2}CO{sub 3}–KCl system is studied by single-crystal X-ray diffraction. The parameters of the orthorhombic unit cell are as follows: a = 13.490(1), b = 6.9576(3), and c = 4.3930(2) Å; V = 412.32(3) Å{sup 3} and space group Pna2{sub 1}. The structure is refined in the anisotropic approximation of the atomic displacement parameters to R = 4.28% using 972 vertical bar F vertical bar > 4σ(F). It is confirmed that the crystal structure of Ca triborate CaB{sub 3}O{sub 5}(OH) is identical to that described earlier. The hydrogen atom is localized. An SHG signal stronger than that of the quartz standard is registered. The phase transition of calcium triborate into calciborite is found on heating. The comparative crystal-chemical analysis of a series of borates with the general chemical formula 2CaO · 3B{sub 2}O{sub 3} · nH{sub 2}O (n = 0–13) with the constant CaO: B{sub 2}O{sub 3}= 2: 3 ratio and variable content of water is performed.

  10. Synthesis, crystal structure refinement, and nonlinear-optical properties of CaB3O5(OH): Comparative crystal chemistry of calcium triborates

    Yamnova, N. A.; Aksenov, S. M.; Stefanovich, S. Yu.; Volkov, A. S.; Dimitrova, O. V.

    2015-01-01

    Calcium triborate CaB 3 O5(OH) obtained by hydrothermal synthesis in the Ca(OH) 2 –H 3 BO 3 –Na 2 CO 3 –KCl system is studied by single-crystal X-ray diffraction. The parameters of the orthorhombic unit cell are as follows: a = 13.490(1), b = 6.9576(3), and c = 4.3930(2) Å; V = 412.32(3) Å 3 and space group Pna2 1 . The structure is refined in the anisotropic approximation of the atomic displacement parameters to R = 4.28% using 972 vertical bar F vertical bar > 4σ(F). It is confirmed that the crystal structure of Ca triborate CaB 3 O 5 (OH) is identical to that described earlier. The hydrogen atom is localized. An SHG signal stronger than that of the quartz standard is registered. The phase transition of calcium triborate into calciborite is found on heating. The comparative crystal-chemical analysis of a series of borates with the general chemical formula 2CaO · 3B 2 O 3 · nH 2 O (n = 0–13) with the constant CaO: B 2 O 3 = 2: 3 ratio and variable content of water is performed

  11. Identification methods for structural health monitoring

    Papadimitriou, Costas

    2016-01-01

    The papers in this volume provide an introduction to well known and established system identification methods for structural health monitoring and to more advanced, state-of-the-art tools, able to tackle the challenges associated with actual implementation. Starting with an overview on fundamental methods, introductory concepts are provided on the general framework of time and frequency domain, parametric and non-parametric methods, input-output or output only techniques. Cutting edge tools are introduced including, nonlinear system identification methods; Bayesian tools; and advanced modal identification techniques (such as the Kalman and particle filters, the fast Bayesian FFT method). Advanced computational tools for uncertainty quantification are discussed to provide a link between monitoring and structural integrity assessment. In addition, full scale applications and field deployments that illustrate the workings and effectiveness of the introduced monitoring schemes are demonstrated.

  12. Methadone Detoxification Versus Traditional Gradual Decrease in the Consumed Amount of Refined Opium Dross (Shireh: The Preferred Method for Controlling Withdrawal Syndrome

    Mohammadreza Farsinejad

    2012-08-01

    Full Text Available Background: The aim of this study was to compare the effectiveness of methadone detoxification with traditional method of gradual decrement in the abused amount of the refined opium dross (Shireh to control withdrawal syndrome in Shireh-addicted patients. Methods: In this study, two groups of Shireh addicts were compared. The first group was treated by methadone and the second group by gradual decrement in the amount of consumed Shireh. Those experiencing the adverse effects of the treatment were excluded from the study. Methadone dose was calculated based on the amount of the Shireh consumed and detoxification was performed during a 21-day period. In the second group, the amount of the consumed Shireh was gradually decreased within 21 days and some of the withdrawal symptoms were selected as indicators for patient evaluation. Results: A total of 35 patients (16 versus 19 patients in the first and second groups were evaluated. Their mean age was 43 ± 4 years and all were male. A statistically significant difference was found between these two groups in terms of severity and duration of withdrawal symptoms within the first five days and their duration after the 21st day of the onset of detoxification (P< 0.05. Conclusion: In comparison with methadone detoxification, traditional method of gradually decreasing the consumed amount of Shireh controls the severity and duration of withdrawal symptoms better in the course of detoxification.

  13. Comparing Syntactic and Semantics Action Refinement

    Goltz, Ursula; Gorrieri, Roberto; Rensink, Arend

    The semantic definition of action refinement on labelled configuration structures is compared with the notion of syntactic substitution, which can be used as another notion of action refinement in a process algebraic setting. The comparison is done by studying a process algebra equipped with

  14. On Syntactic and Semantic Action Refinement

    Hagiya, M.; Goltz, U.; Mitchell, J.C.; Gorrieri, R.; Rensink, Arend

    1994-01-01

    The semantic definition of action refinement on labelled event structures is compared with the notion of syntactic substitution, which can be used as another notion of action refinement in a process algebraic setting. This is done by studying a process algebra equipped with the ACP sequential

  15. Bauxite Mining and Alumina Refining

    Frisch, Neale; Olney, David

    2014-01-01

    Objective: To describe bauxite mining and alumina refining processes and to outline the relevant physical, chemical, biological, ergonomic, and psychosocial health risks. Methods: Review article. Results: The most important risks relate to noise, ergonomics, trauma, and caustic soda splashes of the skin/eyes. Other risks of note relate to fatigue, heat, and solar ultraviolet and for some operations tropical diseases, venomous/dangerous animals, and remote locations. Exposures to bauxite dust, alumina dust, and caustic mist in contemporary best-practice bauxite mining and alumina refining operations have not been demonstrated to be associated with clinically significant decrements in lung function. Exposures to bauxite dust and alumina dust at such operations are also not associated with the incidence of cancer. Conclusions: A range of occupational health risks in bauxite mining and alumina refining require the maintenance of effective control measures. PMID:24806720

  16. Multigrid for refined triangle meshes

    Shapira, Yair

    1997-02-01

    A two-level preconditioning method for the solution of (locally) refined finite element schemes using triangle meshes is introduced. In the isotropic SPD case, it is shown that the condition number of the preconditioned stiffness matrix is bounded uniformly for all sufficiently regular triangulations. This is also verified numerically for an isotropic diffusion problem with highly discontinuous coefficients.

  17. Intelligent structural optimization: Concept, Model and Methods

    Lu, Dagang; Wang, Guangyuan; Peng, Zhang

    2002-01-01

    Structural optimization has many characteristics of Soft Design, and so, it is necessary to apply the experience of human experts to solving the uncertain and multidisciplinary optimization problems in large-scale and complex engineering systems. With the development of artificial intelligence (AI) and computational intelligence (CI), the theory of structural optimization is now developing into the direction of intelligent optimization. In this paper, a concept of Intelligent Structural Optimization (ISO) is proposed. And then, a design process model of ISO is put forward in which each design sub-process model are discussed. Finally, the design methods of ISO are presented

  18. Concurrent semantics for structured design methods

    Nixon, Patrick

    1996-01-01

    Also in Jelly, I., Gordon, I., & Groll, P. Software Engineering for Parallel and Distributed Systems. London: Chapman Hall. Design methods can be ambiguous due to di#11;erent interpretations of symbols or concepts. This paper presents a formal semantics for the Ward/Mellor Structured Analysis Method for Real Time systems. These semantics ensures that an unambiguous meaning can be attributed to a particular design. Speci#12;cally, it ensures that concurrent and real-time propert...

  19. Relational Demonic Fuzzy Refinement

    Fairouz Tchier

    2014-01-01

    Full Text Available We use relational algebra to define a refinement fuzzy order called demonic fuzzy refinement and also the associated fuzzy operators which are fuzzy demonic join (⊔fuz, fuzzy demonic meet (⊓fuz, and fuzzy demonic composition (□fuz. Our definitions and properties are illustrated by some examples using mathematica software (fuzzy logic.

  20. Refinement of La1.5Ba1.5Cu3O7-x from a Twinned Crystal

    Hjorth, Michael

    1996-01-01

    The structure of the title compound (barium copper lanthanum oxide, Ba1.50Cu3La1.50O6.66) has been refined from a twinned crystal using single-crystal methods. The results of the present investigation show lower standard deviations than the results of earlier powder diffraction refinements...

  1. Refining cost-effectiveness analyses using the net benefit approach and econometric methods: an example from a trial of anti-depressant treatment.

    Sabes-Figuera, Ramon; McCrone, Paul; Kendricks, Antony

    2013-04-01

    Economic evaluation analyses can be enhanced by employing regression methods, allowing for the identification of important sub-groups and to adjust for imperfect randomisation in clinical trials or to analyse non-randomised data. To explore the benefits of combining regression techniques and the standard Bayesian approach to refine cost-effectiveness analyses using data from randomised clinical trials. Data from a randomised trial of anti-depressant treatment were analysed and a regression model was used to explore the factors that have an impact on the net benefit (NB) statistic with the aim of using these findings to adjust the cost-effectiveness acceptability curves. Exploratory sub-samples' analyses were carried out to explore possible differences in cost-effectiveness. Results The analysis found that having suffered a previous similar depression is strongly correlated with a lower NB, independent of the outcome measure or follow-up point. In patients with previous similar depression, adding an selective serotonin reuptake inhibitors (SSRI) to supportive care for mild-to-moderate depression is probably cost-effective at the level used by the English National Institute for Health and Clinical Excellence to make recommendations. This analysis highlights the need for incorporation of econometric methods into cost-effectiveness analyses using the NB approach.

  2. Study on Separation of Structural Isomer with Magneto-Archimedes method

    Kobayashi, T.; Mori, T.; Akiyama, Y.; Mishima, F.; Nishijima, S.

    2017-09-01

    Organic compounds are refined by separating their structural isomers, however each separation method has some problems. For example, distillation consumes large energy. In order to solve these problems, new separation method is needed. Considering organic compounds are diamagnetic, we focused on magneto-Archimedes method. With this method, particle mixture dispersed in a paramagnetic medium can be separated in a magnetic field due to the difference of the density and magnetic susceptibility of the particles. In this study, we succeeded in separating isomers of phthalic acid as an example of structural isomer using MnCl2 solution as the paramagnetic medium. In order to use magneto-Archimedes method for separating materials for food or medicine, we proposed harmless medium using oxygen and fluorocarbon instead of MnCl2 aqueous solution. As a result, the possibility of separating every structural isomer was shown.

  3. A Direct Method of Hamiltonian Structure

    Li Qi; Chen Dengyuan; Su Shuhua

    2011-01-01

    A direct method of constructing the Hamiltonian structure of the soliton hierarchy with self-consistent sources is proposed through computing the functional derivative under some constraints. The Hamiltonian functional is related with the conservation densities of the corresponding hierarchy. Three examples and their two reductions are given. (general)

  4. The Fourier modal method for aperiodic structures

    Pisarenco, M.; Maubach, J.M.L.; Setija, I.D.; Mattheij, R.M.M.

    2010-01-01

    This paper extends the area of application of the Fourier modal method from periodic structures to non-periodic ones illuminated under arbitrary angles. This is achieved by placing perfectly matched layers at the lateral boundaries and reformulating the problem in terms of a contrast field.

  5. Method of dismantling cylindrical structure by cutting

    Harada, Minoru; Mitsuo, Kohei; Yokota, Isoya; Nakamura, Kenjiro.

    1989-01-01

    This invention concerns a method of cutting and removing cylindrical structures, for example, iron-reinforced concrete materials such as thermal shielding walls in BWR type power plants into block-like form. That is, in a method of cutting and removing the cylindrical structure from the side of the outer wall, the structural material is cut from above to below successively in the axial direction and the circumferential direction by means abrasive jet by remote operation and cut into blocks each of a predetermined size. The cut out blocks are successively taken out. Cutting of the material from above to below by remote operation and taking out of small blocks causes no hazards to human body. Upon practicing the present invention, it is preferred to use a processing device for slurry and exhaust gases for preventing scattering of activated dismantled pieces or powdery dusts. (K.M.)

  6. Enstatite, Mg2Si2O6: A neutron diffraction refinement of the crystal structure and a rigid-body analysis of the thermal vibration

    Ghose, S.; Schomaker, V.; McMullan, R.K.

    1986-01-01

    Synthetic enstatite, Mg 2 Si 2 O 6 , is orthorhombic, space group Pbca, with eight formula units per cell and lattice parameters a = 18.235(3), b = 8.818(1), c = 5.179(1) A at 23 0 C. A least-squares structure refinement based on 1790 neutron intensity data converged with an agreement factor R(F 2 ) = 0.032, yielding Mg-O and Si-O bond lengths with standard deviations of 0.0007 and 0.0008 A, respectively. The variations observed in the Si-O bond lengths within the silicate tetrahedra A and B are caused by the differences in primary coordination of the oxygen atoms and the proximity of the magnesium ions to the silicon atoms. The latter effect is most pronounced for the bridging bonds of tetrahedron. A. The smallest O-Si-O angle is the result of edge-sharing by the Mg(2) octahedron and the A tetrahedron. An analysis of rigid-body thermal vibrations of the two crystallographically independent [SiO 4 ] tetrahedra indicates considerable librational motion, leading to a thermal correction of apparent Si-O bond lengths as large as +0.002 A at room temperature. (orig.)

  7. Rietveld refinement of the crystal structure of perovskite solar cells using CH3NH3PbI3 and other compounds

    Ando, Yuji; Ohishi, Yuya; Suzuki, Kohei; Suzuki, Atsushi; Oku, Takeo

    2018-01-01

    The crystal structures of perovskite thin films including CH3NH3PbI3, CH3NH3Pb1-xSbxI3, and CH3NH3PbI3-yCly in the solar cell configuration were studied by using Rietveld refinement. For the CH3NH3PbI3 and CH3NH3Pb1-xSbxI3 samples, satisfactory agreement with the measured profiles was obtained with a weighted profile R-factor (Rwp) of as low as 3%. It was shown that the site occupancy of methylammonium (MA) was decreased in the antimonized cell due to the compensation effect of an increased positive charge brought about by replacing Pb2+ with Sb3+. Photovoltaic measurements showed that the power conversion efficiency was enhanced by adding a small amount of Sb to the CH3NH3PbI3 cell, but it was monotonically decreased as the mole fraction of Sb exceeded 0.03. This variation of the conversion efficiency was considered as a result of suppressed crystallization of PbI2 and carrier recombination via MA vacancies in the antimonized cells. In the case of CH3NH3PbI2.88Cl0.12 sample, the agreement with the measured profile with an Rwp of as high as 7% suggested the co-existence of cubic and tetragonal phases in the chlorinated cell.

  8. A crystal-structure refinement of synthetic brannerite, UTi2O6, and its bearing on rate of alkaline-carbonate leaching of brannerite in ore

    Szymanski, J.T.; Scott, J.D.

    1982-01-01

    The crystal structure of synthetic, stoichiometric brannerite, UTi 2 O 6 , has been refined to R=2.23% from MoKα radiation. Monoclinic, with space group C2/m, a 9.8123(15), b 3.7697(6), c 6.9253(9) A, β 118.957(6) 0 , brannerite is isostructural with thoruitite, ThTi 2 O 6 (Ruh β Wadsley 1966). The co-ordination of U by O is distorted octahedral, the bond distances being 2 x 2.252(2), 4 x 2.296(1) A. There is an additional pair of short nonbonded U-O contacts, 2 x 2.824(2) A. The co-ordination around Ti is also distorted octahedral, with the Ti-O distance between 1.854(3) and 2.104(3) A. The depth of penetration of an alkaline-carbonate leaching solution into natural brannerite from Eldorado, Saskatchewan, has been found to vary nonuniformly with both time and crystallographic direction of leaching attack. The rate of dissolution for a free crystal is 1.33 cubic micrometers per second or, using the density calculated from the cell data, 8.5 x 10 -12 g/s

  9. METHODS OF FORMING THE STRUCTURE OF KNOWLEDGE

    Tatyana A. Snegiryova

    2015-01-01

    Full Text Available The aim of the study is to describe the method of forming thestructure of knowledge of students on the basis of an integrated approach (expert, taxonomy and thesaurus and the presentation of the results of its use in the study of medical and biological physics at the Izhevsk State Medical Academy.Methods. The methods used in the work involve: an integrated approach that includes group expert method, developed by V. S. Cherepanov; taxonomy and thesaurus approach when creating a model of taxonomic structure of knowledge, as well as models of the formation of the knowledge structure.Results. The algorithm, stages and procedures of knowledge structure formation of trainees are considered in detail; the model of the given process is created; the technology of content selection of a teaching material due to the fixed time that has been released on studying of concrete discipline is shown.Scientific novelty and practical significance. Advantage of the proposed method and model of students’ knowledge structure formation consists in their flexibility: at certain adaptation they can be used while training to any discipline apart of its specificity and educational institution. Observance of all stages of the presented technology of content selection of a teaching material on the basis of an expert estimation will promote substantial increase of quality of training; make it possible to develop the unified method uniting the various points of view of teachers on knowledge formation of trainees.

  10. Bayesian ensemble refinement by replica simulations and reweighting

    Hummer, Gerhard; Köfinger, Jürgen

    2015-12-01

    We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.

  11. Creating a simplified model of oil refining and solution of the model using a linear programming method. Part 1, Model presentation

    Duric, M; Novakovic, M; Stojkanovic, L

    1983-01-01

    Based on a detailed analysis of technological limitations in oil refining at an oil refinery (NPZ) in the separation of petroleum products, specifications with regard to quality and market limitations, a general model is created of oil refining. The number of actual variables is reduced to a minimum, while the number of linear limitations is adapted to the selected technology and raw material quality. The nonlinearity of certain characteristics is overcome using the so called movement factor.

  12. Analysis and development of spatial hp-refinement methods for solving the neutron transport equation; Analyse et developpement de methodes de raffinement hp en espace pour l'equation de transport des neutrons

    Fournier, D.

    2011-10-10

    The different neutronic parameters have to be calculated with a higher accuracy in order to design the 4. generation reactor cores. As memory storage and computation time are limited, adaptive methods are a solution to solve the neutron transport equation. The neutronic flux, solution of this equation, depends on the energy, angle and space. The different variables are successively discretized. The energy with a multigroup approach, considering the different quantities to be constant on each group, the angle by a collocation method called SN approximation. Once the energy and angle variable are discretized, a system of spatially-dependent hyperbolic equations has to be solved. Discontinuous finite elements are used to make possible the development of hp-refinement methods. Thus, the accuracy of the solution can be improved by spatial refinement (h-refinement), consisting into subdividing a cell into sub-cells, or by order refinement (p-refinement), by increasing the order of the polynomial basis. In this thesis, the properties of this methods are analyzed showing the importance of the regularity of the solution to choose the type of refinement. Thus, two error estimators are used to lead the refinement process. Whereas the first one requires high regularity hypothesis (analytical solution), the second one supposes only the minimal hypothesis required for the solution to exist. The comparison of both estimators is done on benchmarks where the analytic solution is known by the method of manufactured solutions. Thus, the behaviour of the solution as a regard of the regularity can be studied. It leads to a hp-refinement method using the two estimators. Then, a comparison is done with other existing methods on simplified but also realistic benchmarks coming from nuclear cores. These adaptive methods considerably reduces the computational cost and memory footprint. To further improve these two points, an approach with energy-dependent meshes is proposed. Actually, as the

  13. Structural equation modeling methods and applications

    Wang, Jichuan

    2012-01-01

    A reference guide for applications of SEM using Mplus Structural Equation Modeling: Applications Using Mplus is intended as both a teaching resource and a reference guide. Written in non-mathematical terms, this book focuses on the conceptual and practical aspects of Structural Equation Modeling (SEM). Basic concepts and examples of various SEM models are demonstrated along with recently developed advanced methods, such as mixture modeling and model-based power analysis and sample size estimate for SEM. The statistical modeling program, Mplus, is also featured and provides researchers with a

  14. Method of fabricating patterned crystal structures

    Yu, Liyang

    2016-12-15

    A method of manufacturing a patterned crystal structure for includes depositing an amorphous material. The amorphous material is modified such that a first portion of the amorphous thin-film layer has a first height/volume and a second portion of the amorphous thin-film layer has a second height/volume greater than the first portion. The amorphous material is annealed to induce crystallization, wherein crystallization is induced in the second portion first due to the greater height/volume of the second portion relative to the first portion to form patterned crystal structures.

  15. A refined, rapid and reproducible high resolution melt (HRM-based method suitable for quantification of global LINE-1 repetitive element methylation

    Tse M Yat

    2011-12-01

    Full Text Available Abstract Background The methylation of DNA is recognized as a key mechanism in the regulation of genomic stability and evidence for its role in the development of cancer is accumulating. LINE-1 methylation status represents a surrogate measure of genome-wide methylation. Findings Using high resolution melt (HRM curve analysis technology, we have established an in-tube assay that is linear (r > 0.9986 with a high amplification efficiency (90-105%, capable of discriminating between partcipant samples with small differences in methylation, and suitable for quantifying a wide range of LINE-1 methylation levels (0-100%--including the biologically relevant range of 50-90% expected in human DNA. We have optimized this procedure to perform using 2 μg of starting DNA and 2 ng of bisulfite-converted DNA for each PCR reaction. Intra- and inter-assay coefficients of variation were 1.44% and 0.49%, respectively, supporting the high reproducibility and precision of this approach. Conclusions In summary, this is a completely linear, quantitative HRM PCR method developed for the measurement of LINE-1 methylation. This cost-efficient, refined and reproducible assay can be performed using minimal amounts of starting DNA. These features make our assay suitable for high throughput analysis of multiple samples from large population-based studies.

  16. Refining margins and prospects

    Baudouin, C.; Favennec, J.P.

    1997-01-01

    Refining margins throughout the world have remained low in 1996. In Europe, in spite of an improvement, particularly during the last few weeks, they are still not high enough to finance new investments. Although the demand for petroleum products is increasing, experts are still sceptical about any rapid recovery due to prevailing overcapacity and to continuing capacity growth. After a historical review of margins and an analysis of margins by regions, we analyse refining over-capacities in Europe and the unbalances between production and demand. Then we discuss the current situation concerning barriers to the rationalization, agreements between oil companies, and the consequences on the future of refining capacities and margins. (author)

  17. North American refining

    Osten, James; Haltmaier, Susan

    2000-01-01

    This article examines the current status of the North American refining industry, and considers the North American economy and the growth in demand in the petroleum industry, petroleum product demand and quality, crude oil upgrading to meet product standards, and changes in crude oil feedstocks such as the use of heavier crudes and bitumens. Refining expansion, the declining profits in refining, and changes due to environmental standards are discussed. The Gross Domestic Product and oil demand for the USA, Canada, Mexico, and Venezuela for the years 1995-2020 are tabulated

  18. Mesh Generation via Local Bisection Refinement of Triangulated Grids

    2015-06-01

    Science and Technology Organisation DSTO–TR–3095 ABSTRACT This report provides a comprehensive implementation of an unstructured mesh generation method...and Technology Organisation 506 Lorimer St, Fishermans Bend, Victoria 3207, Australia Telephone: 1300 333 362 Facsimile: (03) 9626 7999 c© Commonwealth...their behaviour is critically linked to Maubach’s method and the data structures N and T . The top- level mesh refinement algorithm is also presented

  19. Grain refinement through severe plastic deformation (SPD) processing

    Izairi, N.; Vevecka - Priftaj, A.

    2012-01-01

    There is considerable current interest in processing metallic samples through procedures involving the imposition of severe plastic deformation (SPD). These procedures lead to very significant grain refinement to the submicrometer or even the nanometer level, resulting in advanced physical properties. Among various SPD processes, Equal Channel Angular Pressing, High pressure Torsion and Accumulated Roll Bonding have been widely used for many metals and alloys. In the present work, we present an overview of the most used methods of SPD for grain refinement and the production of bulk nano structured materials with enhancement in their mechanical and functional properties. In order to examine the potential for using ECAP to refine the grain size and improve the mechanical properties, two commercial 5754 Al alloy and AA 3004 , were selected for study. Processing by ECAP gives a reduction in the grain size and an increase in the microhardness. (Author)

  20. Numerical solution of plasma fluid equations using locally refined grids

    Colella, P.

    1997-01-01

    This paper describes a numerical method for the solution of plasma fluid equations on block-structured, locally refined grids. The plasma under consideration is typical of those used for the processing of semiconductors. The governing equations consist of a drift-diffusion model of the electrons and an isothermal model of the ions coupled by Poisson's equation. A discretization of the equations is given for a uniform spatial grid, and a time-split integration scheme is developed. The algorithm is then extended to accommodate locally refined grids. This extension involves the advancement of the discrete system on a hierarchy of levels, each of which represents a degree of refinement, together with synchronization steps to ensure consistency across levels. A brief discussion of a software implementation is followed by a presentation of numerical results

  1. Adaptive multilevel mesh refinement method for the solution of low Mach number reactive flows; Methode adaptative de raffinement local multi-niveaux pour le calcul d'ecoulements reactifs a faible nombre de Mach

    Core, X.

    2002-02-01

    The isobar approximation for the system of the balance equations of mass, momentum, energy and chemical species is a suitable approximation to represent low Mach number reactive flows. In this approximation, which neglects acoustics phenomena, the mixture is hydrodynamically incompressible and the thermodynamic effects lead to an uniform compression of the system. We present a novel numerical scheme for this approximation. An incremental projection method, which uses the original form of mass balance equation, discretizes in time the Navier-Stokes equations. Spatial discretization is achieved through a finite volume approach on MAC-type staggered mesh. A higher order de-centered scheme is used to compute the convective fluxes. We associate to this discretization a local mesh refinement method, based on Flux Interface Correction technique. A first application concerns a forced flow with variable density which mimics a combustion problem. The second application is natural convection with first small temperature variations and then beyond the limit of validity of the Boussinesq approximation. Finally, we treat a third application which is a laminar diffusion flame. For each of these test problems, we demonstrate the robustness of the proposed numerical scheme, notably for the density spatial variations. We analyze the gain in accuracy obtained with the local mesh refinement method. (author)

  2. Hybrid Method Simulation of Slender Marine Structures

    Christiansen, Niels Hørbye

    This present thesis consists of an extended summary and five appended papers concerning various aspects of the implementation of a hybrid method which combines classical simulation methods and artificial neural networks. The thesis covers three main topics. Common for all these topics...... only recognize patterns similar to those comprised in the data used to train the network. Fatigue life evaluation of marine structures often considers simulations of more than a hundred different sea states. Hence, in order for this method to be useful, the training data must be arranged so...... that a single neural network can cover all relevant sea states. The applicability and performance of the present hybrid method is demonstrated on a numerical model of a mooring line attached to a floating offshore platform. The second part of the thesis demonstrates how sequential neural networks can be used...

  3. Measurement methods of building structures deflections

    Wróblewska Magdalena

    2018-01-01

    Full Text Available Underground mining exploitation is leading to the occurrence of deformations manifested by, in particular, sloping terrain. The structures situated on the deforming subsoil are subject to uneven subsidence which is leading in consequence to their deflection. Before a building rectification process takes place by, e.g. uneven raising, the structure's deflection direction and value is determined so that the structure is restored to its vertical position as a result of the undertaken remedial measures. Deflection can be determined by applying classical as well as modern measurement techniques. The article presents examples of measurement methods used considering the measured elements of building structures’ constructions and field measurements. Moreover, for a given example of a mining area, the existing deflections of buildings were compared with mining terrain sloping.

  4. Lagrangian based methods for coherent structure detection

    Allshouse, Michael R., E-mail: mallshouse@chaos.utexas.edu [Center for Nonlinear Dynamics and Department of Physics, University of Texas at Austin, Austin, Texas 78712 (United States); Peacock, Thomas, E-mail: tomp@mit.edu [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

    2015-09-15

    There has been a proliferation in the development of Lagrangian analytical methods for detecting coherent structures in fluid flow transport, yielding a variety of qualitatively different approaches. We present a review of four approaches and demonstrate the utility of these methods via their application to the same sample analytic model, the canonical double-gyre flow, highlighting the pros and cons of each approach. Two of the methods, the geometric and probabilistic approaches, are well established and require velocity field data over the time interval of interest to identify particularly important material lines and surfaces, and influential regions, respectively. The other two approaches, implementing tools from cluster and braid theory, seek coherent structures based on limited trajectory data, attempting to partition the flow transport into distinct regions. All four of these approaches share the common trait that they are objective methods, meaning that their results do not depend on the frame of reference used. For each method, we also present a number of example applications ranging from blood flow and chemical reactions to ocean and atmospheric flows.

  5. Structural modeling techniques by finite element method

    Kang, Yeong Jin; Kim, Geung Hwan; Ju, Gwan Jeong

    1991-01-01

    This book includes introduction table of contents chapter 1 finite element idealization introduction summary of the finite element method equilibrium and compatibility in the finite element solution degrees of freedom symmetry and anti symmetry modeling guidelines local analysis example references chapter 2 static analysis structural geometry finite element models analysis procedure modeling guidelines references chapter 3 dynamic analysis models for dynamic analysis dynamic analysis procedures modeling guidelines and modeling guidelines.

  6. Refinement by interface instantiation

    Hallerstede, Stefan; Hoang, Thai Son

    2012-01-01

    be easily refined. Our first contribution hence is a proposal for a new construct called interface that encapsulates the external variables, along with a mechanism for interface instantiation. Using the new construct and mechanism, external variables can be refined consistently. Our second contribution...... is an approach for verifying the correctness of Event-B extensions using the supporting Rodin tool. We illustrate our approach by proving the correctness of interface instantiation....

  7. Relational Demonic Fuzzy Refinement

    Tchier, Fairouz

    2014-01-01

    We use relational algebra to define a refinement fuzzy order called demonic fuzzy refinement and also the associated fuzzy operators which are fuzzy demonic join $({\\bigsqcup }_{\\mathrm{\\text{f}}\\mathrm{\\text{u}}\\mathrm{\\text{z}}})$ , fuzzy demonic meet $({\\sqcap }_{\\mathrm{\\text{f}}\\mathrm{\\text{u}}\\mathrm{\\text{z}}})$ , and fuzzy demonic composition $({\\square }_{\\mathrm{\\text{f}}\\mathrm{\\text{u}}\\mathrm{\\text{z}}})$ . Our definitions and properties are illustrated by some examples using ma...

  8. Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

    Borbulevych, Oleg Y; Plumley, Joshua A; Martin, Roger I; Merz, Kenneth M; Westerhoff, Lance M

    2014-05-01

    Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein-ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

  9. [Hierarchy structuring for mammography technique by interpretive structural modeling method].

    Kudo, Nozomi; Kurowarabi, Kunio; Terashita, Takayoshi; Nishimoto, Naoki; Ogasawara, Katsuhiko

    2009-10-20

    Participation in screening mammography is currently desired in Japan because of the increase in breast cancer morbidity. However, the pain and discomfort of mammography is recognized as a significant deterrent for women considering this examination. Thus quick procedures, sufficient experience, and advanced skills are required for radiologic technologists. The aim of this study was to make the point of imaging techniques explicit and to help understand the complicated procedure. We interviewed 3 technologists who were highly skilled in mammography, and 14 factors were retrieved by using brainstorming and the KJ method. We then applied Interpretive Structural Modeling (ISM) to the factors and developed a hierarchical concept structure. The result showed a six-layer hierarchy whose top node was explanation of the entire procedure on mammography. Male technologists were related to as a negative factor. Factors concerned with explanation were at the upper node. We gave attention to X-ray techniques and considerations. The findings will help beginners improve their skills.

  10. Grain refinement of zinc-aluminium alloys

    Zaid, A.I.O.

    2006-01-01

    It is now well-established that the structure of the zinc-aluminum die casting alloys can be modified by the binary Al-Ti or the ternary Al-Ti-B master alloys. in this paper, grain refinement of zinc-aluminum alloys by rare earth materials is reviewed and discussed. The importance of grain refining of these alloys and parameters affecting it are presented and discussed. These include parameters related to the Zn-Al alloys cast, parameters related to the grain refining elements or alloys and parameters related to the process. The effect of addition of other alloying elements e.g. Zr either alone or in the presence of the main grain refiners Ti or Ti + B on the grain refining efficiency is also reviewed and discussed. Furthermore, based on the grain refinement and the parameters affecting it, a criterion for selection of the optimum grain refiner is suggested. Finally, the recent research work on the effect of grain refiners on the mechanical behaviour, impact strength, wear resistance, and fatigue life of these alloys are presented and discussed. (author)

  11. Optimal algebraic multilevel preconditioning for local refinement along a line

    Margenov, S.D.; Maubach, J.M.L.

    1995-01-01

    The application of some recently proposed algebraic multilevel methods for the solution of two-dimensional finite element problems on nonuniform meshes is studied. The locally refined meshes are created by the newest vertex mesh refinement method. After the introduction of this refinement technique

  12. A Method to Increase Current Density in a Mono Element Internal Tin Processed Superconductor Utilizing Zr Oxide to Refine Grain Size; Final Report Phase 2

    Zeitlin, Bruce A.; Gregory, Eric

    2008-01-01

    The effect of Oxygen on (Nb1Zr)3Sn multifilament conductors manufactured by the Mono Element Internal Tin (MEIT) process was explored to improve the current density by refining the grain size. This followed work first done by General Electric on the Nb3Sn tape process. Techniques to fabricate the more difficult Nb1Zr composites are described and allowed fabrication of long lengths of .254 mm diameter wire from an 88.9 mm diameter billet. Oxygen was incorporated through the use of SnO2 mixed with tin powder and incorporated into the core. These were compared to samples with Ti+Sn and Cu+Sn cores. Heat treatments covered the range of 700 C to 1000 C. Current density vs. H, grain size, and reaction percentages are provided for the materials tested. The Oxygen gave superior results in the temperature range of 815-1000 C. It also stabilized the filament geometry of the array in comparison to the other additions at the higher temperatures. At 815 C a peak in layer Jc yielded values of 2537 A/mm2 at 12 T and 1353 A/mm2 at 15T, 8-22% and 30-73% greater respectively than 700 C values. Results with Oxygen at high temperature show the possibility of high speed continuous reaction of the composite versus the current batch or react in place methods. In general the Ti additions gave superior results at the lower reaction temperature. Future work is suggested to determine if the 815 C reaction temperature can lead to higher current density in high tin (Nb1Zr+Ox)3Sn conductors. A second technique incorporated oxygen directly into the Nb1Zr rods through heat treatment with Nb2O5 at 1100 C for 100 hours in vacuum prior to extrusion. The majority of the filaments reduced properly in the composite but some local variations in hardness led to breakage at smaller diameters.

  13. European refining: evolution or revolution?

    Cuthbert, N.

    1999-01-01

    A recent detailed analysis of the refining business in Europe (by Purvin and Gurtz) was used to highlight some key issues facing the industry. The article was written under five sub-sections: (i) economic environment (assessment of the economic prospects for Europe), (ii) energy efficiency and global warming (lists the four points of the EU car makers' voluntary agreement), (iii) fuel quality and refinery investment (iv) refinery capacity and utilisation and (v) industry structure and development. Diagrams show GDP per capita for East and West, European road fuel demand to 2015 and European net trade and European refinery ownership by crude capacity. It was concluded that the future of refining in Europe is 'exciting and challenging' and there are likely to be more large joint venture refineries. (UK)

  14. Bauxite Mining and Alumina Refining

    Donoghue, A. Michael; Frisch, Neale; Olney, David

    2014-01-01

    Objective: To describe bauxite mining and alumina refining processes and to outline the relevant physical, chemical, biological, ergonomic, and psychosocial health risks. Methods: Review article. Results: The most important risks relate to noise, ergonomics, trauma, and caustic soda splashes of the skin/eyes. Other risks of note relate to fatigue, heat, and solar ultraviolet and for some operations tropical diseases, venomous/dangerous animals, and remote locations. Exposures to bauxite dust,...

  15. New insights into the crystal chemistry of agardite-(Ce): refinement of the crystal structure, hydrogen bonding, and epitaxial intergrowths with the Sb-analogue of auriacusite

    Aksenov, Sergey M.; Chukanov, Nikita V.; Göttlicher, Jörg; Möckel, Steffen; Varlamov, Dmitriy; Van, Konstantin V.; Rastsvetaeva, Ramiza K.

    2018-01-01

    Agardite-(Ce) from Clara Mine, Schwarzwald, Germany, has been investigated by means of electron microprobe analysis, single-crystal X-ray analysis, XANES spectroscopy and IR spectroscopy. Hexagonal unit-cell parameters are: a = 13.598(6), c = 5.954(3) Å; V = 953.5(2) Å3; space group P63/ m. The structure has been solved and refined to final R 1 = 3.87%, w R 2 = 5.02 for 786 I > 3 σ( I). Hydrogen atoms have been localized. The crystal-chemical formula is ( Z = 2): A(1)(Ce0.82Ca0.14Sr0.04)Σ1.00 A(2)(Ca0.03Ce0.02)Σ0.05 [Cu5.75(Fe3+, Mn)0.20]Σ5.95 [ T(1)(AsO4) 2.96 T(2) (SbO4)0.04)]Σ3.00 (OH)5.96O0.04·3H2O. Hydrogen bonding in agardite-series minerals has been characterized for the first time. IR spectra of agardite-(Ce) and agardite-(Nd) from Lavrion used for comparison, as well as structural data indicate the presence of isolated H+ cations that do not form strong covalent bonds with coordinating O atoms. Agardite-(Ce) from Clara Mine forms epitaxial growths with the Sb-analogue of auriacusite. The latter mineral was characterized by EDS analyses; its typical empirical formulae are {Ca}_{0.0 6} {Ce}_{0.0 4} {Fe}^{ 3+ }{}_{ 1.0 6} {Cu}_{0. 8 9}[(SbO4)0.58(AsO4)0.38(SiO4)0.04]Σ1.00(O,OH) and {Ca}_{0.0 7 5} {Ce}_{0.0 4} {Fe}^{ 3+ }{}_{0. 9 3} {Cu}_{0. 9 7}[(SbO4)0.59(AsO4)0.35(SiO4)0.06]Σ1.00(O,OH). The formation of uniaxial growths of the Sb-analogue of auriacusite and agardite-(Ce) is caused by the close values of their c parameters (for auriacusite s.s. c = 5.9501(5) Å). Three-valence state of iron and five-valence of antimony in both minerals has been validated by means of Fe K- and Sb L 2,3-edge XANES spectroscopy.

  16. Scientific methods for developing ultrastable structures

    Gamble, M.; Thompson, T.; Miller, W.

    1990-01-01

    Scientific methods used by the Los Alamos National Laboratory for developing an ultrastable structure for study of silicon-based elementary particle tracking systems are addressed. In particular, the design, analysis, and monitoring of this system are explored. The development methodology was based on a triad of analytical, computational, and experimental techniques. These were used to achieve a significant degree of mechanical stability (alignment accuracy >1 μrad) and yet allow dynamic manipulation of the system. Estimates of system thermal and vibratory stability and component performance are compared with experimental data collected using laser interferometry and accelerometers. 8 refs., 5 figs., 4 tabs

  17. Effect of grain refinement on the fluidity of two commercial Al-Si foundry alloys

    Dahle, A. K.; Tøndel, P. A.; Paradies, C. J.; Arnberg, L.

    1996-08-01

    The effect of grain refinement on the fluidity of AlSi7Mg and AlSi11Mg has been investigated by spiral tests. Two different types of grain refiners have been evaluated. An AlTi5Bl master alloy was added to different Ti contents. Since the commercial alloys had a high initial content of titanium, model alloys were made to investigate the fluidity at low grain refiner additions. Commercial alloys grain refined only by boron additions have also been investigated. The results from the fluidity measurements have been verified by measuring the dendrite coherency point of the different cast alloys. Although different, the two methods show similar trends. The spirals from each fraction grain refiner cast were subsequently investigated metallographically at the tip of the spirals and at a reference point a distance behind, but no obvious difference in structure was observed. For both alloys, an increase in fluidity is observed as the content of grain refiner increases above 0.12 pct Ti, while the fluidity is impaired with increased grain refinement below 0.12 pct Ti. The alloys grain refined with ~0.015 pct B show the highest fraction solid at dendrite coherency, the smallest grain size, and the best fluidity.

  18. Profile fitting and the two-stage method in neutron powder diffractometry for structure and texture analysis

    Jansen, E.; Schaefer, W.; Will, G.; Kernforschungsanlage Juelich G.m.b.H.

    1988-01-01

    An outline and an application of the two-stage method in neutron powder diffractometry are presented. Stage (1): Individual reflection data like position, half-width and integrated intensity are analysed by profile fitting. The profile analysis is based on an experimentally determined instrument function and can be applied without prior knowledge of a structural model. A mathematical procedure is described which results in a variance-covariance matrix containing standard deviations and correlations of the refined reflection parameters. Stage (2): The individual reflection data derived from the profile fitting procedure can be used for appropriate purposes either in structure determination or in texture and strain or stress analysis. The integrated intensities are used in the non-diagonal weighted least-squares routine POWLS for structure refinement. The weight matrix is given by the inverted variance-covariance matrix of stage (1). This procedure is the basis for reliable and real Bragg R values and for a realistic estimation of standard deviations of structural parameters. In the case of texture analysis the integrated intensities are compiled into pole figures representing the intensity distribution for all sample orientations of individual hkl. Various examples for the wide application of the two-stage method in structure and texture analysis are given: Structure refinement of a standard quartz specimen, magnetic ordering in the system Tb x Y 1-x Ag, preferred orientation effects in deformed marble and texture investigations of a triclinic plagioclase. (orig.)

  19. Refining margins: recent trends

    Baudoin, C.; Favennec, J.P.

    1999-01-01

    Despite a business environment that was globally mediocre due primarily to the Asian crisis and to a mild winter in the northern hemisphere, the signs of improvement noted in the refining activity in 1996 were borne out in 1997. But the situation is not yet satisfactory in this sector: the low return on invested capital and the financing of environmental protection expenditure are giving cause for concern. In 1998, the drop in crude oil prices and the concomitant fall in petroleum product prices was ultimately rather favorable to margins. Two elements tended to put a damper on this relative optimism. First of all, margins continue to be extremely volatile and, secondly, the worsening of the economic and financial crisis observed during the summer made for a sharp decline in margins in all geographic regions, especially Asia. Since the beginning of 1999, refining margins are weak and utilization rates of refining capacities have decreased. (authors)

  20. Refining and petrochemicals

    Constancio, Silva

    2006-07-01

    In 2004, refining margins showed a clear improvement that persisted throughout the first three quarters of 2005. This enabled oil companies to post significantly higher earnings for their refining activity in 2004 compared to 2003, with the results of the first half of 2005 confirming this trend. As for petrochemicals, despite a steady rise in the naphtha price, higher cash margins enabled a turnaround in 2004 as well as a clear improvement in oil company financial performance that should continue in 2005, judging by the net income figures reported for the first half-year. Despite this favorable business environment, capital expenditure in refining and petrochemicals remained at a low level, especially investment in new capacity, but a number of projects are being planned for the next five years. (author)

  1. Refining and petrochemicals

    Constancio, Silva

    2006-01-01

    In 2004, refining margins showed a clear improvement that persisted throughout the first three quarters of 2005. This enabled oil companies to post significantly higher earnings for their refining activity in 2004 compared to 2003, with the results of the first half of 2005 confirming this trend. As for petrochemicals, despite a steady rise in the naphtha price, higher cash margins enabled a turnaround in 2004 as well as a clear improvement in oil company financial performance that should continue in 2005, judging by the net income figures reported for the first half-year. Despite this favorable business environment, capital expenditure in refining and petrochemicals remained at a low level, especially investment in new capacity, but a number of projects are being planned for the next five years. (author)

  2. Indian refining industry

    Singh, I.J.

    2002-01-01

    The author discusses the history of the Indian refining industry and ongoing developments under the headings: the present state; refinery configuration; Indian capabilities for refinery projects; and reforms in the refining industry. Tables lists India's petroleum refineries giving location and capacity; new refinery projects together with location and capacity; and expansion projects of Indian petroleum refineries. The Indian refinery industry has undergone substantial expansion as well as technological changes over the past years. There has been progressive technology upgrading, energy efficiency, better environmental control and improved capacity utilisation. Major reform processes have been set in motion by the government of India: converting the refining industry from a centrally controlled public sector dominated industry to a delicensed regime in a competitive market economy with the introduction of a liberal exploration policy; dismantling the administered price mechanism; and a 25 year hydrocarbon vision. (UK)

  3. COSMOLOGICAL ADAPTIVE MESH REFINEMENT MAGNETOHYDRODYNAMICS WITH ENZO

    Collins, David C.; Xu Hao; Norman, Michael L.; Li Hui; Li Shengtai

    2010-01-01

    In this work, we present EnzoMHD, the extension of the cosmological code Enzo to include the effects of magnetic fields through the ideal magnetohydrodynamics approximation. We use a higher order Godunov method for the computation of interface fluxes. We use two constrained transport methods to compute the electric field from those interface fluxes, which simultaneously advances the induction equation and maintains the divergence of the magnetic field. A second-order divergence-free reconstruction technique is used to interpolate the magnetic fields in the block-structured adaptive mesh refinement framework already extant in Enzo. This reconstruction also preserves the divergence of the magnetic field to machine precision. We use operator splitting to include gravity and cosmological expansion. We then present a series of cosmological and non-cosmological test problems to demonstrate the quality of solution resulting from this combination of solvers.

  4. Refining - Panorama 2008

    2008-01-01

    Investment rallied in 2007, and many distillation and conversion projects likely to reach the industrial stage were announced. With economic growth sustained in 2006 and still pronounced in 2007, oil demand remained strong - especially in emerging countries - and refining margins stayed high. Despite these favorable business conditions, tensions persisted in the refining sector, which has fallen far behind in terms of investing in refinery capacity. It will take renewed efforts over a long period to catch up. Looking at recent events that have affected the economy in many countries (e.g. the sub-prime crisis), prudence remains advisable

  5. (Na,□)5[MnO2]13 nanorods: a new tunnel structure for electrode materials determined ab initio and refined through a combination of electron and synchrotron diffraction data

    Mugnaioli, Enrico; Gemmi, Mauro; Merlini, Marco; Gregorkiewitz, Michele

    2016-01-01

    (Nax□1 − x)5[MnO2]13 has been synthesized with x = 0.80 (4), corresponding to Na0.31[MnO2]. This well known material is usually cited as Na0.4[MnO2] and is believed to have a romanèchite-like framework. Here, its true structure is determined, ab initio, by single-crystal electron diffraction tomography (EDT) and refined both by EDT data applying dynamical scattering theory and by the Rietveld method based on synchrotron powder diffraction data (χ2 = 0.690, R wp = 0.051, R p = 0.037, R F2 = 0.035). The unit cell is monoclinic C2/m, a = 22.5199 (6), b = 2.83987 (6), c = 14.8815 (4) Å, β = 105.0925 (16)°, V = 918.90 (4) Å3, Z = 2. A hitherto unknown [MnO2] framework is found, which is mainly based on edge- and corner-sharing octahedra and comprises three types of tunnels: per unit cell, two are defined by S-shaped 10-rings, four by egg-shaped 8-rings, and two by slightly oval 6-rings of Mn polyhedra. Na occupies all tunnels. The so-determined structure excellently explains previous reports on the electrochemistry of (Na,□)5[MnO2]13. The trivalent Mn3+ ions concentrate at two of the seven Mn sites where larger Mn—O distances and Jahn–Teller distortion are observed. One of the Mn3+ sites is five-coordinated in a square pyramid which, on oxidation to Mn4+, may easily undergo topotactic transformation to an octahedron suggesting a possible pathway for the transition among different tunnel structures. PMID:27910840

  6. Computational methods in sequence and structure prediction

    Lang, Caiyi

    This dissertation is organized into two parts. In the first part, we will discuss three computational methods for cis-regulatory element recognition in three different gene regulatory networks as the following: (a) Using a comprehensive "Phylogenetic Footprinting Comparison" method, we will investigate the promoter sequence structures of three enzymes (PAL, CHS and DFR) that catalyze sequential steps in the pathway from phenylalanine to anthocyanins in plants. Our result shows there exists a putative cis-regulatory element "AC(C/G)TAC(C)" in the upstream of these enzyme genes. We propose this cis-regulatory element to be responsible for the genetic regulation of these three enzymes and this element, might also be the binding site for MYB class transcription factor PAP1. (b) We will investigate the role of the Arabidopsis gene glutamate receptor 1.1 (AtGLR1.1) in C and N metabolism by utilizing the microarray data we obtained from AtGLR1.1 deficient lines (antiAtGLR1.1). We focus our investigation on the putatively co-regulated transcript profile of 876 genes we have collected in antiAtGLR1.1 lines. By (a) scanning the occurrence of several groups of known abscisic acid (ABA) related cisregulatory elements in the upstream regions of 876 Arabidopsis genes; and (b) exhaustive scanning of all possible 6-10 bps motif occurrence in the upstream regions of the same set of genes, we are able to make a quantative estimation on the enrichment level of each of the cis-regulatory element candidates. We finally conclude that one specific cis-regulatory element group, called "ABRE" elements, are statistically highly enriched within the 876-gene group as compared to their occurrence within the genome. (c) We will introduce a new general purpose algorithm, called "fuzzy REDUCE1", which we have developed recently for automated cis-regulatory element identification. In the second part, we will discuss our newly devised protein design framework. With this framework we have developed

  7. Method of fitting a cage structure

    Takeuchi, Mamoru; Iwasaki, Tsutomu; Ishida, Akira; Yokota, Hirakazu.

    1971-01-01

    Herein disclosed is a method of fitting together cage structures, each made of a different material. The cage structure may be an ultrahigh speed rotary drum for a centrifuge. An inner cylinder of, for example, Al alloy, to be inserted in an outer cylinder made of a material such as carbon fiber reinforced plastic is filament-wound with a resin-impregnated carbon fiber under application of an axial tensile force to the inner cylinder so as to contract the radius thereof, and then after-cured to cool down to room temperature. The tensile force is then released to permit the radially contracted inner cylinder to elastically recover its original form and to thereby eliminate a gap formed between both cylinders due to aftercure, providing that the width of the gap is equal to that of the radial contraction, determined by Poisson's ratio, of the Al alloy material. Thus, the inner cylinder can be firmly fitted within the outer cylinder in accordance with the elastic deformation of the material. (Ohno, Y.)

  8. Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: Two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum

    Banks, K.M.; Hare, D.R.; Reid, B.R.

    1989-01-01

    A three-dimensional solution structure for the self-complementary dodecanucleotide [(d-GCCTGATCAGGC)] 2 has been determined by distance geometry with further refinements being performed after back-calculation of the NOESY spectrum. This DNA dodecamer contains the hexamer [d(TGATCA)] 2 recognized and cut by the restriction endonuclease BclI, and its structure was determined in hopes of obtaining a better understanding of the sequence-specific interactions which occur between proteins and DNA. Preliminary examination of the structure indicates the structure is underwound with respect to idealized B-form DNA though some of the local structural parameters (glycosyl torsion angle and pseudorotation angle) suggest a B-family type of structure is present. This research demonstrates the requirements (resonance assignments, interproton distance measurements, distance geometry calculations, and NOESY spectra back-calculation) to generate experimentally self-consistent solution structures for short DNA sequences

  9. Structures for capturing CO.sub.2, methods of making the structures, and methods of capturing CO.sub.2

    Jones, Christopher W; Hicks, Jason C; Fauth, Daniel J; McMahan, Gray

    2012-10-30

    Briefly described, embodiments of this disclosure, among others, include carbon dioxide (CO.sub.2) sorption structures, methods of making CO.sub.2 sorption structures, and methods of using CO.sub.2 sorption structures.

  10. Hirshfeld atom refinement for modelling strong hydrogen bonds.

    Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon

    2014-09-01

    High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

  11. Crystal structures of iron bearing tetrahedrite and tennantite at 25 and 250 degrees C by means of Rietveld refinement of synchrotron data

    Friese, K.; Grzechnik, A.; Makovicky, E.

    2008-01-01

    Rietveld refinement of X-ray synchrotron data was performed for two synthetic tetrahedrite samples, with 0.61 and 1.83 Fe atoms, and two synthetic tennantite samples with 0.10 and 1.23 Fe atoms p.f.u. M-12(Sb,As)(4)S-13. Measurements were performed at 25 and 250 degrees C. For both the phases...

  12. Opportunities and future directions for visual soil evaluation methods in soil structure research

    Guimaraes, R.M.L.; Lamandé, Mathieu; Munkholm, Lars Juhl

    2017-01-01

    to provide spatial information for soil process models, e.g. compaction models. VSE could be combined with sensing techniques at the field or landscape scale for better management of fields in the context of precision farming. Further work should be done to integrate plant vigour, roots and soil fauna......As the use of visual soil evaluation (VSE) methods has spread globally, they have been exposed to different climatic and pedological scenarios, resulting in the need to elucidate limitations, encourage refinements and open up new avenues of research. The main objective of this paper is to outline...... the potential of VSE methods to develop novel soil structure research and how this potential could be developed and integrated within existing research. We provide a brief overview of VSE methods in order to summarize the soil information that is obtained by VSE. More detailed VSE methods could be developed...

  13. Critical assessment of methods of protein structure prediction (CASP) - round x

    Moult, John; Fidelis, Krzysztof; Kryshtafovych, Andriy; Schwede, Torsten; Tramontano, Anna

    2013-01-01

    This article is an introduction to the special issue of the journal PROTEINS, dedicated to the tenth Critical Assessment of Structure Prediction (CASP) experiment to assess the state of the art in protein structure modeling. The article describes the conduct of the experiment, the categories of prediction included, and outlines the evaluation and assessment procedures. The 10 CASP experiments span almost 20 years of progress in the field of protein structure modeling, and there have been enormous advances in methods and model accuracy in that period. Notable in this round is the first sustained improvement of models with refinement methods, using molecular dynamics. For the first time, we tested the ability of modeling methods to make use of sparse experimental three-dimensional contact information, such as may be obtained from new experimental techniques, with encouraging results. On the other hand, new contact prediction methods, though holding considerable promise, have yet to make an impact in CASP testing. The nature of CASP targets has been changing in recent CASPs, reflecting shifts in experimental structural biology, with more irregular structures, more multi-domain and multi-subunit structures, and less standard versions of known folds. When allowance is made for these factors, we continue to see steady progress in the overall accuracy of models, particularly resulting from improvement of non-template regions.

  14. Critical assessment of methods of protein structure prediction (CASP) - round x

    Moult, John

    2013-12-17

    This article is an introduction to the special issue of the journal PROTEINS, dedicated to the tenth Critical Assessment of Structure Prediction (CASP) experiment to assess the state of the art in protein structure modeling. The article describes the conduct of the experiment, the categories of prediction included, and outlines the evaluation and assessment procedures. The 10 CASP experiments span almost 20 years of progress in the field of protein structure modeling, and there have been enormous advances in methods and model accuracy in that period. Notable in this round is the first sustained improvement of models with refinement methods, using molecular dynamics. For the first time, we tested the ability of modeling methods to make use of sparse experimental three-dimensional contact information, such as may be obtained from new experimental techniques, with encouraging results. On the other hand, new contact prediction methods, though holding considerable promise, have yet to make an impact in CASP testing. The nature of CASP targets has been changing in recent CASPs, reflecting shifts in experimental structural biology, with more irregular structures, more multi-domain and multi-subunit structures, and less standard versions of known folds. When allowance is made for these factors, we continue to see steady progress in the overall accuracy of models, particularly resulting from improvement of non-template regions.

  15. Anomalies in the refinement of isoleucine

    Berntsen, K.R.M.; Vriend, G.

    2014-01-01

    A study of isoleucines in protein structures solved using X-ray crystallography revealed a series of systematic trends for the two side-chain torsion angles chi1 and chi2 dependent on the resolution, secondary structure and refinement software used. The average torsion angles for the nine rotamers

  16. US refining reviewed

    Yamaguchi, N.D.

    1998-01-01

    The paper reviews the history, present position and future prospects of the petroleum industry in the USA. The main focus is on supply and demand, the high quality of the products, refinery capacity and product trade balances. Diagrams show historical trends in output, product demand, demand for transport fuels and oil, refinery capacity, refinery closures, and imports and exports. Some particularly salient points brought out were (i) production of US crude shows a marked downward trend but imports of crude will continue to increase, (ii) product demand will continue to grow even though the levels are already high, (iii) the demand is dominated by those products that typically yield the highest income for the refiner, (i.e. high quality transport fuels for environmental compliance), (iv) refinery capacity has decreased since 1980 and (v) refining will continue to have financial problems but will still be profitable. (UK)

  17. Outlook for Canadian refining

    Boje, G.

    1998-01-01

    The petroleum supply and demand balance was discussed and a comparison between Canadian and U.S. refineries was provided. The impact of changing product specifications on the petroleum industry was also discussed. The major changes include sulphur reductions in gasoline, benzene and MMT additives. These changes have been made in an effort to satisfy environmental needs. Geographic margin variations in refineries between east and west were reviewed. An overview of findings from the Solomon Refining Study of Canadian and American refineries, which has been very complimentary of the Canadian refining industry, was provided. From this writer's point of view refinery utilization has improved but there is a threat from increasing efficiency of US competitors. Environmental issues will continue to impact upon the industry and while the chances for making economic returns on investment are good for the years ahead, it will be a challenge to maintain profitability

  18. Computational structural biology: methods and applications

    Schwede, Torsten; Peitsch, Manuel Claude

    2008-01-01

    ... sequencing reinforced the observation that structural information is needed to understand the detailed function and mechanism of biological molecules such as enzyme reactions and molecular recognition events. Furthermore, structures are obviously key to the design of molecules with new or improved functions. In this context, computational structural biology...

  19. Future of French refining

    Calvet, B.

    1993-01-01

    Over recent years, the refining industry has had to grapple with a growing burden of environmental and safety regulations concerning not only its plants and other facilities, but also its end products. At the same time, it has had to bear the effects of the reduction of the special status that used to apply to petroleum, and the consequences of economic freedom, to which we should add, as specifically concerns the French market, the impact of energy policy and the pro-nuclear option. The result is a drop in heavy fuel oil from 36 million tonnes per year in 1973 to 6.3 million in 1992, and in home-heating fuel from 37 to 18 million per year. This fast-moving market is highly competitive. The French market in particular is wide open to imports, but the refining companies are still heavy exporters for those products with high added-value, like lubricants, jet fuel, and lead-free gasolines. The competition has led the refining companies to commit themselves to quality, and to publicize their efforts in this direction. This is why the long-term perspectives for petroleum fuels are still wide open. This is supported by the probable expectation that the goal of economic efficiency is likely to soften the effects of the energy policy, which penalizes petroleum products, in that they have now become competitive again. In the European context, with the challenge of environmental protection and the decline in heavy fuel outlets, French refining has to keep on improving the quality of its products and plants, which means major investments. The industry absolutely must return to a more normal level of profitability, in order to sustain this financial effort, and generate the prosperity of its high-performance plants and equipment. 1 fig., 5 tabs

  20. Process for refining hydrocarbons

    Risenfeld, E H

    1924-11-26

    A process is disclosed for the refining of hydrocarbons or other mixtures through treatment in vapor form with metal catalysts, characterized by such metals being used as catalysts, which are obtained by reduction of the oxide of minerals containing the iron group, and by the vapors of the hydrocarbons, in the presence of the water vapor, being led over these catalysts at temperatures from 200 to 300/sup 0/C.

  1. Unit-cell refinement from powder diffraction scans

    Pawley, G.S.

    1981-01-01

    A procedure for the refinement of the crystal unit cell from a powder diffraction scan is presented. In this procedure knowledge of the crystal structure is not required, and at the end of the refinement a list of indexed intensities is produced. This list may well be usable as the starting point for the application of direct methods. The problems of least-squares ill-conditioning due to overlapping reflections are overcome by constraints. An example using decafluorocyclohexene, C 6 F 10 , shows the quality of fit obtained in a case which may even be a false minimum. The method should become more relevant as powder scans of improved resolution become available, through the use of pulsed neutron sources. (Auth.)

  2. Panorama 2009 - refining

    2008-01-01

    For oil companies to invest in new refining and conversion capacity, favorable conditions over time are required. In other words, refining margins must remain high and demand sustained over a long period. That was the situation prevailing before the onset of the financial crisis in the second half of 2008. The economic conjuncture has taken a substantial turn for the worse since then and the forecasts for 2009 do not look bright. Oil demand is expected to decrease in the OECD countries and to grow much more slowly in the emerging countries. It is anticipated that refining margins will fall in 2009 - in 2008, they slipped significantly in the United States - as a result of increasingly sluggish demand, especially for light products. The next few months will probably be unfavorable to investment. In addition to a gloomy business outlook, there may also be a problem of access to sources of financing. As for investment projects, a mainstream trend has emerged in the last few years: a shift away from the regions that have historically been most active (the OECD countries) towards certain emerging countries, mostly in Asia or the Middle East. The new conjuncture will probably not change this trend

  3. Refining discordant gene trees.

    Górecki, Pawel; Eulenstein, Oliver

    2014-01-01

    Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism. We propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs. Our binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.

  4. Refining processes of selected copper alloys

    S. Rzadkosz

    2009-04-01

    Full Text Available The analysis of the refining effectiveness of the liquid copper and selected copper alloys by various micro additions and special refiningsubstances – was performed. Examinations of an influence of purifying, modifying and deoxidation operations performed in a metal bath on the properties of certain selected alloys based on copper matrix - were made. Refining substances, protecting-purifying slag, deoxidation and modifying substances containing micro additions of such elements as: zirconium, boron, phosphor, sodium, lithium, or their compounds introduced in order to change micro structures and properties of alloys, were applied in examinations. A special attention was directed to macro and micro structures of alloys, their tensile and elongation strength and hot-cracks sensitivity. Refining effects were estimated by comparing the effectiveness of micro structure changes with property changes of copper and its selected alloys from the group of tin bronzes.

  5. Macromolecular refinement by model morphing using non-atomic parameterizations.

    Cowtan, Kevin; Agirre, Jon

    2018-02-01

    Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model.

  6. Refinement of protein termini in template-based modeling using conformational space annealing.

    Park, Hahnbeom; Ko, Junsu; Joo, Keehyoung; Lee, Julian; Seok, Chaok; Lee, Jooyoung

    2011-09-01

    The rapid increase in the number of experimentally determined protein structures in recent years enables us to obtain more reliable protein tertiary structure models than ever by template-based modeling. However, refinement of template-based models beyond the limit available from the best templates is still needed for understanding protein function in atomic detail. In this work, we develop a new method for protein terminus modeling that can be applied to refinement of models with unreliable terminus structures. The energy function for terminus modeling consists of both physics-based and knowledge-based potential terms with carefully optimized relative weights. Effective sampling of both the framework and terminus is performed using the conformational space annealing technique. This method has been tested on a set of termini derived from a nonredundant structure database and two sets of termini from the CASP8 targets. The performance of the terminus modeling method is significantly improved over our previous method that does not employ terminus refinement. It is also comparable or superior to the best server methods tested in CASP8. The success of the current approach suggests that similar strategy may be applied to other types of refinement problems such as loop modeling or secondary structure rearrangement. Copyright © 2011 Wiley-Liss, Inc.

  7. Stable grid refinement and singular source discretization for seismic wave simulations

    Petersson, N A; Sjogreen, B

    2009-10-30

    An energy conserving discretization of the elastic wave equation in second order formulation is developed for a composite grid, consisting of a set of structured rectangular component grids with hanging nodes on the grid refinement interface. Previously developed summation-by-parts properties are generalized to devise a stable second order accurate coupling of the solution across mesh refinement interfaces. The discretization of singular source terms of point force and point moment tensor type are also studied. Based on enforcing discrete moment conditions that mimic properties of the Dirac distribution and its gradient, previous single grid formulas are generalized to work in the vicinity of grid refinement interfaces. These source discretization formulas are shown to give second order accuracy in the solution, with the error being essentially independent of the distance between the source and the grid refinement boundary. Several numerical examples are given to illustrate the properties of the proposed method.

  8. Design methods for structures under thermal ratchet

    Branca, T.R.; McLean, J.L.

    1975-01-01

    Previous work on the thermal ratchet analysis of a simple pipe is extended to the case of an intersection of a pipe with a spherical shell. The chosen nozzle configuration is subjected to an internal pressure which remains constant, and a cyclic thermal transient which is representative of the type of transient that might be expected for components of a LMFBR. A number of cross-sections through the nozzle were examined, each yielding a different combination of elastic primary and secondary stress. These stresses, together with their associated cyclic strain growth, as determined from an elastic-plastic-creep analysis of the nozzle, were then plotted on a Miller or Bree-type diagram. Thus, a number of points, one for each cross-section considered, were available for comparison with the data obtained from the ratchet analysis of simple pipe sections. Both the elastic and inelastic analyses on the nozzle were performed using the finite element method of structural analysis of the ANSYS computer code. The pipe ratchetting cases were computed using the Oak Ridge National Laboratory PLACRE code. For a simple pipe ratchet case, a brief comparison is given between the version of ANSYS used in this study, the ANSYS version used in previous work and PLACRE code. The three programs did not yield identical results. Further study is needed to resolve the discrepancies that were observed. The results of the comparison between the nozzle ratchet and pipe ratchet solutions indicate that reasonable predictions can be made for the nozzle ratchet strains based on elastic parameters and design curves developed from pipe ratchetting solutions. (author)

  9. In situ study the effect of refiner on the microstructure evolution of variable cross-section structure by synchrotron X-ray radiography

    Li, Faguo; Zhang, Jiao; Dai, Yongbing; Bian, Fenggang; Fu, Yanan; Yin, Fucheng; Sun, Baode

    2015-10-01

    The formation of microstructures during solidification is strongly affected by the interaction that occurs between factors, such as heat field, melt flow, solute distribution, and number of effective nucleation cores. In this study, the microstructure evolution of a high-purity hypoeutectic Al-Cu alloy at its region of variable cross-section was studied using synchrotron radiation imaging. The characteristics of the thermal field, solute field, and flow field were analyzed according to these radiographs. The results showed that the region of variable cross-section is the site that is more prone to dendrite arms fracture. These dendrites spread radially from the center of the thin wall and the isotherms distribute as an arc-shape. These are the main reasons for the uneven distribution of the microstructure, which lead to undesirable phase formation and aggregation at the region of variable cross-section. The microstructure can be significantly refined and solute enrichment can be eliminated by adding refiners to alloys. Comparing these two conditions, it can be concluded that the solute and flow field distribution at the variable cross-section region is significantly affected, uniformity of the solidification microstructure is improved, and undesirable phases are eliminated by increase in effective heterogeneous nucleation cores.

  10. Optical feedback structures and methods of making

    None

    2014-11-18

    An optical resonator can include an optical feedback structure disposed on a substrate, and a composite including a matrix including a chromophore. The composite disposed on the substrate and in optical communication with the optical feedback structure. The chromophore can be a semiconductor nanocrystal. The resonator can provide laser emission when excited.

  11. Application of the Rietveld method in structural analysis of catalysts based on CuO/CeO2

    Neiva, L.S.; Ribeiro, M.A.; Bispo, A.; Simoes, A.N.; Gama, L.

    2011-01-01

    This work has as aim to synthesize catalysts composed by CuO/CeO 2 by means two distinct methods of synthesis, they are: combustion synthesis and Pechini. The catalysts composed by CuO/CeO 2 were synthesized with CuO in condition of dopant element. The value of the CuO concentration ranged between 0 and 0.5 mol. Has been done a structural analysis related to how the kind of synthesis method used influences over physical characteristic of the catalytic material. The obtained catalysts were characterized by X-ray diffraction with refinement by Rietveld method. According to results, the synthesized catalysts showed crystalline structures formed mostly by CeO 2 phase, as expected, since this is the host matrix for the dopant element. The catalysts obtained by the Pechini method presented structures with a smaller amount of segregated phases formed by CuO, according to the results of the structural analysis. (author)

  12. Method of using triaxial magnetic fields for making particle structures

    Martin, James E.; Anderson, Robert A.; Williamson, Rodney L.

    2005-01-18

    A method of producing three-dimensional particle structures with enhanced magnetic susceptibility in three dimensions by applying a triaxial energetic field to a magnetic particle suspension and subsequently stabilizing said particle structure. Combinations of direct current and alternating current fields in three dimensions produce particle gel structures, honeycomb structures, and foam-like structures.

  13. Refining and petrochemicals

    Benazzi, E.

    2003-01-01

    Down sharply in 2002, refining margins showed a clear improvement in the first half-year of 2003. As a result, the earnings reported by oil companies for financial year 2002 were significantly lower than in 2001, but the prospects are brighter for 2003. In the petrochemicals sector, slow demand and higher feedstock prices eroded margins in 2002, especially in Europe and the United States. The financial results for the first part of 2003 seem to indicate that sector profitability will not improve before 2004. (author)

  14. Refining and petrochemicals

    Benazzi, E.; Alario, F.

    2004-01-01

    In 2003, refining margins showed a clear improvement that continued throughout the first three quarters of 2004. Oil companies posted significantly higher earnings in 2003 compared to 2002, with the results of first quarter 2004 confirming this trend. Due to higher feedstock prices, the implementation of new capacity and more intense competition, the petrochemicals industry was not able to boost margins in 2003. In such difficult business conditions, aggravated by soaring crude prices, the petrochemicals industry is not likely to see any improvement in profitability before the second half of 2004. (author)

  15. Refining mineral oils

    1946-07-05

    A process is described refining raw oils such as mineral oils, shale oils, tar, their fractions and derivatives, by extraction with a selected solvent or a mixture of solvents containing water, forming a solvent more favorable for the hydrocarbons poor in hydrogen than for hydrocarbons rich in hydrogen, this process is characterized by the addition of an aiding solvent for the water which can be mixed or dissolved in the water and the solvent or in the dissolving mixture and increasing in this way the solubility of the water in the solvent or the dissolving mixture.

  16. Crystallography of quasicrystals concepts, methods and structures

    Walter, Steurer

    2009-01-01

    From tilings to quasicrystal structures and from surfaces to the n-dimensional approach, this book gives a full, self-contained in-depth description of the crystallography of quasicrystals. It aims not only at conveying the concepts and a precise picture of the structures of quasicrystals, butit also enables the interested reader to enter the field of quasicrystal structure analysis. Going beyond metallic quasicrystals, it also describes the new, dynamically growing field of photonic quasicrystals. The readership will be graduate students and researchers in crystallography, solid-state physics, materials science, solid- state chemistry and applied mathematics.

  17. Efficient protein structure search using indexing methods.

    Kim, Sungchul; Sael, Lee; Yu, Hwanjo

    2013-01-01

    Understanding functions of proteins is one of the most important challenges in many studies of biological processes. The function of a protein can be predicted by analyzing the functions of structurally similar proteins, thus finding structurally similar proteins accurately and efficiently from a large set of proteins is crucial. A protein structure can be represented as a vector by 3D-Zernike Descriptor (3DZD) which compactly represents the surface shape of the protein tertiary structure. This simplified representation accelerates the searching process. However, computing the similarity of two protein structures is still computationally expensive, thus it is hard to efficiently process many simultaneous requests of structurally similar protein search. This paper proposes indexing techniques which substantially reduce the search time to find structurally similar proteins. In particular, we first exploit two indexing techniques, i.e., iDistance and iKernel, on the 3DZDs. After that, we extend the techniques to further improve the search speed for protein structures. The extended indexing techniques build and utilize an reduced index constructed from the first few attributes of 3DZDs of protein structures. To retrieve top-k similar structures, top-10 × k similar structures are first found using the reduced index, and top-k structures are selected among them. We also modify the indexing techniques to support θ-based nearest neighbor search, which returns data points less than θ to the query point. The results show that both iDistance and iKernel significantly enhance the searching speed. In top-k nearest neighbor search, the searching time is reduced 69.6%, 77%, 77.4% and 87.9%, respectively using iDistance, iKernel, the extended iDistance, and the extended iKernel. In θ-based nearest neighbor serach, the searching time is reduced 80%, 81%, 95.6% and 95.6% using iDistance, iKernel, the extended iDistance, and the extended iKernel, respectively.

  18. Contextual Distance Refining for Image Retrieval

    Islam, Almasri

    2014-01-01

    Recently, a number of methods have been proposed to improve image retrieval accuracy by capturing context information. These methods try to compensate for the fact that a visually less similar image might be more relevant because it depicts the same object. We propose a new quick method for refining any pairwise distance metric, it works by iteratively discovering the object in the image from the most similar images, and then refine the distance metric accordingly. Test show that our technique improves over the state of art in terms of accuracy over the MPEG7 dataset.

  19. Contextual Distance Refining for Image Retrieval

    Islam, Almasri

    2014-09-16

    Recently, a number of methods have been proposed to improve image retrieval accuracy by capturing context information. These methods try to compensate for the fact that a visually less similar image might be more relevant because it depicts the same object. We propose a new quick method for refining any pairwise distance metric, it works by iteratively discovering the object in the image from the most similar images, and then refine the distance metric accordingly. Test show that our technique improves over the state of art in terms of accuracy over the MPEG7 dataset.

  20. On the Use of Dynamical Diffraction Theory To Refine Crystal Structure from Electron Diffraction Data: Application to KLa5O5(VO4)2, a Material with Promising Luminescent Properties.

    Colmont, Marie; Palatinus, Lukas; Huvé, Marielle; Kabbour, Houria; Saitzek, Sébastien; Djelal, Nora; Roussel, Pascal

    2016-03-07

    A new lanthanum oxide, KLa5O5(VO4)2, was synthesized using a flux growth technique that involved solid-state reaction under an air atmosphere at 900 °C. The crystal structure was solved and refined using an innovative approach recently established and based on three-dimensional (3D) electron diffraction data, using precession of the electron beam and then validated against Rietveld refinement and denisty functional theory (DFT) calculations. It crystallizes in a monoclinic unit cell with space group C2/m and has unit cell parameters of a = 20.2282(14) Å, b = 5.8639(4) Å, c = 12.6060(9) Å, and β = 117.64(1)°. Its structure is built on Cresnel-like two-dimensional (2D) units (La5O5) of 4*3 (OLa4) tetrahedra, which run parallel to (001) plane, being surrounded by isolated VO4 tetrahedra. Four isolated vanadate groups create channels that host K(+) ions. Substitution of K(+) cations by another alkali metal is possible, going from lithium to rubidium. Li substitution led to a similar phase with a primitive monoclinic unit cell. A complementary selected area electron diffraction (SAED) study highlighted diffuse streaks associated with stacking faults observed on high-resolution electron microscopy (HREM) images of the lithium compound. Finally, preliminary catalytic tests for ethanol oxidation are reported, as well as luminescence evidence. This paper also describes how solid-state chemists can take advantages of recent progresses in electron crystallography, assisted by DFT calculations and powder X-ray diffraction (PXRD) refinements, to propose new structural types with potential applications to the physicist community.

  1. Inverse Finite Method Investigation for Adaptive Structures

    National Aeronautics and Space Administration — This research project is evaluating an innovative technique that uses fiber optic strain sensors to measure structural deformations and full field strains. An...

  2. Synthesis of hydroxyapatite and structural refinement by X-ray diffraction; Sintese da hidroxiapatita e refinamento estrutural por difracao de raios-X

    Araujo, Jorge Correa de [Universidade do Estado do Rio de Janeiro (UERJ), Sao Goncalo, RJ (Brazil). Faculdade de Formacao de Professores; Sena, Lidia [Instituto Nacional de Metrologia, Normalizacao e Qualidade Industrial (INMETRO), Duque de Caxias, RJ (Brazil). Div. de Metrologia de Materiais; Bastos, Ivan Napoleao [Universidade do Estado do Rio de Janeiro (UERJ), Nova Friburgo, RJ (Brazil). Inst. Politecnico]. E-mail: jcaraujo@iprj.uerj.br; Soares, Gloria Dulce de Almeida [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil)

    2007-07-01

    A sample of hydroxyapatite was synthesized and its crystalline structure was analyzed by X-ray diffraction by means of the Rietveld method. Two functions were used to fit the peak profiles, modified Voigt (TCHZ) and Pearson VII. The occupational factors and lattice parameters obtained by both models show that the sample does not contain relevant cationic substitutions. The interatomic distances from Ca1 to oxygens O1, O2 and O3 were adequate for a pure hydroxyapatite without defect at site Ca1. Besides, the use of multiple lines in planes (300) and (002) associated with the model Pearson VII resulted in good agreement with the TCHZ model with respect to the size-strain effects with an ellipsoidal shape of crystallites. In conclusion, the procedures adopted in the synthesis of hydroxyapatite produced a pure and crystalline material. The experimental results of transmission electron microscopy confirmed the predicted shape of crystals. (author)

  3. A new crystal structure fragment-based pharmacophore method for G protein-coupled receptors

    Fidom, Kimberley; Isberg, Vignir; Hauser, Alexander Sebastian

    2015-01-01

    and receptor residue pairs, from crystal structure complexes. We describe the procedure to collect a library with more than 250 fragments covering 29 residue positions within the generic transmembrane binding pocket. We describe how the library fragments are recombined and inferred to build pharmacophores...... for new targets. A validating retrospective virtual screening of histamine H1 and H3 receptor pharmacophores yielded area-under-the-curves of 0.88 and 0.82, respectively. The fragment-based method has the unique advantage that it can be applied to targets for which no (homologous) crystal structures...... or ligands are known. 47% of the class A G protein-coupled receptors can be targeted with at least four-element pharmacophores. The fragment libraries can also be used to grow known ligands or for rotamer refinement of homology models. Researchers can download the complete fragment library or a subset...

  4. Atlantic Basin refining profitability

    Jones, R.J.

    1998-01-01

    A review of the profitability margins of oil refining in the Atlantic Basin was presented. Petroleum refiners face the continuous challenge of balancing supply with demand. It would appear that the profitability margins in the Atlantic Basin will increase significantly in the near future because of shrinking supply surpluses. Refinery capacity utilization has reached higher levels than ever before. The American Petroleum Institute reported that in August 1997, U.S. refineries used 99 per cent of their capacity for several weeks in a row. U.S. gasoline inventories have also declined as the industry has focused on reducing capital costs. This is further evidence that supply and demand are tightly balanced. Some of the reasons for tightening supplies were reviewed. It was predicted that U.S. gasoline demand will continue to grow in the near future. Gasoline demand has not declined as expected because new vehicles are not any more fuel efficient today than they were a decade ago. Although federally-mandated fuel efficiency standards were designed to lower gasoline consumption, they may actually have prevented consumption from falling. Atlantic margins were predicted to continue moving up because of the supply and demand evidence: high capacity utilization rates, low operating inventories, limited capacity addition resulting from lower capital spending, continued U.S. gasoline demand growth, and steady total oil demand growth. 11 figs

  5. Refining intra-protein contact prediction by graph analysis

    Eyal Eran

    2007-05-01

    Full Text Available Abstract Background Accurate prediction of intra-protein residue contacts from sequence information will allow the prediction of protein structures. Basic predictions of such specific contacts can be further refined by jointly analyzing predicted contacts, and by adding information on the relative positions of contacts in the protein primary sequence. Results We introduce a method for graph analysis refinement of intra-protein contacts, termed GARP. Our previously presented intra-contact prediction method by means of pair-to-pair substitution matrix (P2PConPred was used to test the GARP method. In our approach, the top contact predictions obtained by a basic prediction method were used as edges to create a weighted graph. The edges were scored by a mutual clustering coefficient that identifies highly connected graph regions, and by the density of edges between the sequence regions of the edge nodes. A test set of 57 proteins with known structures was used to determine contacts. GARP improves the accuracy of the P2PConPred basic prediction method in whole proteins from 12% to 18%. Conclusion Using a simple approach we increased the contact prediction accuracy of a basic method by 1.5 times. Our graph approach is simple to implement, can be used with various basic prediction methods, and can provide input for further downstream analyses.

  6. Verifying large modular systems using iterative abstraction refinement

    Lahtinen, Jussi; Kuismin, Tuomas; Heljanko, Keijo

    2015-01-01

    Digital instrumentation and control (I&C) systems are increasingly used in the nuclear engineering domain. The exhaustive verification of these systems is challenging, and the usual verification methods such as testing and simulation are typically insufficient. Model checking is a formal method that is able to exhaustively analyse the behaviour of a model against a formally written specification. If the model checking tool detects a violation of the specification, it will give out a counter-example that demonstrates how the specification is violated in the system. Unfortunately, sometimes real life system designs are too big to be directly analysed by traditional model checking techniques. We have developed an iterative technique for model checking large modular systems. The technique uses abstraction based over-approximations of the model behaviour, combined with iterative refinement. The main contribution of the work is the concrete abstraction refinement technique based on the modular structure of the model, the dependency graph of the model, and a refinement sampling heuristic similar to delta debugging. The technique is geared towards proving properties, and outperforms BDD-based model checking, the k-induction technique, and the property directed reachability algorithm (PDR) in our experiments. - Highlights: • We have developed an iterative technique for model checking large modular systems. • The technique uses BDD-based model checking, k-induction, and PDR in parallel. • We have tested our algorithm by verifying two models with it. • The technique outperforms classical model checking methods in our experiments

  7. Petroleum refining industry in China

    Walls, W.D.

    2010-01-01

    The oil refining industry in China has faced rapid growth in oil imports of increasingly sour grades of crude with which to satisfy growing domestic demand for a slate of lighter and cleaner finished products sold at subsidized prices. At the same time, the world petroleum refining industry has been moving from one that serves primarily local and regional markets to one that serves global markets for finished products, as world refining capacity utilization has increased. Globally, refined product markets are likely to experience continued globalization until refining investments significantly expand capacity in key demand regions. We survey the oil refining industry in China in the context of the world market for heterogeneous crude oils and growing world trade in refined petroleum products. (author)

  8. A Structural Analysis Method Formulation for Fault-tolerant Control System Design

    Izadi-Zamanabadi, Roozbeh; Staroswiecki, M

    2000-01-01

    An analysis of structural model representation has been used to extract available inherent redundant information in the system. The paper presents a refined structured model representation based on bipartite directed graph definition and the necessary condition for sensor fusion based...... on the structural observability is proposed...

  9. Structural health monitoring system/method using electroactive polymer fibers

    Scott-Carnell, Lisa A. (Inventor); Siochi, Emilie J. (Inventor)

    2013-01-01

    A method for monitoring the structural health of a structure of interest by coupling one or more electroactive polymer fibers to the structure and monitoring the electroactive responses of the polymer fiber(s). Load changes that are experienced by the structure cause changes in the baseline responses of the polymer fiber(s). A system for monitoring the structural health of the structure is also provided.

  10. Speculative Carryover: An Empirical Examination of the U.S. Refined Copper Market

    Walter N. Thurman

    1988-01-01

    This article develops and estimates an empirically tractable model of equilibrium storage. The method bridges the gap between theoretical rational expectations models and applied commodity market work. The application to the U.S. refined copper market provides estimates of structural supply and demand, rational price forecasts, and the risk of copper storage that is consistent with modern portfolio theory.

  11. Method for preventing micromechanical structures from adhering to another object

    Smith, J.H.; Ricco, A.J.

    1998-06-16

    A method for preventing micromechanical structures from adhering to another object includes the step of immersing a micromechanical structure and its associated substrate in a chemical species that does not stick to itself. The method can be employed during the manufacture of micromechanical structures to prevent micromechanical parts from sticking or adhering to one another and their associated substrate surface. 3 figs.

  12. Developments of the neutron scattering analysis method for the determination of magnetic structures

    Park, Je-Geun; Chung, Jae Gwan; Park, Jung Hwan; Kong, Ung Girl [Inha Univ., Incheon (Korea); So, Ji Yong [Seoul National University, Seoul(Korea)

    2001-04-01

    Neutron diffraction is up to now almost the only and very important experimental method of determining the magnetic structure of materials. Unlike the studies of crystallographic structure, however to use neutron diffraction for magnetic structure determination is not easily accessible to non-experts because of the complexity of magnetic group theory: which is very important in the magnetic structure analysis. With the recent development of computer code for magnetic group, it is now time to rethink of these difficulties. In this work, we have used the computer code of the magnetic group (Mody-2) and Fullprof refinement program in order to study the magnetic structure of YMnO{sub 3} and other interesting materials. YMnO{sub 3} forms in the hexagonal structure and show both ferroelectric and antiferromagnetic phase transitions. Since it was recently found that YMnO{sub 3} can be used as a nonvolatile memory device, there has been many numbers of applied research on this material. We used neutron diffraction to determine the magnetic structure, and, in particular, to investigate the correlation between the order parameters of the ferroelectric and antiferromagnetic phase transitions. From this study, we have demonstrated that with a proper use of the computer code of the magnetic group one can overcome most of difficulties arising from the magnetic group theory. 4 refs., 8 figs., 5 tabs. (Author)

  13. Materials refining on the Moon

    Landis, Geoffrey A.

    2007-05-01

    Oxygen, metals, silicon, and glass are raw materials that will be required for long-term habitation and production of structural materials and solar arrays on the Moon. A process sequence is proposed for refining these materials from lunar regolith, consisting of separating the required materials from lunar rock with fluorine. The fluorine is brought to the Moon in the form of potassium fluoride, and is liberated from the salt by electrolysis in a eutectic salt melt. Tetrafluorosilane produced by this process is reduced to silicon by a plasma reduction stage; the fluorine salts are reduced to metals by reaction with metallic potassium. Fluorine is recovered from residual MgF and CaF2 by reaction with K2O.

  14. On Syntactic and Semantic Action Refinement

    Goltz, Ursula; Gorrieri, Roberto; Rensink, Arend

    1992-01-01

    The semantic definition of action refinement on labelled event structures is compared with the notion of syntactic substitution,which can be used as another notion of action refiment in a process algebraic setting. This is done by studying a process algebra equipped with the ACP sequential

  15. Robust Refinement as Implemented in TOPAS

    Stone, K.; Stephens, P

    2010-01-01

    A robust refinement procedure is implemented in the program TOPAS through an iterative reweighting of the data. Examples are given of the procedure as applied to fitting partially overlapped peaks by full and partial models and also of the structures of ibuprofen and acetaminophen in the presence of unmodeled impurity contributions

  16. A refinement methodology for object-oriented programs

    Tafat , Asma; Boulmé , Sylvain; Marché , Claude

    2010-01-01

    International audience; Refinement is a well-known approach for developing correct-byconstruction software. It has been very successful for producing high quality code e.g., as implemented in the B tool. Yet, such refinement techniques are restricted in the sense that they forbid aliasing (and more generally sharing of data-structures), which often happens in usual programming languages. We propose a sound approach for refinement in presence of aliases. Suitable abstractions of programs are d...

  17. Preparation of Al-Ti-B grain refiner by SHS technology

    Nikitin, V.I.; Wanqi, J.I.E.; Kandalova, E.G.; Makarenko, A.G.; Yong, L.

    2000-01-01

    Since the discovery of the grain refinement effect of aluminum by titanium, especially with the existence of B or C in 1950, grain refiners are widely accepted in industry for microstructure control of aluminum alloys. Research on this topic is to obtain the highest grain refinement efficiency with the lowest possible addition of master alloy. It is widely accepted that the morphology and size of TiAl 3 particles, which are known as heterogeneous nucleation centers, are important factors deterring the grain refinement efficiency. Fine TiAl 3 particles are favorable. The grain refinement process shows a heredity phenomenon, which means that structural information from initial materials transfers through a melt to the final product. It is important to find the connection between microstructural parameters of the master alloy and the final product. To improve the quality of Al-Ti-B master alloys for the use as a grain refiner, a new method based on SHS (self-propagating high-temperature synthesis) technology has been developed in Samara State Technical University to produce the master alloys. SHS, as a new method for preparation of materials, was first utilized by Merzhanov in 1967. This method uses the energy from highly exothermic reactions to sustain the chemical reaction in a combustion wave. The advantages of SHS include simplicity, low energy requirement, and higher product purity. Because SHS reactions can take place between elemental reactants, it is easy to control product composition. The purposes of this investigation were to fabricate an SHS Al-5%Ti-1%B master alloy, to analyze its structure and to test its grain refining performance

  18. Structuring Consumer Preferences with the SEM Method

    Rosa, Franco

    2002-01-01

    Structuring preferences has been developed with econometric models using functional flexible parametric form and the exploring the perceptions about expressed and latent needs using different multivariate approaches. Purpose of this research is to explore the demand for a new drink using the mean-end chain (MEC) theory and multivariate SEM procedure. The first part is dedicated to description of specialty foods for their capacity to create new niche markets. The MEC theory is introduced to ex...

  19. Structural refinement and extraction of hydrogen atomic positions in polyoxymethylene crystal based on the first successful measurements of 2-dimensional high-energy synchrotron X-ray diffraction and wide-angle neutron diffraction patterns of hydrogenated and deuterated species

    Tashiro, Kohji; Hanesaka, Makoto; Ohhara, Takashi; Kurihara, Kazuo; Tamada, Taro; Kuroki, Ryota; Fujiwara, Satoru; Ozeki, Tomoji; Kitano, Toshiaki; Nishu, Takashi; Tanaka, Ichiro; Niimura, Nobuo

    2007-01-01

    2-Dimensional X-ray and neutron diffraction patterns have been successfully measured for deuterated and hydrogenated polyoxymethylene (POM) samples obtained by γ-ray induced solid-state polymerization reaction. More than 700 reflections were collected from the X-ray diffraction data at -150degC by utilizing a high-energy synchrotron X-ray beam at SPring-8, Japan, from which the crystal structure of POM has been refined thoroughly including the extraction of hydrogen atomic positions at clearly seen in the difference Fourier synthesis map. As the first trial the nonuniform (9/5) helical model was analyzed with the reliability factor (R factor) 6.9%. The structural analysis was made also using the X-ray reflections of about 400 observed at room temperature (R 8.8%), and the thermal parameters of constituent atoms were compared between the low and high temperatures to discuss the librational thermal motion of the chains. The 2-dimensional neutron diffraction data, collected for the deuterated and hydrogenated POM samples using an imaging plate system specifically built-up for neutron scattering experiment, have allowed us to pick up the D and H atomic positions clearly in the Fourier synthesis maps. Another possible model, (29/16) helix, which was proposed by several researches, has been also investigated on the basis of the X-ray diffraction data at -150degC. The direct method succeeded in extracting this (29/16) model straightforwardly. The R factor was 8.6%, essentially the same as that of (9/5) helical model. This means that the comparison of the diffraction intensity between the data collected from the full-rotation X-ray diffraction pattern and the intensity calculated for both the (9/5) and (29/16) models cannot be used for the unique determination of the superiority of the model, (9/5) or (29/16) helix. However, we have found the existence of 001 and 002 reflections which give the longer repeating period 55.7 A. Besides there observed a series of meridional

  20. An efficicient data structure for three-dimensional vertex based finite volume method

    Akkurt, Semih; Sahin, Mehmet

    2017-11-01

    A vertex based three-dimensional finite volume algorithm has been developed using an edge based data structure.The mesh data structure of the given algorithm is similar to ones that exist in the literature. However, the data structures are redesigned and simplied in order to fit requirements of the vertex based finite volume method. In order to increase the cache efficiency, the data access patterns for the vertex based finite volume method are investigated and these datas are packed/allocated in a way that they are close to each other in the memory. The present data structure is not limited with tetrahedrons, arbitrary polyhedrons are also supported in the mesh without putting any additional effort. Furthermore, the present data structure also supports adaptive refinement and coarsening. For the implicit and parallel implementation of the FVM algorithm, PETSc and MPI libraries are employed. The performance and accuracy of the present algorithm are tested for the classical benchmark problems by comparing the CPU time for the open source algorithms.

  1. Experimental studies of the refined structure within oxide UO{sub 2} clusters (1983); Etudes experimentales de structure fine a l'interieur de grappes d'oxyde UO{sub 2} (1963)

    Palmedo, P F [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1963-07-01

    General measurements of neutron fine structure in various UO{sub 2} clusters are described. The experimental techniques that were found useful are presented, as well as the methods of experimental analysis. The results are given in detail. A semi-empirical relation for the fine structure in clusters is suggested and is compared with the various results. (author) [French] Plusieurs experiences de structure fine de la densite neutronique dans diverses grappes de UO{sub 2} sont decrites. On presente les techniques qui ont ete jugees les plus appropriees pour ce genre de mesure, les methodes d'analyae des experiences, et les resultats detailles. Une expression semi-empirique de la structure fine dans de telles grappes est donnee et elle est comparee avec les divers reaultats obtenue. (auteur)

  2. Uranium refining process using ion exchange membrane

    Yamaguchi, Akira

    1977-01-01

    As for the method of refining uranium ore being carried out in Europe and America at present, uranium ore is roughly refined at the mine sites to yellow cake, then this is transported to refineries and refined by dry method. This method has the following faults, namely the number of processes is large, it requires expensive corrosion-resistant materials because of high temperature treatment, and the impurities in uranium tend to increase. On the other hand, in case of EXCER method, treatment is carried out at low temperature, and high purity uranium can be obtained, but the efficiency of electrolytic reduction process is extremely low, and economically infeasible. In the wet refining method called PNC process, uranium tetrafluoride is produced from uranium ore without making yellow cake, therefore the process is rationalized largely, and highly economical. The electrolytic reduction process in this method was developed by Asahi Chemical Industry Co., Ltd. by constructing the pilot plant in Ningyotoge Mine. The ion exchange membrane, the electrodes, and the problems concerning the process and the engineering for commercial plants were investigated. The electrolytic reduction process, the pilot plant, the development of the elements of electrolytic cells, the establishment of analytical process, the measurement of the electrolytic characteristics, the demonstration operation, and the life time of the electrolytic diaphragm are reported. (Kako, I.)

  3. Crystal structure refinement, dielectric and magnetic properties of Ca/Pb substituted SrFe{sub 12}O{sub 19} hexaferrites

    Hooda, Ashima [Department of Physics, Deenbandhu Chhotu Ram University of Science and Technology, Murthal 131039, Haryana (India); Sanghi, Sujata, E-mail: sutkash@yahoo.com [Department of Applied Physics, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana (India); Agarwal, Ashish [Department of Applied Physics, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana (India); Dahiya, Reetu [Department of Physics, Hindu Girls College, Sonepat 131001, Haryana (India)

    2015-08-01

    SrFe{sub 12}O{sub 19} (SFO), Sr{sub 0.5}Ca{sub 0.5}Fe{sub 12}O{sub 19} (SCFO) and Sr{sub 0.5}Pb{sub 0.5}Fe{sub 12}O{sub 19} (SPFO) hexaferrites have been synthesized by a conventional solid state reaction technique. Powder X-ray diffraction and Rietveld refinement confirm the presence of M-type hexagonal phase in prepared samples. However in SCFO, secondary phase was also present with main phase. Analysis of Nyquist's plots of SFO hexaferrite revealed the contribution of many electrically active regions corresponding to bulk mechanism, distribution of grain boundaries and electrode processes also. Both conductivity and electric modulus formalisms have been employed to study the relaxation dynamics of charge carriers. A perfect overlapping of the normalized plots of modulus isotherms on a single ‘super curve’ for all the studied temperatures reveals a temperature independence of dynamic processes involved in conduction and for relaxation. In SPFO sample coercivity is reduced effectively but accompanied with increase in magnetization, which is requirement for hexaferrites to be used as magnetic recording media. - Highlights: • Samples have hexagonal phase with space group P6{sub 3}/mmc. • SPFO hexaferrite may be used for microwave devices. • SPFO hexaferrite may be used for magnetic recording media.

  4. Comparative study on the welded structure fatigue strength assessment method

    Hu, Tao

    2018-04-01

    Due to the welding structure is widely applied in various industries, especially the pressure container, motorcycle, automobile, aviation, ship industry, such as large crane steel structure, so for welded structure fatigue strength evaluation is particularly important. For welded structure fatigue strength evaluation method mainly has four kinds of, the more from the use of two kinds of welded structure fatigue strength evaluation method, namely the nominal stress method and the hot spot stress evaluation method, comparing from its principle, calculation method for the process analysis and research, compare the similarities and the advantages and disadvantages, the analysis of practical engineering problems to provide the reference for every profession and trade, as well as the future welded structure fatigue strength and life evaluation method put forward outlook.

  5. Linear Prediction Using Refined Autocorrelation Function

    M. Shahidur Rahman

    2007-07-01

    Full Text Available This paper proposes a new technique for improving the performance of linear prediction analysis by utilizing a refined version of the autocorrelation function. Problems in analyzing voiced speech using linear prediction occur often due to the harmonic structure of the excitation source, which causes the autocorrelation function to be an aliased version of that of the vocal tract impulse response. To estimate the vocal tract characteristics accurately, however, the effect of aliasing must be eliminated. In this paper, we employ homomorphic deconvolution technique in the autocorrelation domain to eliminate the aliasing effect occurred due to periodicity. The resulted autocorrelation function of the vocal tract impulse response is found to produce significant improvement in estimating formant frequencies. The accuracy of formant estimation is verified on synthetic vowels for a wide range of pitch frequencies typical for male and female speakers. The validity of the proposed method is also illustrated by inspecting the spectral envelopes of natural speech spoken by high-pitched female speaker. The synthesis filter obtained by the current method is guaranteed to be stable, which makes the method superior to many of its alternatives.

  6. An adaptive grid refinement strategy for the simulation of negative streamers

    Montijn, C.; Hundsdorfer, W.; Ebert, U.

    2006-01-01

    The evolution of negative streamers during electric breakdown of a non-attaching gas can be described by a two-fluid model for electrons and positive ions. It consists of continuity equations for the charged particles including drift, diffusion and reaction in the local electric field, coupled to the Poisson equation for the electric potential. The model generates field enhancement and steep propagating ionization fronts at the tip of growing ionized filaments. An adaptive grid refinement method for the simulation of these structures is presented. It uses finite volume spatial discretizations and explicit time stepping, which allows the decoupling of the grids for the continuity equations from those for the Poisson equation. Standard refinement methods in which the refinement criterion is based on local error monitors fail due to the pulled character of the streamer front that propagates into a linearly unstable state. We present a refinement method which deals with all these features. Tests on one-dimensional streamer fronts as well as on three-dimensional streamers with cylindrical symmetry (hence effectively 2D for numerical purposes) are carried out successfully. Results on fine grids are presented, they show that such an adaptive grid method is needed to capture the streamer characteristics well. This refinement strategy enables us to adequately compute negative streamers in pure gases in the parameter regime where a physical instability appears: branching streamers

  7. Protein homology model refinement by large-scale energy optimization.

    Park, Hahnbeom; Ovchinnikov, Sergey; Kim, David E; DiMaio, Frank; Baker, David

    2018-03-20

    Proteins fold to their lowest free-energy structures, and hence the most straightforward way to increase the accuracy of a partially incorrect protein structure model is to search for the lowest-energy nearby structure. This direct approach has met with little success for two reasons: first, energy function inaccuracies can lead to false energy minima, resulting in model degradation rather than improvement; and second, even with an accurate energy function, the search problem is formidable because the energy only drops considerably in the immediate vicinity of the global minimum, and there are a very large number of degrees of freedom. Here we describe a large-scale energy optimization-based refinement method that incorporates advances in both search and energy function accuracy that can substantially improve the accuracy of low-resolution homology models. The method refined low-resolution homology models into correct folds for 50 of 84 diverse protein families and generated improved models in recent blind structure prediction experiments. Analyses of the basis for these improvements reveal contributions from both the improvements in conformational sampling techniques and the energy function.

  8. Comparing Refinements for Failure and Bisimulation Semantics

    Eshuis, H.; Fokkinga, M.M.

    2002-01-01

    Refinement in bisimulation semantics is defined differently from refinement in failure semantics: in bisimulation semantics refinement is based on simulations between labelled transition systems, whereas in failure semantics refinement is based on inclusions between failure systems. There exist

  9. Development of analysis methods for seismically isolated nuclear structures

    Yoo, Bong; Lee, Jae-Han; Koo, Gyeng-Hoi

    2002-01-01

    KAERI's contributions to the project entitled Development of Analysis Methods for Seismically Isolated Nuclear Structures under IAEA CRP of the intercomparison of analysis methods for predicting the behaviour of seismically isolated nuclear structures during 1996-1999 in effort to develop the numerical analysis methods and to compare the analysis results with the benchmark test results of seismic isolation bearings and isolated nuclear structures provided by participating countries are briefly described. Certain progress in the analysis procedures for isolation bearings and isolated nuclear structures has been made throughout the IAEA CRPs and the analysis methods developed can be improved for future nuclear facility applications. (author)

  10. Structure determinations for Ca3Ti2O7, Ca4Ti3O10, Ca3.6Sr0.4Ti3O10 and a refinement of Sr3Ti2O7

    Elcombe, M.M.; Kisi, E.H.; Hawkins, K.D.; White, T.J.; Goodman, P.; Matheson, S.

    1991-01-01

    The structures of the orthorhombic Ruddlesden-Popper (A n+1 B n X 3n+1 ) phases Ca 3 Ti 2 O 7 (n=2) refined from neutron powder diffraction data at λ=1.893 A. They consist of coherent intergrowths of perovskite (CaTiO 3 ) blocks, n TiO 6 octahedra thick, with single layers of CaO having a distorted NaCl configuration. TiO 6 octahedra are tilted and distorted in a very similar fashion to those in CaTiO 3 (n=∞). This fact was used to determine the space groups of the layered structures. Convergent-beam electron diffraction patterns are best matched by calculations in the above space groups which are thus confirmed. Octahedral tilt angles increase slightly in the sequence n=2, 3, ∞. Strontium addition reduces the octahedral tilt angles because of preferential substitution of Sr on the Ca sites within the perovskite blocks of Ca 4 Ti 3 O 10 . The algorithm used to produce starting models for structure refinements is thought to be generally applicable to Ruddlesden-Popper and possibly other layered perovskite structures. It furnishes the predictions: (a) all n-even compounds in the Ca n+1 Ti n O 3n+1 series will have space group Ccm2 1 , (b) all n-odd compounds in this series will have space group Pcab, (c) all A n+1 B n X 3n+1 series for which the n=∞ end member (ABX 3 ) is isostructural with CaTiO 3 will be isostructural with the compounds reported above (e.g. Ca n+1 Zr n O 3n+1 ). (orig./WL)

  11. Commercial refining in the Mediterranean

    Packer, P.

    1999-01-01

    About 9% of the world's oil refining capacity is on the Mediterranean: some of the world's biggest and most advanced refineries are on Sicily and Sardinia. The Mediterranean refineries are important suppliers to southern Europe and N. Africa. The article discusses commercial refining in the Mediterranean under the headings of (i) historic development, (ii) product demand, (iii) refinery configurations, (iv) refined product trade, (v) financial performance and (vi) future outlook. Although some difficulties are foreseen, refining in the Mediterranean is likely to continue to be important well into the 21st century. (UK)

  12. Chinese refining capacity for Canadian heavy oil

    Bruce, G.W.

    2006-01-01

    This paper discussed China's refining capacity in relation to exports of Canadian heavy oil. Demand for oil is increasing throughout the world, and China is expected to consume 25 per cent of the projected yearly oil supplies. Alberta currently has an estimated 174 billion barrels of recoverable bitumen, and produces 1.06 million barrels per day. Production is expected to increase to 4.5 million barrels per day by the year 2020. Currently bitumen blends are refined and diluted with naphtha and sweet synthetic crude oil. Bitumen is a challenging feedstock for refineries, and requires thermal production methods or gasification processes. Primary conversion into sour synthetic crude is typically followed by hydrocracking and further refining into finished petroleum products. There are currently 50 refineries in China with a 7.4 million barrel per day capacity. Coastal refineries using imported crude oil have a 4 million barrel per day capacity. New facilities are being constructed and existing plants are being upgraded in order to process heavier and more sour crude oils. However, current refining capabilities in Chinese refineries have a limited ability for resid conversion. It was concluded that while China has a refining infrastructure, only refineries on the coast will use oil sands-derived feedstocks. However, there are currently opportunities to design refineries to match future feedstocks. tabs., figs

  13. Zone refining high-purity germanium

    Hubbard, G.S.; Haller, E.E.; Hansen, W.L.

    1977-10-01

    The effects of various parameters on germanium purification by zone refining have been examined. These parameters include the germanium container and container coatings, ambient gas and other operating conditions. Four methods of refining are presented which reproducibly yield 3.5 kg germanium ingots from which high purity (vertical barN/sub A/ - N/sub D/vertical bar less than or equal to2 x 10 10 cm -3 ) single crystals can be grown. A qualitative model involving binary and ternary complexes of Si, O, B, and Al is shown to account for the behavior of impurities at these low concentrations

  14. Method of cutting radioactivated metal structures

    Takimoto, Yoshinori; Sakota, Kotaro; Hamamoto, Noboru; Harada, Keizo.

    1985-01-01

    Purpose: To improve the cutting performance to a level as comparable with that in air, as well as prevent the scattering of the radioactive materials upon cutting to the level as that in water cutting. Method: After igniting a gas cutting torch automatically, water spray by the local water sprayer is started by the actuation of a submerged pump, while a gas cutting manipulator is operated to cut the nuclear reactor pressure vessel. In this way, cutting exhaust gases resulted from the gas cutting torch are water-washed by the spray from the local water sprayer and falls within the nuclear rector pressure vessel in the form of water streams or droplets along the inner wall surface of the pressure vessel. Further, water is fed again to the local water sprayer by the submerged pump. (Kawakami, Y.)

  15. Possibilities and limitations of parametric Rietveld refinement on high pressure data. The case study of LaFeO3

    Etter, Martin; Mueller, Melanie; Dinnebier, Robert E.; Hanfland, Michael

    2014-01-01

    Parametric Rietveld refinement is a powerful technique to apply directly physical or empirical equations to the refinement of in situ powder diffraction data. In order to investigate the possibilities and limitations of parametric Rietveld refinements for high pressure data four competitive crystallographic approaches were used to carry out a full structural investigation of the orthoferrite LaFeO 3 (Pbnm at ambient conditions) under high pressure up to 47 GPa. Approach A with traditional Rietveld refinement using atomic coordinates, Approach B where the Rietveld refinement was done by using the rigid body method, Approach C where symmetry modes were used and Approach D where the newly developed method of the rotational symmetry mode description for a rigid body was used. For all approaches sequential as well as parametric refinements were carried out, confirming a second order phase transition of LaFeO 3 to a higher symmetric phase (space group Ibmm) at around 21.1?GPa and an isostructural first order phase transition at around 38 GPa. Limitations due to non-hydrostatic conditions as well as the possibilities of a direct modeling of phase transitions with parametric Rietveld refinement are discussed in detail. (orig.)

  16. Mirror of the refined topological vertex from a matrix model

    Eynard, B

    2011-01-01

    We find an explicit matrix model computing the refined topological vertex, starting from its representation in terms of plane partitions. We then find the spectral curve of that matrix model, and thus the mirror symmetry of the refined vertex. With the same method we also find a matrix model for the strip geometry, and we find its mirror curve. The fact that there is a matrix model shows that the refined topological string amplitudes also satisfy the remodeling the B-model construction.

  17. Construction of crystal structure prototype database: methods and applications

    Su, Chuanxun; Lv, Jian; Wang, Hui; Wang, Yanchao; Ma, Yanming; Li, Quan; Zhang, Lijun

    2017-01-01

    Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery. (paper)

  18. Construction of crystal structure prototype database: methods and applications.

    Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

    2017-04-26

    Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

  19. A refined method for the calculation of the Non-Methane Volatile Organic Compound emission estimate from Domestic Solvent Usage in Ireland from 1992 to 2014 - A case study for Ireland

    Barry, Stephen; O'Regan, Bernadette

    2016-08-01

    This study describes a new methodology to calculate Non-Methane Volatile Organic Compounds from Domestic Solvent Use including Fungicides over the period 1992-2014. Improved emissions data compiled at a much more refined level can help policy-makers develop more effective policy's to address environmental issues. However, a number of problems were found when member states attempt to use national statistics for Domestic Solvent Use including Fungicides. For instance, EMEP/EEA (2013) provides no guidance regarding which activity data should be used, resulting in emission estimates being potentially inconsistent and un-comparable. Also, previous methods and emission factors described in the EMEP/EEA (2013) guidebook do not exactly match data collected by state agencies. This makes using national statistics difficult. In addition, EMEP/EEA (2013) use broader categories than necessary (e.g. Cosmetics Aerosol/Non Aerosol) to estimate emissions while activity data is available at a more refined level scale (e.g. Personal Cleaning Products, Hair Products, Cosmetics, Deodorants and Perfumes). This can make identifying the drivers of emissions unclear. This study builds upon Tzanidakis et al. (2012) whereby it provides a method for collecting activity data from state statistics, developed country specific emission factors based on a survey of 177 Irish products and importantly, used a new method to account for the volatility of organic compounds found in commonly available domestic solvent containing products. This is the first study to account for volatility based on the characteristics of organic compounds and therefore is considered a more accurate method of accounting for emissions from this emission source. The results of this study can also be used to provide a simple method for other member parties to account for the volatility of organic compounds using sectorial adjustment factors described here. For comparison purposes, emission estimates were calculated using the

  20. Study on structural refinement and electrochemical behaviour of Ba0.5Sr0.5Co0.8Fe0.2O3-δ as cathode materials for intermediate temperature solid oxide fuel cells (IT-SOFC)

    Kautkar, Pranay R.; Shirbhate, Shraddha C.; Acharya, Smita A.

    2018-05-01

    Ba0.5Sr0.5Co0.8Fe0.2O3-δ (BSCF) was prepared by ethylene glycol-citrate combined sol-gel combustion route and calcined at optimized temperature 1050°C. The X-ray Diffraction (XRD) data revealing the crystal purity of BSCF cathode was refined by the Cubic-type structure having the space group Pm-3m by Rietveld analysis. Refined lattice parameter of BSCF cathode is a = 3.9759 Å and unit cell volume is 62.85 (4) Å3, Co/Fe-O bond length from VESTA program figured out to be 1.987 (3) Å. Electron density distribution (EDD) of the unit cell of BSCF cathode shows the bonding feature with oxygen ions, this could represent oxygen vacancies are present in the lattice. These results reflected in electrochemical impedance spectra measurement of symmetric cell. Area of specific resistance (ASR) of the BSCF cathode was found to be 0.17 Ω.cm2 at 700°C and respective activation energy (Ea) 1.15 eV. It shows surface exchange at cathode interface, surface diffusion and self-diffusion happened through Ce0.85Sd0.15O1.95 (SDC15) electrolyte.

  1. Methods for testing the logical structure of plant procedure documents

    Horne, C.P.; Colley, R.; Fahley, J.M.

    1990-01-01

    This paper describes an ongoing EPRI project to investigate computer based methods to improve the development, maintenance, and verification of plant operating procedures. This project began as an evaluation of the applicability of structured software analysis methods to operating procedures. It was found that these methods offer benefits, if procedures are transformed to a structured representation to make them amenable to computer analysis. The next task was to investigate methods to transform procedures into a structured representation. The use of natural language techniques to read and compile the procedure documents appears to be viable for this purpose and supports conformity to guidelines. The final task was to consider possibilities of automated verification methods for procedures. Methods to help verify procedures were defined and information requirements specified. These methods take the structured representation of procedures as input. The software system being constructed in this project is called PASS, standing for Procedures Analysis Software System

  2. Determination of phases of {alpha} - Fe{sub 2}O{sub 3}: SiO{sub 2} compound by the Rietveld refinement

    Palomares S, S.A. [Istituto Materiali Speciali per Elettronica e Magnetismo (MASPEC), Parco Area delle Scienze 37A-43010 Loc. Fontanni, Parma (Italy); Ponce C, S.; Martinez, J.R. [Facultad de Ciencias, Universidad Autonoma de San Luis Potosi, 78000 San Luis Potosi (Mexico); Ruiz, F. [Instituto Potosino de Investigacion Cientifica y Tecnologica, Av. V. Carranza 2025, San Luis Potosi (Mexico)

    2002-07-01

    We use a variation of the Rietveld refinement method to calculate the amorphous content of composites formed by a silica xerogel amorphous matrix and iron particles embedded into. In order to apply the Rietveld refinement to amorphous structures an initial crystalline model is assumed with the same composition as the material to be modelled. In this work we try to refine the structure of compounds using the program MAUD. It is shown how this program can be used to determine the amorphous and crystalline fractions in composites consisting of an amorphous matrix and incorporated iron oxide particles. The analysed compounds underwent different thermal treatments. (Author)

  3. Probabilistic structural analysis methods for space transportation propulsion systems

    Chamis, C. C.; Moore, N.; Anis, C.; Newell, J.; Nagpal, V.; Singhal, S.

    1991-01-01

    Information on probabilistic structural analysis methods for space propulsion systems is given in viewgraph form. Information is given on deterministic certification methods, probability of failure, component response analysis, stress responses for 2nd stage turbine blades, Space Shuttle Main Engine (SSME) structural durability, and program plans. .

  4. Sensitivity Analysis of Structures by Virtual Distortion Method

    Gierlinski, J.T.; Holnicki-Szulc, J.; Sørensen, John Dalsgaard

    1991-01-01

    are used in structural optimization, see Haftka [4]. The recently developed Virtual Distortion Method (VDM) is a numerical technique which offers an efficient approach to calculation of the sensitivity derivatives. This method has been orginally applied to structural remodelling and collapse analysis, see...

  5. Thermodynamic properties and crystal structure refinement of ferricopiapite, coquimbite, rhomboclase, and Fe2(SO4)3(H2O)5

    Majzlan, J.; Navrotsky, A.; McCleskey, R. Blaine; Alpers, Charles N.

    2006-01-01

    Enthalpies of formation of ferricopiapite [nominally Fe4.67(SO4)6(OH)2 (H2O)20]. coquimbite [Fe2(SO4)3(H2O)9], rhomboclase [(H3O)Fe(SO4)2 (H2O)3], and Fe2(SO4)3(H2O)5 were measured by acid (5 N HCl) solution calorimetry. The samples were characterized by wet chemical analyses and synchrotron powder X-ray diffraction (XRD). The refinement of XRD patterns gave lattice parameters, atomic positions, thermal factors, and occupancies of the sites. The calculated formulae differ slightly from the nominal compositions: Fe4.78(SO4)6 (OH)2.34(H2O)20.71 (ferricopiapite), (Fe1.47Al0.53)(SO4)3 (H2O)9.65 (coquimbite), (H3O)1.34Fe(SO4)2.17 (H2O)3.06 (rhomboclase), and Fe2(SO4)3 (H2O)5.03. All thermodynamic data are given per mole of these formulae. The measured standard enthalpies (in kJ/mol) of formation from the elements (crystalline Fe, Al, S, and ideal gases O2 and H2) at T = 298.15 K are -4115.8??4.1 [Fe2(SO4)3 (H2O)5.03], -12045.1??9.2 (ferricopiapite), -5738.4??3.3 (coquimbite), and -3201.1??2.6 (rhomboclase). Standard entropy (S??) was estimated as a sum of entropies of oxide, hydroxide, and sulfate components. The estimated S?? (in J/mol.K) values for the iron sulfates are 488.2 [Fe2(SO4)3 (H2O)5.03], 1449.2 (ferricopiapite), 638.3 (coquimbite), and 380.1 (rhomboclase). The calculated Gibbs free energies of formation (in kJ/mol) are -3499.7??4.2 [Fe2(SO4)3 (H2O)5.03], -10089.8??9.3 (ferricopiapite), -4845.6??3.3 (coquimbite), and -2688.0??2.7 (rhomboclase). These results combined with other available thermodynamic data allow construction of mineral stability diagrams in the FeIII2(SO4)3-FeII SO4-H2O system. One such diagram is provided, indicating that the order of stability of ferric sulfate minerals with decreasing pH in the range of 1.5 to -0.5 is: hydronium jarosite, ferricopiapite, and rhomboclase. ?? 2006 E. Schweizerbart'sche Verlagsbuchhandlung.

  6. Rietveld refinement of the structures of 1.0 C-S-H and 1.5 C-S-H

    Battocchio, Francesco; Monteiro, Paulo J.M.; Wenk, Hans-Rudolf

    2012-01-01

    Low-Q region Rietveld analyses were performed on C-S-H synchrotron XRD patterns, using the software MAUD. Two different crystal structures of tobermorite 11 Å were used as a starting model: monoclinic ordered Merlino tobermorite, and orthorhombic

  7. On Modal Refinement and Consistency

    Nyman, Ulrik; Larsen, Kim Guldstrand; Wasowski, Andrzej

    2007-01-01

    Almost 20 years after the original conception, we revisit several fundamental question about modal transition systems. First, we demonstrate the incompleteness of the standard modal refinement using a counterexample due to Hüttel. Deciding any refinement, complete with respect to the standard...

  8. Modal identification of composite structures using Eigen realization method

    Hamidzadeh, H.R.; Afolabi, D.

    1996-01-01

    Experimental modal analysis has proved to be a useful tool to determine the vibration response of complex composite structures. An accurate method for extracting modal parameters of these type of structures are presented. The method used experimental impulse response of the system as input and provides natural frequencies and damping ratios of a dynamic system. The employed theories are Eigen Realization and Impulse Response methods. The adopted method is superior to other available methods in time and frequency domains. The presented method is proven to provide robustness with respect to measured noise

  9. Endurance time method for Seismic analysis and design of structures

    Estekanchi, H.E.; Vafai, A.; Sadeghazar, M.

    2004-01-01

    In this paper, a new method for performance based earthquake analysis and design has been introduced. In this method, the structure is subjected to accelerograms that impose increasing dynamic demand on the structure with time. Specified damage indexes are monitored up to the collapse level or other performance limit that defines the endurance limit point for the structure. Also, a method for generating standard intensifying accelerograms has been described. Three accelerograms have been generated using this method. Furthermore, the concept of Endurance Time has been described by applying these accelerograms to single and multi degree of freedom linear systems. The application of this method for analysis of complex nonlinear systems has been explained. Endurance Time method provides a uniform approach to seismic analysis and design of complex structures that can be applied in numerical and experimental investigations

  10. New Process for Grain Refinement of Aluminum. Final Report

    Dr. Joseph A. Megy

    2000-09-22

    A new method of grain refining aluminum involving in-situ formation of boride nuclei in molten aluminum just prior to casting has been developed in the subject DOE program over the last thirty months by a team consisting of JDC, Inc., Alcoa Technical Center, GRAS, Inc., Touchstone Labs, and GKS Engineering Services. The Manufacturing process to make boron trichloride for grain refining is much simpler than preparing conventional grain refiners, with attendant environmental, capital, and energy savings. The manufacture of boride grain refining nuclei using the fy-Gem process avoids clusters, salt and oxide inclusions that cause quality problems in aluminum today.

  11. Influence of synthesis method on structural and magnetic properties of cobalt ferrite nanoparticles

    Gyergyek, Saso; Makovec, Darko; Kodre, Alojz; Arcon, Iztok; Jagodic, Marko; Drofenik, Miha

    2010-01-01

    The Co-ferrite nanoparticles having a relatively uniform size distribution around 8 nm were synthesized by three different methods. A simple co-precipitation from aqueous solutions and a co-precipitation in an environment of microemulsions are low temperature methods (50 o C), whereas a thermal decomposition of organo-metallic complexes was performed at elevated temperature of 290 o C. The X-ray diffractometry (XRD) showed spinel structure, and the high-resolution transmission electron microscopy (HRTEM) a good crystallinity of all the nanoparticles. Energy-dispersive X-ray spectroscopy (EDS) showed the composition close to stoichiometric (∼CoFe 2 O 4 ) for both co-precipitated nanoparticles, whereas the nanoparticles prepared by the thermal decomposition were Co-deficient (∼Co 0.6 Fe 2.4 O 4 ). The X-ray absorption near-edge structure (XANES) analysis showed Co valence of 2+ in all the samples, Fe valence 3+ in both co-precipitated samples, but average Fe valence of 2.7+ in the sample synthesized by thermal decomposition. The variations in cation distribution within the spinel lattice were observed by structural refinement of X-ray absorption fine structure (EXAFS). Like the bulk CoFe 2 O 4 , the nanoparticles synthesized at elevated temperature using thermal decomposition displayed inverse spinel structure with the Co ions occupying predominantly octahedral lattice sites, whereas co-precipitated samples showed considerable proportion of cobalt ions occupying tetrahedral sites (nearly 1/3 for the nanoparticles synthesized by co-precipitation from aqueous solutions and almost 1/4 for the nanoparticles synthesized in microemulsions). Magnetic measurements performed at room temperature and at 10 K were in good agreement with the nanoparticles' composition and the cation distribution in their structure. The presented study clearly shows that the distribution of the cations within the spinel lattice of the ferrite nanoparticles, and consequently their magnetic

  12. Mass Spectrometry Coupled Experiments and Protein Structure Modeling Methods

    Lee Sael

    2013-10-01

    Full Text Available With the accumulation of next generation sequencing data, there is increasing interest in the study of intra-species difference in molecular biology, especially in relation to disease analysis. Furthermore, the dynamics of the protein is being identified as a critical factor in its function. Although accuracy of protein structure prediction methods is high, provided there are structural templates, most methods are still insensitive to amino-acid differences at critical points that may change the overall structure. Also, predicted structures are inherently static and do not provide information about structural change over time. It is challenging to address the sensitivity and the dynamics by computational structure predictions alone. However, with the fast development of diverse mass spectrometry coupled experiments, low-resolution but fast and sensitive structural information can be obtained. This information can then be integrated into the structure prediction process to further improve the sensitivity and address the dynamics of the protein structures. For this purpose, this article focuses on reviewing two aspects: the types of mass spectrometry coupled experiments and structural data that are obtainable through those experiments; and the structure prediction methods that can utilize these data as constraints. Also, short review of current efforts in integrating experimental data in the structural modeling is provided.

  13. X-ray and neutron single crystal diffraction on (NH4)3H(SO4)2. II. Refinement of crystal structure of phase II at room temperature

    Reehuis, M.; Wozniak, K.; Dominiak, P.; Smirnov, L.S.; Natkaniec, I.; Baranov, A.I.; Dolbinina, V.V.

    2006-01-01

    The (NH 4 ) 3 H(SO 4 ) 2 is of special interest due to the possible influence of ammonium ions on a series of phase transitions: I => II => III => IV => V => VII. Earlier, the X-ray single crystal diffraction study of phase II of (NH 4 ) 3 H(SO 4 ) 2 showed that the crystal structure of this compound has two crystallographically independent groups of ammonium ions NH 4 (1) and NH 4 (2), but orientational positions of these ammonium ions were not determined exactly. The refinement of NH 4 (1) and NH 4 (2) orientational positions in phase II is carried out with the help of the X-ray and neutron single crystal diffraction study. The analyses of differential Fourier maps of electron charge density and nuclear density point out the possibility of disordering of NH 4 (2) ammonium ions

  14. STRUCTURE OF THE METHOD OF EDUCATION AND ITS PROGNOSTIC FUNCTION

    Azat Minabutdinovich Gaifutdinov

    2018-05-01

    Full Text Available Aim. The article is devoted to a poorly studied issue in the theory of upbringing – the structure of methods of upbringing. The subject of analysis is the content of methods of upbringing. The authors aim to determine the method of strict fixation and description of the method, the main elements of the structure of the method of upbringing and its species. Methodology. The basis of the research is historical and pedagogical analysis, theoretical generalization and interpretation of the results of pedagogical and historical pedagogical research, the method of analogy. Results. Authors, on the basis of studying the content of methods of upbringing, determine the basic elements of their structure: the nature of the actions, the sequence of their implementation, the result of applying the method. A unified approach to the description of methods is proposed, which includes: the goal (the planned results of applying this method of upbringing; initial data (age of students and other features; nature of actions; actions (methods of the method and the sequence of their execution. One of the three main types of the structure of the method of education is determined on the basis of the nature of the method’s actions in practice: linear, cyclic or branching. Practical implications. The results of the research can be applied in the field of pedagogical design and organization of the educational process, scientific and pedagogical search and training of pedagogical personnel.

  15. A sub-structure method for multidimensional integral transport calculations

    Kavenoky, A.; Stankovski, Z.

    1983-03-01

    A new method has been developed for fine structure burn-up calculations of very heterogeneous large size media. It is a generalization of the well-known surface-source method, allowing coupling actual two-dimensional heterogeneous assemblies, called sub-structures. The method has been applied to a rectangular medium, divided into sub-structures, containing rectangular and/or cylindrical fuel, moderator and structure elements. The sub-structures are divided into homogeneous zones. A zone-wise flux expansion is used to formulate a direct collision probability problem within it (linear or flat flux expansion in the rectangular zones, flat flux in the others). The coupling of the sub-structures is performed by making extra assumptions on the currents entering and leaving the interfaces. The accuracies and computing times achieved are illustrated by numerical results on two benchmark problems

  16. Methods and devices for fabricating three-dimensional nanoscale structures

    Rogers, John A.; Jeon, Seokwoo; Park, Jangung

    2010-04-27

    The present invention provides methods and devices for fabricating 3D structures and patterns of 3D structures on substrate surfaces, including symmetrical and asymmetrical patterns of 3D structures. Methods of the present invention provide a means of fabricating 3D structures having accurately selected physical dimensions, including lateral and vertical dimensions ranging from 10s of nanometers to 1000s of nanometers. In one aspect, methods are provided using a mask element comprising a conformable, elastomeric phase mask capable of establishing conformal contact with a radiation sensitive material undergoing photoprocessing. In another aspect, the temporal and/or spatial coherence of electromagnetic radiation using for photoprocessing is selected to fabricate complex structures having nanoscale features that do not extend entirely through the thickness of the structure fabricated.

  17. A method for rapid similarity analysis of RNA secondary structures

    Liu Na

    2006-11-01

    Full Text Available Abstract Background Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures. Results Three sets of real data have been used as input for the example applications. Set I includes the structures from 5S rRNAs. Set II includes the secondary structures from RNase P and RNase MRP. Set III includes the structures from 16S rRNAs. Reasonable phylogenetic trees are derived for these three sets of data by using our method. Moreover, our program runs faster as compared to some existing ones. Conclusion The famous Lempel-Ziv algorithm can efficiently extract the information on repeated patterns encoded in RNA secondary structures and makes our method an alternative to analyze the similarity of RNA secondary structures. This method will also be useful to researchers who are interested in evolutionary analysis.

  18. Validating neural-network refinements of nuclear mass models

    Utama, R.; Piekarewicz, J.

    2018-01-01

    Background: Nuclear astrophysics centers on the role of nuclear physics in the cosmos. In particular, nuclear masses at the limits of stability are critical in the development of stellar structure and the origin of the elements. Purpose: We aim to test and validate the predictions of recently refined nuclear mass models against the newly published AME2016 compilation. Methods: The basic paradigm underlining the recently refined nuclear mass models is based on existing state-of-the-art models that are subsequently refined through the training of an artificial neural network. Bayesian inference is used to determine the parameters of the neural network so that statistical uncertainties are provided for all model predictions. Results: We observe a significant improvement in the Bayesian neural network (BNN) predictions relative to the corresponding "bare" models when compared to the nearly 50 new masses reported in the AME2016 compilation. Further, AME2016 estimates for the handful of impactful isotopes in the determination of r -process abundances are found to be in fairly good agreement with our theoretical predictions. Indeed, the BNN-improved Duflo-Zuker model predicts a root-mean-square deviation relative to experiment of σrms≃400 keV. Conclusions: Given the excellent performance of the BNN refinement in confronting the recently published AME2016 compilation, we are confident of its critical role in our quest for mass models of the highest quality. Moreover, as uncertainty quantification is at the core of the BNN approach, the improved mass models are in a unique position to identify those nuclei that will have the strongest impact in resolving some of the outstanding questions in nuclear astrophysics.

  19. Thermal-chemical Mantle Convection Models With Adaptive Mesh Refinement

    Leng, W.; Zhong, S.

    2008-12-01

    In numerical modeling of mantle convection, resolution is often crucial for resolving small-scale features. New techniques, adaptive mesh refinement (AMR), allow local mesh refinement wherever high resolution is needed, while leaving other regions with relatively low resolution. Both computational efficiency for large- scale simulation and accuracy for small-scale features can thus be achieved with AMR. Based on the octree data structure [Tu et al. 2005], we implement the AMR techniques into the 2-D mantle convection models. For pure thermal convection models, benchmark tests show that our code can achieve high accuracy with relatively small number of elements both for isoviscous cases (i.e. 7492 AMR elements v.s. 65536 uniform elements) and for temperature-dependent viscosity cases (i.e. 14620 AMR elements v.s. 65536 uniform elements). We further implement tracer-method into the models for simulating thermal-chemical convection. By appropriately adding and removing tracers according to the refinement of the meshes, our code successfully reproduces the benchmark results in van Keken et al. [1997] with much fewer elements and tracers compared with uniform-mesh models (i.e. 7552 AMR elements v.s. 16384 uniform elements, and ~83000 tracers v.s. ~410000 tracers). The boundaries of the chemical piles in our AMR code can be easily refined to the scales of a few kilometers for the Earth's mantle and the tracers are concentrated near the chemical boundaries to precisely trace the evolvement of the boundaries. It is thus very suitable for our AMR code to study the thermal-chemical convection problems which need high resolution to resolve the evolvement of chemical boundaries, such as the entrainment problems [Sleep, 1988].

  20. Escherichia coli MltA : MAD phasing and refinement of a tetartohedrally twinned protein crystal structure (vol D61, pg 613, 2005)

    Barends, Thomas R.M.; Jong, René M. de; Straaten, Karin E. van; Thunnissen, Andy-Mark W.H.; Dijkstra, Bauke W.

    Crystals were grown of a mutant form of the bacterial cell-wall maintenance protein MltA that diffracted to 2.15 Å resolution. When phasing with molecular replacement using the native structure failed, selenium MAD was used to obtain initial phases. However, after MAD phasing the crystals were found

  1. Refinement of the concept of uncertainty.

    Penrod, J

    2001-04-01

    To analyse the conceptual maturity of uncertainty; to develop an expanded theoretical definition of uncertainty; to advance the concept using methods of concept refinement; and to analyse congruency with the conceptualization of uncertainty presented in the theory of hope, enduring, and suffering. Uncertainty is of concern in nursing as people experience complex life events surrounding health. In an earlier nursing study that linked the concepts of hope, enduring, and suffering into a single theoretical scheme, a state best described as 'uncertainty' arose. This study was undertaken to explore how this conceptualization fit with the scientific literature on uncertainty and to refine the concept. Initially, a concept analysis using advanced methods described by Morse, Hupcey, Mitcham and colleagues was completed. The concept was determined to be partially mature. A theoretical definition was derived and techniques of concept refinement using the literature as data were applied. The refined concept was found to be congruent with the concept of uncertainty that had emerged in the model of hope, enduring and suffering. Further investigation is needed to explore the extent of probabilistic reasoning and the effects of confidence and control on feelings of uncertainty and certainty.

  2. Local grid refinement for free-surface flow simulations

    van der Plas, Peter

    2017-01-01

    The principal goal of the current study is to explore and investigate the potential of local grid refinement for increasing the numerical efficiency of free-surface flow simulations in a practical context. In this thesis we propose a method for local grid refinement in the free-surface flow model

  3. RBT—A Tool for Building Refined Buneman Trees

    Besenbacher, Søren; Mailund; Westh-Nielsen, Lasse

    2005-01-01

    We have developed a tool implementing an efficient algorithm for refined Buneman tree reconstruction. The algorithm—which has the same complexity as the neighbour-joining method and the (plain) Buneman tree construction—enables refined Buneman tree reconstruction on large taxa sets....

  4. The Scottish Structural Proteomics Facility: targets, methods and outputs

    Oke, Muse; Carter, Lester G; Johnson, Kenneth A

    2010-01-01

    The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report...... reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers...

  5. Electronic structure and magnetic properties of FeWO{sub 4} nanocrystals synthesized by the microwave-hydrothermal method

    Almeida, M.A.P. [INCTMN-DQ-Universidade Federal de Sao Carlos, Sao Carlos, P.O. Box 676, 13565-905, SP (Brazil); Cavalcante, L.S., E-mail: laeciosc@bol.com.br [INCTMN-Universidade Estadual, Paulista, P.O. Box 355, 14801-907, Araraquara, SP (Brazil); Morilla-Santos, C.; Filho, P.N. Lisboa [MAv-Universidade Estadual, Paulista, P.O. Box 473, 17033-360, Bauru, SP (Brazil); Beltran, A.; Andres, J.; Gracia, L. [Department de Quimica Fisica i Analitica, Universitat Jaume I, E-12071 Castello (Spain); Longo, E. [INCTMN-DQ-Universidade Federal de Sao Carlos, Sao Carlos, P.O. Box 676, 13565-905, SP (Brazil); INCTMN-Universidade Estadual, Paulista, P.O. Box 355, 14801-907, Araraquara, SP (Brazil)

    2012-11-15

    This communication reports that FeWO{sub 4} nanocrystals were successfully synthesized by the microwave-hydrothermal method at 443 K for 1 h. The structure and shape of these nanocrystals were characterized by X-ray diffraction, Rietveld refinement, and transmission electron microscopy. The experimental results and first principles calculations were combined to explain the electronic structure and magnetic properties. Experimental data were obtained by magnetization measurements for different applied magnetic fields. Theoretical calculations revealed that magnetic properties of FeWO{sub 4} nanocrystals can be assigned to two magnetic orderings with parallel or antiparallel spins in adjacent chains. These factors are crucial to understanding of competition between ferro- and antiferromagnetic behavior. Highlights: Black-Right-Pointing-Pointer Monophasic FeWO{sub 4} nanocrystals were synthesized by the microwave-hydrothermal method. Black-Right-Pointing-Pointer Rietveld refinement and clusters model for monoclinic structure Black-Right-Pointing-Pointer Magnetic properties of FeWO{sub 4} nanocrystals at different temperatures.

  6. Grain refinement of permanent mold cast copper base alloys. Final report

    Sadayappan, M.; Thomson, J. P.; Elboujdaini, M.; Gu, G. Ping; Sahoo, M.

    2004-04-29

    Grain refinement behavior of copper alloys cast in permanent molds was investigated. This is one of the least studied subjects in copper alloy castings. Grain refinement is not widely practiced for leaded copper alloys cast in sand molds. Aluminum bronzes and high strength yellow brasses, cast in sand and permanent molds, were usually fine grained due to the presence of more than 2% iron. Grain refinement of the most common permanent mold casting alloys, leaded yellow brass and its lead-free replacement EnviroBrass III, is not universally accepted due to the perceived problem of hard spots in finished castings and for the same reason these alloys contain very low amounts of iron. The yellow brasses and Cu-Si alloys are gaining popularity in North America due to their low lead content and amenability for permanent mold casting. These alloys are prone to hot tearing in permanent mold casting. Grain refinement is one of the solutions for reducing this problem. However, to use this technique it is necessary to understand the mechanism of grain refinement and other issues involved in the process. The following issues were studied during this three year project funded by the US Department of Energy and the copper casting industry: (1) Effect of alloying additions on the grain size of Cu-Zn alloys and their interaction with grain refiners; (2) Effect of two grain refining elements, boron and zirconium, on the grain size of four copper alloys, yellow brass, EnviroBrass II, silicon brass and silicon bronze and the duration of their effect (fading); (3) Prediction of grain refinement using cooling curve analysis and use of this method as an on-line quality control tool; (4) Hard spot formation in yellow brass and EnviroBrass due to grain refinement; (5) Corrosion resistance of the grain refined alloys; (6) Transfer the technology to permanent mold casting foundries; It was found that alloying elements such as tin and zinc do not change the grain size of Cu-Zn alloys

  7. Architectural Refinement for the Design of Survivable Systems

    Ellison, Robert

    2001-01-01

    ...; that is, have no central administration and no unified security policy. The survivable architecture refinement is an iterative risk-driven process which adopts the structure of Boehm's Spiral Model Boehm 88...

  8. Three-dimensional protein structure prediction: Methods and computational strategies.

    Dorn, Márcio; E Silva, Mariel Barbachan; Buriol, Luciana S; Lamb, Luis C

    2014-10-12

    A long standing problem in structural bioinformatics is to determine the three-dimensional (3-D) structure of a protein when only a sequence of amino acid residues is given. Many computational methodologies and algorithms have been proposed as a solution to the 3-D Protein Structure Prediction (3-D-PSP) problem. These methods can be divided in four main classes: (a) first principle methods without database information; (b) first principle methods with database information; (c) fold recognition and threading methods; and (d) comparative modeling methods and sequence alignment strategies. Deterministic computational techniques, optimization techniques, data mining and machine learning approaches are typically used in the construction of computational solutions for the PSP problem. Our main goal with this work is to review the methods and computational strategies that are currently used in 3-D protein prediction. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. A new hierarchical method to find community structure in networks

    Saoud, Bilal; Moussaoui, Abdelouahab

    2018-04-01

    Community structure is very important to understand a network which represents a context. Many community detection methods have been proposed like hierarchical methods. In our study, we propose a new hierarchical method for community detection in networks based on genetic algorithm. In this method we use genetic algorithm to split a network into two networks which maximize the modularity. Each new network represents a cluster (community). Then we repeat the splitting process until we get one node at each cluster. We use the modularity function to measure the strength of the community structure found by our method, which gives us an objective metric for choosing the number of communities into which a network should be divided. We demonstrate that our method are highly effective at discovering community structure in both computer-generated and real-world network data.

  10. Refinements of the attending equations for several spectral methods that provide improved quantification of B-carotene and/or lycopene in selected foods

    Developing and maintaining maximal levels of carotenoids in fruits and vegetables that contain them is a concern of the produce industry. Toward this end, reliable methods for quantifying lycopene and B-carotene, two of the major health-enhancing carotenoids, are necessary. The goal of this resear...

  11. Verification of fluid-structure-interaction algorithms through the method of manufactured solutions for actuator-line applications

    Vijayakumar, Ganesh; Sprague, Michael

    2017-11-01

    Demonstrating expected convergence rates with spatial- and temporal-grid refinement is the ``gold standard'' of code and algorithm verification. However, the lack of analytical solutions and generating manufactured solutions presents challenges for verifying codes for complex systems. The application of the method of manufactured solutions (MMS) for verification for coupled multi-physics phenomena like fluid-structure interaction (FSI) has only seen recent investigation. While many FSI algorithms for aeroelastic phenomena have focused on boundary-resolved CFD simulations, the actuator-line representation of the structure is widely used for FSI simulations in wind-energy research. In this work, we demonstrate the verification of an FSI algorithm using MMS for actuator-line CFD simulations with a simplified structural model. We use a manufactured solution for the fluid velocity field and the displacement of the SMD system. We demonstrate the convergence of both the fluid and structural solver to second-order accuracy with grid and time-step refinement. This work was funded by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Wind Energy Technologies Office, under Contract No. DE-AC36-08-GO28308 with the National Renewable Energy Laboratory.

  12. Methods for excluding cliff swallows from nesting on highway structures.

    2009-08-01

    Cliff swallows (Petrochelidon pyrrhonota) are colonially breeding migratory birds that frequently nest on highway : structures. Protected by the Migratory Bird Treaty Act of 1918, nesting control methods cannot harm swallows or active : nests. This c...

  13. 2-(2-Chlorobenzoylimino)-1,3-thiazolidine: structure refinement from neutron diffraction data at 113 K and charge density deformation maps

    Cohen-Addad, C.; Savariault, J.-M.; Lehmann, M.S.

    1981-01-01

    The structure of 2-(2-chlorobenzoylimino)-1,3-thiazolidine, C 10 H 9 ClN 2 OS, has been redetermined by neutron diffraction at 113 K. The space group is P2 1 /c with lattice parameters a = 19.950 (4), b = 7.420 (2), c = 11.566 (3) A, β = 109.10 (3) 0 , Z = 4, Msub(r) = 240.7 and dsub(calc) = 1.52 Mg m -3 . The final R(F 2 ) was 0.045 for 1768 reflections. The structural results show unambiguously that the molecule is found in the imino form with an H atom located near the endocyclic N atom of the thiazolidine group. Based on deformation electron density maps and the interatomic distances it is speculated that the difference in geometry between the two tautomeric forms (imino and amino) is small and that the occurrence of one or the other is strongly dependent on the substituents. A short intramolecular S-O contact of 2.68 A is found and is believed to constitute a very weak bond. (Auth.)

  14. The crystal structure of a coxsackievirus B3-RD variant and a refined 9-angstrom cryo-electron microscopy reconstruction of the virus complexed with decay-accelerating factor (DAF) provide a new footprint of DAF on the virus surface.

    Yoder, Joshua D; Cifuente, Javier O; Pan, Jieyan; Bergelson, Jeffrey M; Hafenstein, Susan

    2012-12-01

    The coxsackievirus-adenovirus receptor (CAR) and decay-accelerating factor (DAF) have been identified as cellular receptors for coxsackievirus B3 (CVB3). The first described DAF-binding isolate was obtained during passage of the prototype strain, Nancy, on rhabdomyosarcoma (RD) cells, which express DAF but very little CAR. Here, the structure of the resulting variant, CVB3-RD, has been solved by X-ray crystallography to 2.74 Å, and a cryo-electron microscopy reconstruction of CVB3-RD complexed with DAF has been refined to 9.0 Å. This new high-resolution structure permits us to correct an error in our previous view of DAF-virus interactions, providing a new footprint of DAF that bridges two adjacent protomers. The contact sites between the virus and DAF clearly encompass CVB3-RD residues recently shown to be required for binding to DAF; these residues interact with DAF short consensus repeat 2 (SCR2), which is known to be essential for virus binding. Based on the new structure, the mode of the DAF interaction with CVB3 differs significantly from the mode reported previously for DAF binding to echoviruses.

  15. A reliable method for the stability analysis of structures ...

    The detection of structural configurations with singular tangent stiffness matrix is essential because they can be unstable. The secondary paths, especially in unstable buckling, can play the most important role in the loss of stability and collapse of the structure. A new method for reliable detection and accurate computation of ...

  16. Matrix Methods for Solving Hartree-Fock Equations in Atomic Structure Calculations and Line Broadening

    Thomas Gomez

    2018-04-01

    Full Text Available Atomic structure of N-electron atoms is often determined by solving the Hartree-Fock equations, which are a set of integro-differential equations. The integral part of the Hartree-Fock equations treats electron exchange, but the Hartree-Fock equations are not often treated as an integro-differential equation. The exchange term is often approximated as an inhomogeneous or an effective potential so that the Hartree-Fock equations become a set of ordinary differential equations (which can be solved using the usual shooting methods. Because the Hartree-Fock equations are an iterative-refinement method, the inhomogeneous term relies on the previous guess of the wavefunction. In addition, there are numerical complications associated with solving inhomogeneous differential equations. This work uses matrix methods to solve the Hartree-Fock equations as an integro-differential equation. It is well known that a derivative operator can be expressed as a matrix made of finite-difference coefficients; energy eigenvalues and eigenvectors can be obtained by using linear-algebra packages. The integral (exchange part of the Hartree-Fock equation can be approximated as a sum and written as a matrix. The Hartree-Fock equations can be solved as a matrix that is the sum of the differential and integral matrices. We compare calculations using this method against experiment and standard atomic structure calculations. This matrix method can also be used to solve for free-electron wavefunctions, thus improving how the atoms and free electrons interact. This technique is important for spectral line broadening in two ways: it improves the atomic structure calculations, and it improves the motion of the plasma electrons that collide with the atom.

  17. Adaptive Mesh Refinement in CTH

    Crawford, David

    1999-01-01

    This paper reports progress on implementing a new capability of adaptive mesh refinement into the Eulerian multimaterial shock- physics code CTH. The adaptivity is block-based with refinement and unrefinement occurring in an isotropic 2:1 manner. The code is designed to run on serial, multiprocessor and massive parallel platforms. An approximate factor of three in memory and performance improvements over comparable resolution non-adaptive calculations has-been demonstrated for a number of problems

  18. Steel refining possibilities in LF

    Dumitru, M. G.; Ioana, A.; Constantin, N.; Ciobanu, F.; Pollifroni, M.

    2018-01-01

    This article presents the main possibilities for steel refining in Ladle Furnace (LF). These, are presented: steelmaking stages, steel refining through argon bottom stirring, online control of the bottom stirring, bottom stirring diagram during LF treatment of a heat, porous plug influence over the argon stirring, bottom stirring porous plug, analysis of porous plugs disposal on ladle bottom surface, bottom stirring simulation with ANSYS, bottom stirring simulation with Autodesk CFD.

  19. Refining mass formulas for astrophysical applications: A Bayesian neural network approach

    Utama, R.; Piekarewicz, J.

    2017-10-01

    Background: Exotic nuclei, particularly those near the drip lines, are at the core of one of the fundamental questions driving nuclear structure and astrophysics today: What are the limits of nuclear binding? Exotic nuclei play a critical role in both informing theoretical models as well as in our understanding of the origin of the heavy elements. Purpose: Our aim is to refine existing mass models through the training of an artificial neural network that will mitigate the large model discrepancies far away from stability. Methods: The basic paradigm of our two-pronged approach is an existing mass model that captures as much as possible of the underlying physics followed by the implementation of a Bayesian neural network (BNN) refinement to account for the missing physics. Bayesian inference is employed to determine the parameters of the neural network so that model predictions may be accompanied by theoretical uncertainties. Results: Despite the undeniable quality of the mass models adopted in this work, we observe a significant improvement (of about 40%) after the BNN refinement is implemented. Indeed, in the specific case of the Duflo-Zuker mass formula, we find that the rms deviation relative to experiment is reduced from σrms=0.503 MeV to σrms=0.286 MeV. These newly refined mass tables are used to map the neutron drip lines (or rather "drip bands") and to study a few critical r -process nuclei. Conclusions: The BNN approach is highly successful in refining the predictions of existing mass models. In particular, the large discrepancy displayed by the original "bare" models in regions where experimental data are unavailable is considerably quenched after the BNN refinement. This lends credence to our approach and has motivated us to publish refined mass tables that we trust will be helpful for future astrophysical applications.

  20. Effect of zirconium addition on welding of aluminum grain refined by titanium

    Zaid, A.I.O.

    2011-01-01

    Aluminum and its alloys solidify in large grains columnar structure which tends to reduce their mechanical behaviour and surface quality. Therefore, they are industrially grain refined by titanium or titanium + boron. Furthermore, aluminum oxidizes in ordinary atmosphere which makes its weldability difficult and weak. Therefore, it is anticipated that the effect of addition of zirconium at a weight percentages of 0.1% (which proved to be an effective grain refiner on the weldability of aluminum grain refined by Ti) is worthwhile investigating. This formed the objective of this research work. In this paper, the effect of zirconium addition at a weight percentage of 0.1%, which corresponds to the peritctic limit on the aluminum-zirconium phase diagram, on the weldability of aluminum grain refined by Ti is investigated. Rolled sheets of commercially pure aluminum, Al grain refined Ti of 3 mm thickness were welded together using Gas Tungsten Arc Welding method (GTAW), formerly known as TIG. A constant air gap was maintained at a constant current level, 30 ampere AC, was used because it removes the oxides of the welding process under the same process parameters. Metallographic examination of weldments of the different combinations of aluminum and its microalloys at the heat affected zone, HAZ, and base metal was carried out and examined for width, porosity, cracks and microhardness. It was found that grain refining of commercially pure aluminum by Ti resulted in enhancement of its weldability. Similarly, addition of zirconium to Al grain refined by Ti resulted in further enhancement of the weldment. Photomicrographs of the HAZ regions are presented and discussed. (author)