Implementation of a parallel protein structure alignment service on cloud.

PubMed

Hung, Che-Lun; Lin, Yaw-Ling

2013-01-01

Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

Implementation of a Parallel Protein Structure Alignment Service on Cloud

PubMed Central

Hung, Che-Lun; Lin, Yaw-Ling

2013-01-01

Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics.

PubMed

Kumar, Avishek; Campitelli, Paul; Thorpe, M F; Ozkan, S Banu

2015-12-01

The most successful protein structure prediction methods to date have been template-based modeling (TBM) or homology modeling, which predicts protein structure based on experimental structures. These high accuracy predictions sometimes retain structural errors due to incorrect templates or a lack of accurate templates in the case of low sequence similarity, making these structures inadequate in drug-design studies or molecular dynamics simulations. We have developed a new physics based approach to the protein refinement problem by mimicking the mechanism of chaperons that rehabilitate misfolded proteins. The template structure is unfolded by selectively (targeted) pulling on different portions of the protein using the geometric based technique FRODA, and then refolded using hierarchically restrained replica exchange molecular dynamics simulations (hr-REMD). FRODA unfolding is used to create a diverse set of topologies for surveying near native-like structures from a template and to provide a set of persistent contacts to be employed during re-folding. We have tested our approach on 13 previous CASP targets and observed that this method of folding an ensemble of partially unfolded structures, through the hierarchical addition of contact restraints (that is, first local and then nonlocal interactions), leads to a refolding of the structure along with refinement in most cases (12/13). Although this approach yields refined models through advancement in sampling, the task of blind selection of the best refined models still needs to be solved. Overall, the method can be useful for improved sampling for low resolution models where certain of the portions of the structure are incorrectly modeled. © 2015 Wiley Periodicals, Inc.

Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment.

PubMed

Khoury, George A; Smadbeck, James; Kieslich, Chris A; Koskosidis, Alexandra J; Guzman, Yannis A; Tamamis, Phanourios; Floudas, Christodoulos A

2017-06-01

Protein structure refinement is the challenging problem of operating on any protein structure prediction to improve its accuracy with respect to the native structure in a blind fashion. Although many approaches have been developed and tested during the last four CASP experiments, a majority of the methods continue to degrade models rather than improve them. Princeton_TIGRESS (Khoury et al., Proteins 2014;82:794-814) was developed previously and utilizes separate sampling and selection stages involving Monte Carlo and molecular dynamics simulations and classification using an SVM predictor. The initial implementation was shown to consistently refine protein structures 76% of the time in our own internal benchmarking on CASP 7-10 targets. In this work, we improved the sampling and selection stages and tested the method in blind predictions during CASP11. We added a decomposition of physics-based and hybrid energy functions, as well as a coordinate-free representation of the protein structure through distance-binning Cα-Cα distances to capture fine-grained movements. We performed parameter estimation to optimize the adjustable SVM parameters to maximize precision while balancing sensitivity and specificity across all cross-validated data sets, finding enrichment in our ability to select models from the populations of similar decoys generated for targets in CASPs 7-10. The MD stage was enhanced such that larger structures could be further refined. Among refinement methods that are currently implemented as web-servers, Princeton_TIGRESS 2.0 demonstrated the most consistent and most substantial net refinement in blind predictions during CASP11. The enhanced refinement protocol Princeton_TIGRESS 2.0 is freely available as a web server at http://atlas.engr.tamu.edu/refinement/. Proteins 2017; 85:1078-1098. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Structure refinement of membrane proteins via molecular dynamics simulations.

PubMed

Dutagaci, Bercem; Heo, Lim; Feig, Michael

2018-07-01

A refinement protocol based on physics-based techniques established for water soluble proteins is tested for membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer and aqueous solvent systems. Snapshots from the simulations were selected based on scoring with either knowledge-based or implicit membrane-based scoring functions and averaged to obtain refined models. The protocol resulted in consistent and significant refinement of the membrane protein structures similar to the performance of refinement methods for soluble proteins. Refinement success was similar between sampling in the presence of lipid bilayers and aqueous solvent but the presence of lipid bilayers may benefit the improvement of lipid-facing residues. Scoring with knowledge-based functions (DFIRE and RWplus) was found to be as good as scoring using implicit membrane-based scoring functions suggesting that differences in internal packing is more important than orientations relative to the membrane during the refinement of membrane protein homology models. © 2018 Wiley Periodicals, Inc.

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

PubMed

Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank

2016-09-26

Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

Improving the accuracy of macromolecular structure refinement at 7 Å resolution.

PubMed

Brunger, Axel T; Adams, Paul D; Fromme, Petra; Fromme, Raimund; Levitt, Michael; Schröder, Gunnar F

2012-06-06

In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models, moving them further away from the true structure and leading to high R(free)-values. In contrast, DEN refinement improved even the most distant starting model as judged by R(free), atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution. Copyright © 2012 Elsevier Ltd. All rights reserved.

Improving virtual screening of G protein-coupled receptors via ligand-directed modeling

PubMed Central

Simms, John; Christopoulos, Arthur; Wootten, Denise

2017-01-01

G protein-coupled receptors (GPCRs) play crucial roles in cell physiology and pathophysiology. There is increasing interest in using structural information for virtual screening (VS) of libraries and for structure-based drug design to identify novel agonist or antagonist leads. However, the sparse availability of experimentally determined GPCR/ligand complex structures with diverse ligands impedes the application of structure-based drug design (SBDD) programs directed to identifying new molecules with a select pharmacology. In this study, we apply ligand-directed modeling (LDM) to available GPCR X-ray structures to improve VS performance and selectivity towards molecules of specific pharmacological profile. The described method refines a GPCR binding pocket conformation using a single known ligand for that GPCR. The LDM method is a computationally efficient, iterative workflow consisting of protein sampling and ligand docking. We developed an extensive benchmark comparing LDM-refined binding pockets to GPCR X-ray crystal structures across seven different GPCRs bound to a range of ligands of different chemotypes and pharmacological profiles. LDM-refined models showed improvement in VS performance over origin X-ray crystal structures in 21 out of 24 cases. In all cases, the LDM-refined models had superior performance in enriching for the chemotype of the refinement ligand. This likely contributes to the LDM success in all cases of inhibitor-bound to agonist-bound binding pocket refinement, a key task for GPCR SBDD programs. Indeed, agonist ligands are required for a plethora of GPCRs for therapeutic intervention, however GPCR X-ray structures are mostly restricted to their inactive inhibitor-bound state. PMID:29131821

KoBaMIN: a knowledge-based minimization web server for protein structure refinement.

PubMed

Rodrigues, João P G L M; Levitt, Michael; Chopra, Gaurav

2012-07-01

The KoBaMIN web server provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on minimization of a knowledge-based potential of mean force. The server can be used to refine either a single protein structure or an ensemble of proteins starting from their unrefined coordinates in PDB format. The refinement method is particularly fast and accurate due to the underlying knowledge-based potential derived from structures deposited in the PDB; as such, the energy function implicitly includes the effects of solvent and the crystal environment. Our server allows for an optional but recommended step that optimizes stereochemistry using the MESHI software. The KoBaMIN server also allows comparison of the refined structures with a provided reference structure to assess the changes brought about by the refinement protocol. The performance of KoBaMIN has been benchmarked widely on a large set of decoys, all models generated at the seventh worldwide experiments on critical assessment of techniques for protein structure prediction (CASP7) and it was also shown to produce top-ranking predictions in the refinement category at both CASP8 and CASP9, yielding consistently good results across a broad range of model quality values. The web server is fully functional and freely available at http://csb.stanford.edu/kobamin.

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

PubMed

Joosten, Robbie P; Salzemann, Jean; Bloch, Vincent; Stockinger, Heinz; Berglund, Ann-Charlott; Blanchet, Christophe; Bongcam-Rudloff, Erik; Combet, Christophe; Da Costa, Ana L; Deleage, Gilbert; Diarena, Matteo; Fabbretti, Roberto; Fettahi, Géraldine; Flegel, Volker; Gisel, Andreas; Kasam, Vinod; Kervinen, Timo; Korpelainen, Eija; Mattila, Kimmo; Pagni, Marco; Reichstadt, Matthieu; Breton, Vincent; Tickle, Ian J; Vriend, Gert

2009-06-01

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

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

PubMed

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

2008-02-01

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

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

PubMed

Zhu, Tong; Zhang, John Z H; He, Xiao

2014-09-14

In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters.

PubMed

Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K

2013-04-01

When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å. Copyright © 2013 Elsevier Inc. All rights reserved.

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.

PubMed

Singharoy, Abhishek; Teo, Ivan; McGreevy, Ryan; Stone, John E; Zhao, Jianhua; Schulten, Klaus

2016-07-07

Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.

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

PubMed Central

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

2016-01-01

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/. PMID:27131371

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

PubMed

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.

Overview of refinement procedures within REFMAC5: utilizing data from different sources.

PubMed

Kovalevskiy, Oleg; Nicholls, Robert A; Long, Fei; Carlon, Azzurra; Murshudov, Garib N

2018-03-01

Refinement is a process that involves bringing into agreement the structural model, available prior knowledge and experimental data. To achieve this, the refinement procedure optimizes a posterior conditional probability distribution of model parameters, including atomic coordinates, atomic displacement parameters (B factors), scale factors, parameters of the solvent model and twin fractions in the case of twinned crystals, given observed data such as observed amplitudes or intensities of structure factors. A library of chemical restraints is typically used to ensure consistency between the model and the prior knowledge of stereochemistry. If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in REFMAC5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. The refinement procedure also generates the `best' weighted electron-density maps, which are useful for further model (re)building. Here, the refinement of macromolecular structures using REFMAC5 and related tools distributed as part of the CCP4 suite is discussed.

Conformational Sampling of a Biomolecular Rugged Energy Landscape.

PubMed

Rydzewski, Jakub; Jakubowski, Rafal; Nicosia, Giuseppe; Nowak, Wieslaw

2018-01-01

The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper, we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of sampling conformations. The method was tested on the x-ray structure and 30 decoys of the mutant of [Leu]Enkephalin, a paradigmatic example of the biomolecular multiple-minima problem. In order to score the refined conformations, we used a standard potential energy function with the OPLSAA force field. The effectiveness of the search was assessed using a variety of methods. The robustness of sampling was checked by the energy yield function which measures quantitatively the number of the peptide decoys residing in an energetic funnel. Furthermore, the potential energy-dependent Pareto fronts were calculated to elucidate dissimilarities between peptide conformations and the native state as observed by x-ray crystallography. Our results showed that the probed potential energy landscape of [Leu]Enkephalin is self-similar on different metric scales and that the local potential energy minima of the peptide decoys are metastable, thus they can be refined to conformations whose potential energy is decreased by approximately 250 kJ/mol.

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

PubMed

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.

Structure resolution by electron diffraction tomography of the complex layered iron-rich Fe-2234-type Sr{sub 5}Fe{sub 6}O{sub 15.4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lepoittevin, Christophe, E-mail: christophe.lepoittevin@neel.cnrs.fr

2016-10-15

The crystal structure of the strontium ferrite Sr{sub 5}Fe{sub 6}O{sub 15.4}, was solved by direct methods on electron diffraction tomography data acquired on a transmission electron microscope. The refined cell parameters are a=27.4047(3) Å, b=5.48590(7) Å and c=42.7442(4) Å in Fm2m symmetry. Its structure is built up from the intergrowth sequence between a quadruple perovskite-type layer with a complex rock-salt (RS)-type block. In the latter iron atoms are found in two different environments : tetragonal pyramid and tetrahedron. The structural model was refined by Rietveld method based on the powder X-ray diffraction pattern. - Highlights: • Complex structure of Sr{submore » 5}Fe{sub 6}O{sub 15.4} solved by electron diffraction tomography. • Observed Fourier maps allow determining missing oxygen atoms in the structure. • Structural model refined from powder X-ray diffraction data. • Intergrowth between quadruple perovskite layer with double rock-salt-type layer.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borbulevych, Oleg Y.; Plumley, Joshua A.; Martin, Roger I.

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)more » 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.« less

GRAIN REFINEMENT OF URANIUM BILLETS

DOEpatents

Lewis, L.

1964-02-25

A method of refining the grain structure of massive uranium billets without resort to forging is described. The method consists in the steps of beta- quenching the billets, annealing the quenched billets in the upper alpha temperature range, and extrusion upset of the billets to an extent sufficient to increase the cross sectional area by at least 5 per cent. (AEC)

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

PubMed Central

Singharoy, Abhishek; Teo, Ivan; McGreevy, Ryan; Stone, John E; Zhao, Jianhua; Schulten, Klaus

2016-01-01

Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services. DOI: http://dx.doi.org/10.7554/eLife.16105.001 PMID:27383269

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

PubMed

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.

Adaptive mesh refinement and load balancing based on multi-level block-structured Cartesian mesh

NASA Astrophysics Data System (ADS)

Misaka, Takashi; Sasaki, Daisuke; Obayashi, Shigeru

2017-11-01

We developed a framework for a distributed-memory parallel computer that enables dynamic data management for adaptive mesh refinement and load balancing. We employed simple data structure of the building cube method (BCM) where a computational domain is divided into multi-level cubic domains and each cube has the same number of grid points inside, realising a multi-level block-structured Cartesian mesh. Solution adaptive mesh refinement, which works efficiently with the help of the dynamic load balancing, was implemented by dividing cubes based on mesh refinement criteria. The framework was investigated with the Laplace equation in terms of adaptive mesh refinement, load balancing and the parallel efficiency. It was then applied to the incompressible Navier-Stokes equations to simulate a turbulent flow around a sphere. We considered wall-adaptive cube refinement where a non-dimensional wall distance y+ near the sphere is used for a criterion of mesh refinement. The result showed the load imbalance due to y+ adaptive mesh refinement was corrected by the present approach. To utilise the BCM framework more effectively, we also tested a cube-wise algorithm switching where an explicit and implicit time integration schemes are switched depending on the local Courant-Friedrichs-Lewy (CFL) condition in each cube.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smart, Oliver S., E-mail: osmart@globalphasing.com; Womack, Thomas O.; Flensburg, Claus

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 thanmore » 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.« less

Conformational Analysis of Free and Bound Retinoic Acid

PubMed Central

Fu, Zheng; Li, Xue; Merz, Kenneth M.

2012-01-01

The conformational profiles of unbound all-trans and 9-cis retinoic acid (RA) have been determined using classical and quantum mechanical calculations. Sixty-six all-trans-RA (ATRA) and forty-eight 9-cis-RA energy minimum conformers were identified via HF/6-31G* geometry optimizations in vacuo. Their relative conformational energies were estimated utilizing the M06, M06-2x and MP2 methods combined with the 6-311+G(d,p), aug-cc-pVDZ and aug-cc-pVTZ basis sets, as well as complete basis set MP2 extrapolations using the latter two basis sets. Single-point energy calculations performed with the M06-2x density functional were found to yield similar results to MP2/CBS for the low-energy retinoic acid conformations. Not unexpectedly, the conformational propensities of retinoic acid were governed by the orientation and arrangement of the torsion angles associated with the polyene tail. We also used previously reported QM/MM X-ray refinement results on four ATRA-protein crystal structures plus one newly refined 9-cis-RA complex (PDB ID 1XDK) in order to investigate the conformational preferences of bound retinoic acid. In the re-refined RA conformers the conjugated double bonds are nearly coplanar, which is consistent with the global minimum identified by the Omega/QM method rather than the corresponding crystallographically determined conformations given in the PDB. Consequently, a 91.3% average reduction of the local strain energy in the gas phase, as well as 92.1% in PCM solvent, was observed using the QM/MM refined structures versus the PDB deposited RA conformations. These results thus demonstrate that our QM/MM X-ray refinement approach can significantly enhance the quality of X-ray crystal structures refined by conventional refinement protocols, thereby providing reliable drug-target structural information for use in structure-based drug discovery applications. PMID:22844234

GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution

PubMed Central

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results. PMID:27493524

[Can the local energy minimization refine the PDB structures of different resolution universally?].

PubMed

Godzi, M G; Gromova, A P; Oferkin, I V; Mironov, P V

2009-01-01

The local energy minimization was statistically validated as the refinement strategy for PDB structure pairs of different resolution. Thirteen pairs of structures with the only difference in resolution were extracted from PDB, and the structures of 11 identical proteins obtained by different X-ray diffraction techniques were represented. The distribution of RMSD value was calculated for these pairs before and after the local energy minimization of each structure. The MMFF94 field was used for energy calculations, and the quasi-Newton method was used for local energy minimization. By comparison of these two RMSD distributions, the local energy minimization was proved to statistically increase the structural differences in pairs so that it cannot be used for refinement purposes. To explore the prospects of complex refinement strategies based on energy minimization, randomized structures were obtained by moving the initial PDB structures as far as the minimized structures had been moved in a multidimensional space of atomic coordinates. For these randomized structures, the RMSD distribution was calculated and compared with that for minimized structures. The significant differences in their mean values proved the energy surface of the protein to have only few minima near the conformations of different resolution obtained by X-ray diffraction for PDB. Some other results obtained by exploring the energy surface near these conformations are also presented. These results are expected to be very useful for the development of new protein refinement strategies based on energy minimization.

Computational methods for global/local analysis

NASA Technical Reports Server (NTRS)

Ransom, Jonathan B.; Mccleary, Susan L.; Aminpour, Mohammad A.; Knight, Norman F., Jr.

1992-01-01

Computational methods for global/local analysis of structures which include both uncoupled and coupled methods are described. In addition, global/local analysis methodology for automatic refinement of incompatible global and local finite element models is developed. Representative structural analysis problems are presented to demonstrate the global/local analysis methods.

Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins.

PubMed

Emperador, Agustí; Orozco, Modesto

2017-03-14

We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.

Mesh Convergence Requirements for Composite Damage Models

NASA Technical Reports Server (NTRS)

Davila, Carlos G.

2016-01-01

The ability of the finite element method to accurately represent the response of objects with intricate geometry and loading renders the finite element method as an extremely versatile analysis technique for structural analysis. Finite element analysis is routinely used in industry to calculate deflections, stress concentrations, natural frequencies, buckling loads, and much more. The method works by discretizing complex problems into smaller, simpler approximations that are valid over small uniform domains. For common analyses, the maximum size of the elements that can be used is often be determined by experience. However, to verify the quality of a solution, analyses with several levels of mesh refinement should be performed to ensure that the solution has converged. In recent years, the finite element method has been used to calculate the resistance of structures, and in particular that of composite structures. A number of techniques such as cohesive zone modeling, the virtual crack closure technique, and continuum damage modeling have emerged that can be used to predict cracking, delaminations, fiber failure, and other composite damage modes that lead to structural collapse. However, damage models present mesh refinement requirements that are not well understood. In this presentation, we examine different mesh refinement issues related to the representation of damage in composite materials. Damage process zone sizes and their corresponding mesh requirements will be discussed. The difficulties of modeling discontinuities and the associated need for regularization techniques will be illustrated, and some unexpected element size constraints will be presented. Finally, some of the difficulties in constructing models of composite structures capable of predicting transverse matrix cracking will be discussed. It will be shown that to predict the initiation and propagation of transverse matrix cracks, their density, and their saturation may require models that are significantly more refined than those that have been contemplated in the past.

3D magnetospheric parallel hybrid multi-grid method applied to planet–plasma interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leclercq, L., E-mail: ludivine.leclercq@latmos.ipsl.fr; Modolo, R., E-mail: ronan.modolo@latmos.ipsl.fr; Leblanc, F.

2016-03-15

We present a new method to exploit multiple refinement levels within a 3D parallel hybrid model, developed to study planet–plasma interactions. This model is based on the hybrid formalism: ions are kinetically treated whereas electrons are considered as a inertia-less fluid. Generally, ions are represented by numerical particles whose size equals the volume of the cells. Particles that leave a coarse grid subsequently entering a refined region are split into particles whose volume corresponds to the volume of the refined cells. The number of refined particles created from a coarse particle depends on the grid refinement rate. In order tomore » conserve velocity distribution functions and to avoid calculations of average velocities, particles are not coalesced. Moreover, to ensure the constancy of particles' shape function sizes, the hybrid method is adapted to allow refined particles to move within a coarse region. Another innovation of this approach is the method developed to compute grid moments at interfaces between two refinement levels. Indeed, the hybrid method is adapted to accurately account for the special grid structure at the interfaces, avoiding any overlapping grid considerations. Some fundamental test runs were performed to validate our approach (e.g. quiet plasma flow, Alfven wave propagation). Lastly, we also show a planetary application of the model, simulating the interaction between Jupiter's moon Ganymede and the Jovian plasma.« less

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.

PubMed

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-09-01

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

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

PubMed

Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît

2015-10-01

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 agreement with the consensus model of the resting state VSD and the spin-spin distance histograms from ESR/DEER experiments on T4 lysozyme are accurately reproduced.

Computational Amide I Spectroscopy for Refinement of Disordered Peptide Ensembles: Maximum Entropy and Related Approaches

NASA Astrophysics Data System (ADS)

Reppert, Michael; Tokmakoff, Andrei

The structural characterization of intrinsically disordered peptides (IDPs) presents a challenging biophysical problem. Extreme heterogeneity and rapid conformational interconversion make traditional methods difficult to interpret. Due to its ultrafast (ps) shutter speed, Amide I vibrational spectroscopy has received considerable interest as a novel technique to probe IDP structure and dynamics. Historically, Amide I spectroscopy has been limited to delivering global secondary structural information. More recently, however, the method has been adapted to study structure at the local level through incorporation of isotope labels into the protein backbone at specific amide bonds. Thanks to the acute sensitivity of Amide I frequencies to local electrostatic interactions-particularly hydrogen bonds-spectroscopic data on isotope labeled residues directly reports on local peptide conformation. Quantitative information can be extracted using electrostatic frequency maps which translate molecular dynamics trajectories into Amide I spectra for comparison with experiment. Here we present our recent efforts in the development of a rigorous approach to incorporating Amide I spectroscopic restraints into refined molecular dynamics structural ensembles using maximum entropy and related approaches. By combining force field predictions with experimental spectroscopic data, we construct refined structural ensembles for a family of short, strongly disordered, elastin-like peptides in aqueous solution.

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

PubMed Central

Christensen, Anders S.; Linnet, Troels E.; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H.

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 QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3 JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding. PMID:24391900

Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement.

PubMed

McCoy, Airlie J; Oeffner, Robert D; Millán, Claudia; Sammito, Massimo; Usón, Isabel; Read, Randy J

2018-04-01

Descriptions are given of the maximum-likelihood gyre method implemented in Phaser for optimizing the orientation and relative position of rigid-body fragments of a model after the orientation of the model has been identified, but before the model has been positioned in the unit cell, and also the related gimble method for the refinement of rigid-body fragments of the model after positioning. Gyre refinement helps to lower the root-mean-square atomic displacements between model and target molecular-replacement solutions for the test case of antibody Fab(26-10) and improves structure solution with ARCIMBOLDO_SHREDDER.

Global/local stress analysis of composite structures. M.S. Thesis

NASA Technical Reports Server (NTRS)

Ransom, Jonathan B.

1989-01-01

A method for performing a global/local stress analysis is described and its capabilities are demonstrated. The method employs spline interpolation functions which satisfy the linear plate bending equation to determine displacements and rotations from a global model which are used as boundary conditions for the local model. Then, the local model is analyzed independent of the global model of the structure. This approach can be used to determine local, detailed stress states for specific structural regions using independent, refined local models which exploit information from less-refined global models. The method presented is not restricted to having a priori knowledge of the location of the regions requiring local detailed stress analysis. This approach also reduces the computational effort necessary to obtain the detailed stress state. Criteria for applying the method are developed. The effectiveness of the method is demonstrated using a classical stress concentration problem and a graphite-epoxy blade-stiffened panel with a discontinuous stiffener.

Adaptive h -refinement for reduced-order models: ADAPTIVE h -refinement for reduced-order models

DOE PAGES

Carlberg, Kevin T.

2014-11-05

Our work presents a method to adaptively refine reduced-order models a posteriori without requiring additional full-order-model solves. The technique is analogous to mesh-adaptive h-refinement: it enriches the reduced-basis space online by ‘splitting’ a given basis vector into several vectors with disjoint support. The splitting scheme is defined by a tree structure constructed offline via recursive k-means clustering of the state variables using snapshot data. This method identifies the vectors to split online using a dual-weighted-residual approach that aims to reduce error in an output quantity of interest. The resulting method generates a hierarchy of subspaces online without requiring large-scale operationsmore » or full-order-model solves. Furthermore, it enables the reduced-order model to satisfy any prescribed error tolerance regardless of its original fidelity, as a completely refined reduced-order model is mathematically equivalent to the original full-order model. Experiments on a parameterized inviscid Burgers equation highlight the ability of the method to capture phenomena (e.g., moving shocks) not contained in the span of the original reduced basis.« less

Improving consensus structure by eliminating averaging artifacts

PubMed Central

KC, Dukka B

2009-01-01

Background Common structural biology methods (i.e., NMR and molecular dynamics) often produce ensembles of molecular structures. Consequently, averaging of 3D coordinates of molecular structures (proteins and RNA) is a frequent approach to obtain a consensus structure that is representative of the ensemble. However, when the structures are averaged, artifacts can result in unrealistic local geometries, including unphysical bond lengths and angles. Results Herein, we describe a method to derive representative structures while limiting the number of artifacts. Our approach is based on a Monte Carlo simulation technique that drives a starting structure (an extended or a 'close-by' structure) towards the 'averaged structure' using a harmonic pseudo energy function. To assess the performance of the algorithm, we applied our approach to Cα models of 1364 proteins generated by the TASSER structure prediction algorithm. The average RMSD of the refined model from the native structure for the set becomes worse by a mere 0.08 Å compared to the average RMSD of the averaged structures from the native structure (3.28 Å for refined structures and 3.36 A for the averaged structures). However, the percentage of atoms involved in clashes is greatly reduced (from 63% to 1%); in fact, the majority of the refined proteins had zero clashes. Moreover, a small number (38) of refined structures resulted in lower RMSD to the native protein versus the averaged structure. Finally, compared to PULCHRA [1], our approach produces representative structure of similar RMSD quality, but with much fewer clashes. Conclusion The benchmarking results demonstrate that our approach for removing averaging artifacts can be very beneficial for the structural biology community. Furthermore, the same approach can be applied to almost any problem where averaging of 3D coordinates is performed. Namely, structure averaging is also commonly performed in RNA secondary prediction [2], which could also benefit from our approach. PMID:19267905

NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.

PubMed

Ryu, Hyojung; Lim, GyuTae; Sung, Bong Hyun; Lee, Jinhyuk

2016-02-15

Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores. NMRe is available at http://psb.kobic.re.kr/nmre/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Simplified and refined structural modeling for economical flutter analysis and design

NASA Technical Reports Server (NTRS)

Ricketts, R. H.; Sobieszczanski, J.

1977-01-01

A coordinated use of two finite-element models of different levels of refinement is presented to reduce the computer cost of the repetitive flutter analysis commonly encountered in structural resizing to meet flutter requirements. One model, termed a refined model (RM), represents a high degree of detail needed for strength-sizing and flutter analysis of an airframe. The other model, called a simplified model (SM), has a relatively much smaller number of elements and degrees-of-freedom. A systematic method of deriving an SM from a given RM is described. The method consists of judgmental and numerical operations to make the stiffness and mass of the SM elements equivalent to the corresponding substructures of RM. The structural data are automatically transferred between the two models. The bulk of analysis is performed on the SM with periodical verifications carried out by analysis of the RM. In a numerical example of a supersonic cruise aircraft with an arrow wing, this approach permitted substantial savings in computer costs and acceleration of the job turn-around.

Protein homology model refinement by large-scale energy optimization.

PubMed

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.

AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra

PubMed Central

Tian, Ye; Schwieters, Charles D.; Opella, Stanley J.; Marassi, Francesca M.

2011-01-01

AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes. PMID:22036904

Mesh Generation via Local Bisection Refinement of Triangulated Grids

DTIC Science & Technology

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

Simplified and refined finite element approaches for determining stresses and internal forces in geometrically nonlinear structural analysis

NASA Technical Reports Server (NTRS)

Robinson, J. C.

1979-01-01

Two methods for determining stresses and internal forces in geometrically nonlinear structural analysis are presented. The simplified approach uses the mid-deformed structural position to evaluate strains when rigid body rotation is present. The important feature of this approach is that it can easily be used with a general-purpose finite-element computer program. The refined approach uses element intrinsic or corotational coordinates and a geometric transformation to determine element strains from joint displacements. Results are presented which demonstrate the capabilities of these potentially useful approaches for geometrically nonlinear structural analysis.

Ultra-high-resolution X-ray structure of proteins.

PubMed

Lecomte, C; Guillot, B; Muzet, N; Pichon-Pesme, V; Jelsch, C

2004-04-01

The constant advances in synchrotron radiation sources and crystallogenesis methods and the impulse of structural genomics projects have brought biocrystallography to a context favorable to subatomic resolution protein and nucleic acid structures. Thus, as soon as such precision can be frequently obtained, the amount of information available in the precise electron density should also be easily and naturally exploited, similarly to the field of small molecule charge density studies. Indeed, the use of a nonspherical model for the atomic electron density in the refinement of subatomic resolution protein structures allows the experimental description of their electrostatic properties. Some methods we have developed and implemented in our multipolar refinement program MoPro for this purpose are presented. Examples of successful applications to several subatomic resolution protein structures, including the 0.66 angstrom resolution human aldose reductase, are described.

Homology‐based hydrogen bond information improves crystallographic structures in the PDB

PubMed Central

van Beusekom, Bart; Touw, Wouter G.; Tatineni, Mahidhar; Somani, Sandeep; Rajagopal, Gunaretnam; Luo, Jinquan; Gilliland, Gary L.; Perrakis, Anastassis

2017-01-01

Abstract The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H‐bond) distances as a source of information. However, H‐bond restraints can improve structures at low resolution where diffraction data are limited. To improve low‐resolution structure refinement, we present methods for deriving H‐bond information either globally from well‐refined high‐resolution structures from the PDB‐REDO databank, or specifically from on‐the‐fly constructed sets of homologous high‐resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low‐resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB‐REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset. PMID:29168245

Homology-based hydrogen bond information improves crystallographic structures in the PDB.

PubMed

van Beusekom, Bart; Touw, Wouter G; Tatineni, Mahidhar; Somani, Sandeep; Rajagopal, Gunaretnam; Luo, Jinquan; Gilliland, Gary L; Perrakis, Anastassis; Joosten, Robbie P

2018-03-01

The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB-REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset. © 2017 The Protein Society.

Arbitrary Lagrangian-Eulerian Method with Local Structured Adaptive Mesh Refinement for Modeling Shock Hydrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, R W; Pember, R B; Elliott, N S

2001-10-22

A new method that combines staggered grid Arbitrary Lagrangian-Eulerian (ALE) techniques with structured local adaptive mesh refinement (AMR) has been developed for solution of the Euler equations. This method facilitates the solution of problems currently at and beyond the boundary of soluble problems by traditional ALE methods by focusing computational resources where they are required through dynamic adaption. Many of the core issues involved in the development of the combined ALEAMR method hinge upon the integration of AMR with a staggered grid Lagrangian integration method. The novel components of the method are mainly driven by the need to reconcile traditionalmore » AMR techniques, which are typically employed on stationary meshes with cell-centered quantities, with the staggered grids and grid motion employed by Lagrangian methods. Numerical examples are presented which demonstrate the accuracy and efficiency of the method.« less

Rietveld refined structural and room temperature vibrational properties of BaTiO3 doped La0.67Ba0.33MnO3 composites

NASA Astrophysics Data System (ADS)

Dar, M. A.; Sheikh, M. W.; Malla, M. S.; Varshney, Dinesh

2016-05-01

The composites of (1-x) La0.67Ba0.33MnO3 (LBMO) + xBaTiO3 (BTO) (x = 0, 0.25 and 1.0) were synthesized by conventional solid-state reaction method. Rietveld refinement was employed to characterize the structural information of the prepared ceramics. The result of the Rietveld refinement of X-ray powder diffraction of La0.67Ba0.33MnO3 and BaTiO3 shows that these compounds crystallize in rhombohedral (R3c) and tetragonal (P4mm), respectively. The structural parameters and the reliability factors for the LBMO-BTO composite ceramics were successfully determined by the Rietveld refinement. At room temperature, Raman active phonon modes predicted by the group theory were observed only in BaTiO3 and composite sample. Pure LBMO does not show any Raman active Phonon mode at room temperature.

A new adaptive mesh refinement strategy for numerically solving evolutionary PDE's

NASA Astrophysics Data System (ADS)

Burgarelli, Denise; Kischinhevsky, Mauricio; Biezuner, Rodney Josue

2006-11-01

A graph-based implementation of quadtree meshes for dealing with adaptive mesh refinement (AMR) in the numerical solution of evolutionary partial differential equations is discussed using finite volume methods. The technique displays a plug-in feature that allows replacement of a group of cells in any region of interest for another one with arbitrary refinement, and with only local changes occurring in the data structure. The data structure is also specially designed to minimize the number of operations needed in the AMR. Implementation of the new scheme allows flexibility in the levels of refinement of adjacent regions. Moreover, storage requirements and computational cost compare competitively with mesh refinement schemes based on hierarchical trees. Low storage is achieved for only the children nodes are stored when a refinement takes place. These nodes become part of a graph structure, thus motivating the denomination autonomous leaves graph (ALG) for the new scheme. Neighbors can then be reached without accessing their parent nodes. Additionally, linear-system solvers based on the minimization of functionals can be easily employed. ALG was not conceived with any particular problem or geometry in mind and can thus be applied to the study of several phenomena. Some test problems are used to illustrate the effectiveness of the technique.

Improved parallel image reconstruction using feature refinement.

PubMed

Cheng, Jing; Jia, Sen; Ying, Leslie; Liu, Yuanyuan; Wang, Shanshan; Zhu, Yanjie; Li, Ye; Zou, Chao; Liu, Xin; Liang, Dong

2018-07-01

The aim of this study was to develop a novel feature refinement MR reconstruction method from highly undersampled multichannel acquisitions for improving the image quality and preserve more detail information. The feature refinement technique, which uses a feature descriptor to pick up useful features from residual image discarded by sparsity constrains, is applied to preserve the details of the image in compressed sensing and parallel imaging in MRI (CS-pMRI). The texture descriptor and structure descriptor recognizing different types of features are required for forming the feature descriptor. Feasibility of the feature refinement was validated using three different multicoil reconstruction methods on in vivo data. Experimental results show that reconstruction methods with feature refinement improve the quality of reconstructed image and restore the image details more accurately than the original methods, which is also verified by the lower values of the root mean square error and high frequency error norm. A simple and effective way to preserve more useful detailed information in CS-pMRI is proposed. This technique can effectively improve the reconstruction quality and has superior performance in terms of detail preservation compared with the original version without feature refinement. Magn Reson Med 80:211-223, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

A multi-block adaptive solving technique based on lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Zhang, Yang; Xie, Jiahua; Li, Xiaoyue; Ma, Zhenghai; Zou, Jianfeng; Zheng, Yao

2018-05-01

In this paper, a CFD parallel adaptive algorithm is self-developed by combining the multi-block Lattice Boltzmann Method (LBM) with Adaptive Mesh Refinement (AMR). The mesh refinement criterion of this algorithm is based on the density, velocity and vortices of the flow field. The refined grid boundary is obtained by extending outward half a ghost cell from the coarse grid boundary, which makes the adaptive mesh more compact and the boundary treatment more convenient. Two numerical examples of the backward step flow separation and the unsteady flow around circular cylinder demonstrate the vortex structure of the cold flow field accurately and specifically.

Adaptively-refined overlapping grids for the numerical solution of systems of hyperbolic conservation laws

NASA Technical Reports Server (NTRS)

Brislawn, Kristi D.; Brown, David L.; Chesshire, Geoffrey S.; Saltzman, Jeffrey S.

1995-01-01

Adaptive mesh refinement (AMR) in conjunction with higher-order upwind finite-difference methods have been used effectively on a variety of problems in two and three dimensions. In this paper we introduce an approach for resolving problems that involve complex geometries in which resolution of boundary geometry is important. The complex geometry is represented by using the method of overlapping grids, while local resolution is obtained by refining each component grid with the AMR algorithm, appropriately generalized for this situation. The CMPGRD algorithm introduced by Chesshire and Henshaw is used to automatically generate the overlapping grid structure for the underlying mesh.

Analysis of multicrystal pump–probe data sets. I. Expressions for the RATIO model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fournier, Bertrand; Coppens, Philip

2014-08-30

The RATIO method in time-resolved crystallography [Coppenset al.(2009).J. Synchrotron Rad.16, 226–230] was developed for use with Laue pump–probe diffraction data to avoid complex corrections due to wavelength dependence of the intensities. The application of the RATIO method in processing/analysis prior to structure refinement requires an appropriate ratio model for modeling the light response. The assessment of the accuracy of pump–probe time-resolved structure refinements based on the observed ratios was discussed in a previous paper. In the current paper, a detailed ratio model is discussed, taking into account both geometric and thermal light-induced changes.

Super-resolution biomolecular crystallography with low-resolution data.

PubMed

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

2010-04-22

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

NASA Langley developments in response calculations needed for failure and life prediction

NASA Technical Reports Server (NTRS)

Housner, Jerrold M.

1993-01-01

NASA Langley developments in response calculations needed for failure and life predictions are discussed. Topics covered include: structural failure analysis in concurrent engineering; accuracy of independent regional modeling demonstrated on classical example; functional interface method accurately joins incompatible finite element models; interface method for insertion of local detail modeling extended to curve pressurized fuselage window panel; interface concept for joining structural regions; motivation for coupled 2D-3D analysis; compression panel with discontinuous stiffener coupled 2D-3D model and axial surface strains at the middle of the hat stiffener; use of adaptive refinement with multiple methods; adaptive mesh refinement; and studies on quantity effect of bow-type initial imperfections on reliability of stiffened panels.

Solution NMR Refinement of a Metal Ion Bound Protein Using Metal Ion Inclusive Restrained Molecular Dynamics Methods

PubMed Central

Chakravorty, Dhruva K.; Wang, Bing; Lee, Chul Won; Guerra, Alfredo J.; Giedroc, David P.; Merz, Kenneth M.

2013-01-01

Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational dynamics in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies. PMID:23609042

Efficient Unstructured Cartesian/Immersed-Boundary Method with Local Mesh Refinement to Simulate Flows in Complex 3D Geometries

NASA Astrophysics Data System (ADS)

de Zelicourt, Diane; Ge, Liang; Sotiropoulos, Fotis; Yoganathan, Ajit

2008-11-01

Image-guided computational fluid dynamics has recently gained attention as a tool for predicting the outcome of different surgical scenarios. Cartesian Immersed-Boundary methods constitute an attractive option to tackle the complexity of real-life anatomies. However, when such methods are applied to the branching, multi-vessel configurations typically encountered in cardiovascular anatomies the majority of the grid nodes of the background Cartesian mesh end up lying outside the computational domain, increasing the memory and computational overhead without enhancing the numerical resolution in the region of interest. To remedy this situation, the method presented here superimposes local mesh refinement onto an unstructured Cartesian grid formulation. A baseline unstructured Cartesian mesh is generated by eliminating all nodes that reside in the exterior of the flow domain from the grid structure, and is locally refined in the vicinity of the immersed-boundary. The potential of the method is demonstrated by carrying out systematic mesh refinement studies for internal flow problems ranging in complexity from a 90 deg pipe bend to an actual, patient-specific anatomy reconstructed from magnetic resonance.

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

PubMed

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 change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift.

An upwind method for the solution of the 3D Euler and Navier-Stokes equations on adaptively refined meshes

NASA Astrophysics Data System (ADS)

Aftosmis, Michael J.

1992-10-01

A new node based upwind scheme for the solution of the 3D Navier-Stokes equations on adaptively refined meshes is presented. The method uses a second-order upwind TVD scheme to integrate the convective terms, and discretizes the viscous terms with a new compact central difference technique. Grid adaptation is achieved through directional division of hexahedral cells in response to evolving features as the solution converges. The method is advanced in time with a multistage Runge-Kutta time stepping scheme. Two- and three-dimensional examples establish the accuracy of the inviscid and viscous discretization. These investigations highlight the ability of the method to produce crisp shocks, while accurately and economically resolving viscous layers. The representation of these and other structures is shown to be comparable to that obtained by structured methods. Further 3D examples demonstrate the ability of the adaptive algorithm to effectively locate and resolve multiple scale features in complex 3D flows with many interacting, viscous, and inviscid structures.

Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems.

PubMed

DiMaio, Frank

2017-01-01

Molecular replacement (MR), a method for solving the crystallographic phase problem using phases derived from a model of the target structure, has proven extremely valuable, accounting for the vast majority of structures solved by X-ray crystallography. However, when the resolution of data is low, or the starting model is very dissimilar to the target protein, solving structures via molecular replacement may be very challenging. In recent years, protein structure prediction methodology has emerged as a powerful tool in model building and model refinement for difficult molecular replacement problems. This chapter describes some of the tools available in Rosetta for model building and model refinement specifically geared toward difficult molecular replacement cases.

A new parallelization scheme for adaptive mesh refinement

DOE PAGES

Loffler, Frank; Cao, Zhoujian; Brandt, Steven R.; ...

2016-05-06

Here, we present a new method for parallelization of adaptive mesh refinement called Concurrent Structured Adaptive Mesh Refinement (CSAMR). This new method offers the lower computational cost (i.e. wall time x processor count) of subcycling in time, but with the runtime performance (i.e. smaller wall time) of evolving all levels at once using the time step of the finest level (which does more work than subcycling but has less parallelism). We demonstrate our algorithm's effectiveness using an adaptive mesh refinement code, AMSS-NCKU, and show performance on Blue Waters and other high performance clusters. For the class of problem considered inmore » this paper, our algorithm achieves a speedup of 1.7-1.9 when the processor count for a given AMR run is doubled, consistent with our theoretical predictions.« less

A new parallelization scheme for adaptive mesh refinement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loffler, Frank; Cao, Zhoujian; Brandt, Steven R.

Here, we present a new method for parallelization of adaptive mesh refinement called Concurrent Structured Adaptive Mesh Refinement (CSAMR). This new method offers the lower computational cost (i.e. wall time x processor count) of subcycling in time, but with the runtime performance (i.e. smaller wall time) of evolving all levels at once using the time step of the finest level (which does more work than subcycling but has less parallelism). We demonstrate our algorithm's effectiveness using an adaptive mesh refinement code, AMSS-NCKU, and show performance on Blue Waters and other high performance clusters. For the class of problem considered inmore » this paper, our algorithm achieves a speedup of 1.7-1.9 when the processor count for a given AMR run is doubled, consistent with our theoretical predictions.« less

The Quality and Validation of Structures from Structural Genomics

PubMed Central

Domagalski, Marcin J.; Zheng, Heping; Zimmerman, Matthew D.; Dauter, Zbigniew; Wlodawer, Alexander; Minor, Wladek

2014-01-01

Quality control of three-dimensional structures of macromolecules is a critical step to ensure the integrity of structural biology data, especially those produced by structural genomics centers. Whereas the Protein Data Bank (PDB) has proven to be a remarkable success overall, the inconsistent quality of structures reveals a lack of universal standards for structure/deposit validation. Here, we review the state-of-the-art methods used in macromolecular structure validation, focusing on validation of structures determined by X-ray crystallography. We describe some general protocols used in the rebuilding and re-refinement of problematic structural models. We also briefly discuss some frontier areas of structure validation, including refinement of protein–ligand complexes, automation of structure redetermination, and the use of NMR structures and computational models to solve X-ray crystal structures by molecular replacement. PMID:24203341

iATTRACT: simultaneous global and local interface optimization for protein-protein docking refinement.

PubMed

Schindler, Christina E M; de Vries, Sjoerd J; Zacharias, Martin

2015-02-01

Protein-protein interactions are abundant in the cell but to date structural data for a large number of complexes is lacking. Computational docking methods can complement experiments by providing structural models of complexes based on structures of the individual partners. A major caveat for docking success is accounting for protein flexibility. Especially, interface residues undergo significant conformational changes upon binding. This limits the performance of docking methods that keep partner structures rigid or allow limited flexibility. A new docking refinement approach, iATTRACT, has been developed which combines simultaneous full interface flexibility and rigid body optimizations during docking energy minimization. It employs an atomistic molecular mechanics force field for intermolecular interface interactions and a structure-based force field for intramolecular contributions. The approach was systematically evaluated on a large protein-protein docking benchmark, starting from an enriched decoy set of rigidly docked protein-protein complexes deviating by up to 15 Å from the native structure at the interface. Large improvements in sampling and slight but significant improvements in scoring/discrimination of near native docking solutions were observed. Complexes with initial deviations at the interface of up to 5.5 Å were refined to significantly better agreement with the native structure. Improvements in the fraction of native contacts were especially favorable, yielding increases of up to 70%. © 2014 Wiley Periodicals, Inc.

Global/local stress analysis of composite panels

NASA Technical Reports Server (NTRS)

Ransom, Jonathan B.; Knight, Norman F., Jr.

1989-01-01

A method for performing a global/local stress analysis is described, and its capabilities are demonstrated. The method employs spline interpolation functions which satisfy the linear plate bending equation to determine displacements and rotations from a global model which are used as boundary conditions for the local model. Then, the local model is analyzed independent of the global model of the structure. This approach can be used to determine local, detailed stress states for specific structural regions using independent, refined local models which exploit information from less-refined global models. The method presented is not restricted to having a priori knowledge of the location of the regions requiring local detailed stress analysis. This approach also reduces the computational effort necessary to obtain the detailed stress state. Criteria for applying the method are developed. The effectiveness of the method is demonstrated using a classical stress concentration problem and a graphite-epoxy blade-stiffened panel with a discontinuous stiffener.

Global/local methods for probabilistic structural analysis

NASA Technical Reports Server (NTRS)

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

1993-01-01

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.

Global/local methods for probabilistic structural analysis

NASA Astrophysics Data System (ADS)

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.

Crystal structure of human tooth enamel studied by neutron diffraction

NASA Astrophysics Data System (ADS)

Ouladdiaf, Bachir; Rodriguez-Carvajal, Juan; Goutaudier, Christelle; Ouladdiaf, Selma; Grosgogeat, Brigitte; Pradelle, Nelly; Colon, Pierre

2015-02-01

Crystal structure of human tooth enamel was investigated using high-resolution neutron powder diffraction. Excellent agreement between observed and refined patterns is obtained, using the hexagonal hydroxyapatite model for the tooth enamel, where a large hydroxyl deficiency ˜70% is found in the 4e site. Rietveld refinements method combined with the difference Fourier maps have revealed, however, that the hydroxyl ions are not only disordered along the c-axis but also within the basal plane. Additional H ions located at the 6h site and forming HPO42- anions were found.

Monitoring the refinement of crystal structures with {sup 15}N solid-state NMR shift tensor data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalakewich, Keyton; Eloranta, Harriet; Harper, James K.

The {sup 15}N chemical shift tensor is shown to be extremely sensitive to lattice structure and a powerful metric for monitoring density functional theory refinements of crystal structures. These refinements include lattice effects and are applied here to five crystal structures. All structures improve based on a better agreement between experimental and calculated {sup 15}N tensors, with an average improvement of 47.0 ppm. Structural improvement is further indicated by a decrease in forces on the atoms by 2–3 orders of magnitude and a greater similarity in atom positions to neutron diffraction structures. These refinements change bond lengths by more thanmore » the diffraction errors including adjustments to X–Y and X–H bonds (X, Y = C, N, and O) of 0.028 ± 0.002 Å and 0.144 ± 0.036 Å, respectively. The acquisition of {sup 15}N tensors at natural abundance is challenging and this limitation is overcome by improved {sup 1}H decoupling in the FIREMAT method. This decoupling dramatically narrows linewidths, improves signal-to-noise by up to 317%, and significantly improves the accuracy of measured tensors. A total of 39 tensors are measured with shifts distributed over a range of more than 400 ppm. Overall, experimental {sup 15}N tensors are at least 5 times more sensitive to crystal structure than {sup 13}C tensors due to nitrogen’s greater polarizability and larger range of chemical shifts.« less

Building Daily 30-meter Spatial Resolution Maps of Surface Water Bodies from MODIS Data Using a Novel Technique for Transferring Information Across Space and Time

NASA Astrophysics Data System (ADS)

Khandelwal, A.; Karpatne, A.; Kumar, V.

2017-12-01

In this paper, we present novel methods for producing surface water maps at 30 meter spatial resolution at a daily temporal resolution. These new methods will make use of the MODIS spectral data from Terra (available daily since 2000) to produce daily maps at 250 meter and 500 meter resolution, and then refine them using the relative elevation ordering of pixels at 30 meter resolution. The key component of these methods is the use of elevation structure (relative elevation ordering) of a water body. Elevation structure is not explicitly available at desired resolution for most water bodies in the world and hence it will be estimated using our previous work that uses the history of imperfect labels. In this paper, we will present a new technique that uses elevation structure (unlike existing pixel based methods) to enforce temporal consistency in surface water extents (lake area on nearby dates is likely to be very similar). This will greatly improve the quality of the MODIS scale land/water labels since daily MODIS data can have a large amount of missing (or poor quality) data due to clouds and other factors. The quality of these maps will be further improved using elevation based resolution refinement approach that will make use of elevation structure estimated at Landsat scale. With the assumption that elevation structure does not change over time, it provides a very effective way to transfer information between datasets even when they are not observed concurrently. In this work, we will derive elevation structure at Landsat scale from monthly water extent maps spanning 1984-2015, publicly available through a joint effort of Google Earth Engine and the European Commission's Joint Research Centre (JRC). This elevation structure will then be used to refine spatial resolution of Modis scale maps from 2000 onwards. We will present the analysis of these methods on a large and diverse set of water bodies across the world.

Automatic extraction of tree crowns from aerial imagery in urban environment

NASA Astrophysics Data System (ADS)

Liu, Jiahang; Li, Deren; Qin, Xunwen; Yang, Jianfeng

2006-10-01

Traditionally, field-based investigation is the main method to investigate greenbelt in urban environment, which is costly and low updating frequency. In higher resolution image, the imagery structure and texture of tree canopy has great similarity in statistics despite the great difference in configurations of tree canopy, and their surface structures and textures of tree crown are very different from the other types. In this paper, we present an automatic method to detect tree crowns using high resolution image in urban environment without any apriori knowledge. Our method catches unique structure and texture of tree crown surface, use variance and mathematical expectation of defined image window to position the candidate canopy blocks coarsely, then analysis their inner structure and texture to refine these candidate blocks. The possible spans of all the feature parameters used in our method automatically generate from the small number of samples, and HOLE and its distribution as an important characteristics are introduced into refining processing. Also the isotropy of candidate image block and holes' distribution is integrated in our method. After introduction the theory of our method, aerial imageries were used ( with a resolution about 0.3m ) to test our method, and the results indicate that our method is an effective approach to automatically detect tree crown in urban environment.

Deformable complex network for refining low-resolution X-ray structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Chong; Wang, Qinghua; Ma, Jianpeng, E-mail: jpma@bcm.edu

2015-10-27

A new refinement algorithm called the deformable complex network that combines a novel angular network-based restraint with a deformable elastic network model in the target function has been developed to aid in structural refinement in macromolecular X-ray crystallography. In macromolecular X-ray crystallography, building more accurate atomic models based on lower resolution experimental diffraction data remains a great challenge. Previous studies have used a deformable elastic network (DEN) model to aid in low-resolution structural refinement. In this study, the development of a new refinement algorithm called the deformable complex network (DCN) is reported that combines a novel angular network-based restraint withmore » the DEN model in the target function. Testing of DCN on a wide range of low-resolution structures demonstrated that it constantly leads to significantly improved structural models as judged by multiple refinement criteria, thus representing a new effective refinement tool for low-resolution structural determination.« less

Protein structure refinement using a quantum mechanics-based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.

PubMed Central

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 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 change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift. PMID:28451325

Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics

PubMed Central

Shevchuk, Roman; Hub, Jochen S.

2017-01-01

Small-angle X-ray scattering is an increasingly popular technique used to detect protein structures and ensembles in solution. However, the refinement of structures and ensembles against SAXS data is often ambiguous due to the low information content of SAXS data, unknown systematic errors, and unknown scattering contributions from the solvent. We offer a solution to such problems by combining Bayesian inference with all-atom molecular dynamics simulations and explicit-solvent SAXS calculations. The Bayesian formulation correctly weights the SAXS data versus prior physical knowledge, it quantifies the precision or ambiguity of fitted structures and ensembles, and it accounts for unknown systematic errors due to poor buffer matching. The method further provides a probabilistic criterion for identifying the number of states required to explain the SAXS data. The method is validated by refining ensembles of a periplasmic binding protein against calculated SAXS curves. Subsequently, we derive the solution ensembles of the eukaryotic chaperone heat shock protein 90 (Hsp90) against experimental SAXS data. We find that the SAXS data of the apo state of Hsp90 is compatible with a single wide-open conformation, whereas the SAXS data of Hsp90 bound to ATP or to an ATP-analogue strongly suggest heterogenous ensembles of a closed and a wide-open state. PMID:29045407

Seamless image stitching by homography refinement and structure deformation using optimal seam pair detection

NASA Astrophysics Data System (ADS)

Lee, Daeho; Lee, Seohyung

2017-11-01

We propose an image stitching method that can remove ghost effects and realign the structure misalignments that occur in common image stitching methods. To reduce the artifacts caused by different parallaxes, an optimal seam pair is selected by comparing the cross correlations from multiple seams detected by variable cost weights. Along the optimal seam pair, a histogram of oriented gradients is calculated, and feature points for matching are detected. The homography is refined using the matching points, and the remaining misalignment is eliminated using the propagation of deformation vectors calculated from matching points. In multiband blending, the overlapping regions are determined from a distance between the matching points to remove overlapping artifacts. The experimental results show that the proposed method more robustly eliminates misalignments and overlapping artifacts than the existing method that uses single seam detection and gradient features.

Evolutionary Optimization of a Geometrically Refined Truss

NASA Technical Reports Server (NTRS)

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

2007-01-01

Structural optimization is a field of research that has experienced noteworthy growth for many years. Researchers in this area have developed optimization tools to successfully design and model structures, typically minimizing mass while maintaining certain deflection and stress constraints. Numerous optimization studies have been performed to minimize mass, deflection, and stress on a benchmark cantilever truss problem. Predominantly traditional optimization theory is applied to this problem. The cross-sectional area of each member is optimized to minimize the aforementioned objectives. This Technical Publication (TP) presents a structural optimization technique that has been previously applied to compliant mechanism design. This technique demonstrates a method that combines topology optimization, geometric refinement, finite element analysis, and two forms of evolutionary computation: genetic algorithms and differential evolution to successfully optimize a benchmark structural optimization problem. A nontraditional solution to the benchmark problem is presented in this TP, specifically a geometrically refined topological solution. The design process begins with an alternate control mesh formulation, multilevel geometric smoothing operation, and an elastostatic structural analysis. The design process is wrapped in an evolutionary computing optimization toolset.

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.

2015-07-28

A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation–libration–screw refinement strategies produce unique diffuse intensity patterns. Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling andmore » validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls-as-xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

Analysis of macromolecules, ligands and macromolecule-ligand complexes

DOEpatents

Von Dreele, Robert B [Los Alamos, NM

2008-12-23

A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.

Single-crystal growth, structure refinement and the properties of Bis(glycine) Strontium Chloride

NASA Astrophysics Data System (ADS)

Balaji, S. R.; Balu, T.; Rajasekaran, T. R.

2018-02-01

Single crystals of Bis (glycine) Strontium Chloride (BGSC) were grown by means of slow evaporation process by using analar grade Glycine and Strontium Chloride Hexahydrate as a parent compound from its aqueous solution at room temperature. The final chemical composition, [{{Sr}}{({{{C}}}2{{{H}}}5{{{NO}}}2)}2{{{Cl}}}2].{{{H}}}4{{{O}}}3+{{{H}}}8{{{O}}}3, formed were metallic light colorless block, about the size of 28 mm × 9 mm × 8 mm. A single-crystal x-ray diffraction study revealed an ordered superstructure with orthorhombic symmetry that could be assigned to the space group Pbcn. The structure in BGSC, revealed in the electron density distribution was analyzed by the direct methods (SHELXS-2014) and refined by least squares full matrix method (SHELXL-2014). The crystal structure, including anisotropic atomic displacement parameters for each atom and isotropic atomic displacement parameters for hydrogen atom, was refined to R1 = 0.0395, wR2 = 0.0776 using 1097 independent reflections. The FTIR spectrum of BGSC confirms the protonation of amino groups and the different molecular groups present in BGSC vibrate in different modes. Reverse Indentation Size Effect (RISE) was revealed in BGSC in the micro-hardness analysis using Vicker’s micro-hardness analysis. DTA and DSC results ruled out the possibility of structural change independent of mass change. The AFM studies shows fine nano size fiber like structure of the grown crystals.

Concrete Model Checking with Abstract Matching and Refinement

NASA Technical Reports Server (NTRS)

Pasareanu Corina S.; Peianek Radek; Visser, Willem

2005-01-01

We propose an abstraction-based model checking method which relies on refinement of an under-approximation of the feasible behaviors of the system under analysis. The method preserves errors to safety properties, since all analyzed behaviors are feasible by definition. The method does not require an abstract transition relation to he generated, but instead executes the concrete transitions while storing abstract versions of the concrete states, as specified by a set of abstraction predicates. For each explored transition. the method checks, with the help of a theorem prover, whether there is any loss of precision introduced by abstraction. The results of these checks are used to decide termination or to refine the abstraction, by generating new abstraction predicates. If the (possibly infinite) concrete system under analysis has a finite bisimulation quotient, then the method is guaranteed to eventually explore an equivalent finite bisimilar structure. We illustrate the application of the approach for checking concurrent programs. We also show how a lightweight variant can be used for efficient software testing.

An adaptive mesh refinement-multiphase lattice Boltzmann flux solver for simulation of complex binary fluid flows

NASA Astrophysics Data System (ADS)

Yuan, H. Z.; Wang, Y.; Shu, C.

2017-12-01

This paper presents an adaptive mesh refinement-multiphase lattice Boltzmann flux solver (AMR-MLBFS) for effective simulation of complex binary fluid flows at large density ratios. In this method, an AMR algorithm is proposed by introducing a simple indicator on the root block for grid refinement and two possible statuses for each block. Unlike available block-structured AMR methods, which refine their mesh by spawning or removing four child blocks simultaneously, the present method is able to refine its mesh locally by spawning or removing one to four child blocks independently when the refinement indicator is triggered. As a result, the AMR mesh used in this work can be more focused on the flow region near the phase interface and its size is further reduced. In each block of mesh, the recently proposed MLBFS is applied for the solution of the flow field and the level-set method is used for capturing the fluid interface. As compared with existing AMR-lattice Boltzmann models, the present method avoids both spatial and temporal interpolations of density distribution functions so that converged solutions on different AMR meshes and uniform grids can be obtained. The proposed method has been successfully validated by simulating a static bubble immersed in another fluid, a falling droplet, instabilities of two-layered fluids, a bubble rising in a box, and a droplet splashing on a thin film with large density ratios and high Reynolds numbers. Good agreement with the theoretical solution, the uniform-grid result, and/or the published data has been achieved. Numerical results also show its effectiveness in saving computational time and virtual memory as compared with computations on uniform meshes.

NASA/Howard University Large Space Structures Institute

NASA Technical Reports Server (NTRS)

Broome, T. H., Jr.

1984-01-01

Basic research on the engineering behavior of large space structures is presented. Methods of structural analysis, control, and optimization of large flexible systems are examined. Topics of investigation include the Load Correction Method (LCM) modeling technique, stabilization of flexible bodies by feedback control, mathematical refinement of analysis equations, optimization of the design of structural components, deployment dynamics, and the use of microprocessors in attitude and shape control of large space structures. Information on key personnel, budgeting, support plans and conferences is included.

Protein structure modeling and refinement by global optimization in CASP12.

PubMed

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.

Large Eddy simulation of compressible flows with a low-numerical dissipation patch-based adaptive mesh refinement method

NASA Astrophysics Data System (ADS)

Pantano, Carlos

2005-11-01

We describe a hybrid finite difference method for large-eddy simulation (LES) of compressible flows with a low-numerical dissipation scheme and structured adaptive mesh refinement (SAMR). Numerical experiments and validation calculations are presented including a turbulent jet and the strongly shock-driven mixing of a Richtmyer-Meshkov instability. The approach is a conservative flux-based SAMR formulation and as such, it utilizes refinement to computational advantage. The numerical method for the resolved scale terms encompasses the cases of scheme alternation and internal mesh interfaces resulting from SAMR. An explicit centered scheme that is consistent with a skew-symmetric finite difference formulation is used in turbulent flow regions while a weighted essentially non-oscillatory (WENO) scheme is employed to capture shocks. The subgrid stresses and transports are calculated by means of the streched-vortex model, Misra & Pullin (1997)

a Study of the Synchrotron Laue Method for Quantitative Crystal Structure Analysis.

NASA Astrophysics Data System (ADS)

Gomez de Anderez, Dora M.

1990-01-01

Available from UMI in association with The British Library. Quantitative crystal structure analyses have been carried out on small molecule crystals using synchrotron radiation and the Laue method. A variety of single crystal structure determinations and associated refinements are used and compared with the monochromatic analyses. The new molecular structure of 7-amino-5-bromo -4-methyl-2-oxo-1,2,3,4-tetrahidro-1, 6 -naphthyridine-8-carbonitrile (C_{10 }H_9ON_4 Br.H_2O) has been determined, first using monochromatic Mo Kalpha radiation and a four-circle diffractometer, then using synchrotron Laue diffraction photography. The structure refinements showed a R-factor of 4.97 and 14.0% for the Mo Kalpha and Laue data respectively. The molecular structure of (S)-2-chloro-2-fluoro-N-((S)-1-phenylethyl) ethanamide, (C_{10}H _{11}ClFNO), has been determined using the same crystal throughout for X-ray monochromatic analyses (Mo Kalpha and Cu K alpha) followed by synchrotron Laue data collection. The Laue and monochromatic data compare favourably. The R -factors (on F) were 6.23, 6.45 and 8.19% for the Mo K alpha, Cu Kalpha and Laue data sets respectively. The molecular structure of 3-(5-hydroxy-3-methyl-1-phenylpyrazol-4-yl)-1,3-diphenyl -prop- 2-en-1-one, (C_{25 }H_{20}N _2O_2) has been determined using the synchrotron Laue method. The results compare very well with Mo Kalpha monochromatic data. The R-factors (on F) were 4.60 and 5.29% for Mo Kalpha and Laue analysis respectively. The Laue method is assessed in locating the 20 hydrogen atoms in this structure. The structure analysis of the benzil compound ((C_6H_5 O.CO_2)) is carried out using the synchrotron Laue method firstly at room temperature and secondly at low temperature -114 ^circC. The structure shows an R-factor (on F) of 13.06% and 6.85% for each data set respectively. The synchrotron Laue method was used to collect data for ergocalciferol (Vitamin D_2). The same crystal was also used to record oscillation data with the synchrotron radiation monochromatic beam. A new molecular structure of (Dinitrato-(N,N ^'-dimethylethylene-diamine)copper(II)) has been determined using Mo Kalpha radiation on a four circle diffractometer. The refinement resulted in an R-factor (on F) of 4.06%.

A Study of the Synchrotron Laue Method for Quantitative Crystal Structure Analysis

NASA Astrophysics Data System (ADS)

Gomez de Anderez, Dora M.

1990-01-01

Quantitative crystal structure analyses have been carried out on small molecule crystals using synchrotron radiation and the Laue method. A variety of single crystal structure determinations and associated refinements are used and compared with the monochromatic analyses. The new molecular structure of 7-amino-5-bromo -4-methyl-2-oxo-1,2,3,4 -tetrahidro-1,6 -naphthyridine-8-carbonitrile (C_{10 }H_9ON_4 BrcdotH_2O) has been determined, first using monochromatic Mo K alpha radiation and a four-circle diffractometer, then using synchrotron Laue diffraction photography. The structure refinements showed an R-factor of 4.97 and 14.0% for the Mo Kalpha and Laue data respectively. The molecular structure of (S)-2-chloro-2-fluoro-N-((S)-1-phenylethyl) ethanamide, (C_{10}H _{11}ClFNO), has been determined using the same crystal throughout for X-ray monochromatic analyses (Mo Kalpha and Cu K alpha) followed by synchrotron Laue data collection. The Laue and monochromatic data compare favourably. The R -factors (on F) were 6.23, 6.45 and 8.19% for the Mo K alpha, Cu Kalpha and Laue data sets respectively. The molecular structure of 3-(5-hydroxy-3-methyl-1-phenylpyrazol-4-yl)-1,3-diphenyl -prop-2-en-1-one, (C_{25}H _{20}N_2 O_2) has been determined using the synchrotron Laue method. The results compare very well with Mo Kalpha monochromatic data. The R-factors (on F) were 4.60 and 5.29% for Mo Kalpha and Laue analyses respectively. The Laue method is assessed in locating the 20 hydrogen atoms in this structure. The structure analyses of the benzil compound ((C_6H_5 OcdotCO_2)) is carried out using the synchrotron Laue method firstly at room temperature and secondly at low temperature. The structure shows an R-factor (on F) of 13.06% and 6.85% for each data set respectively. The synchrotron Laue method was used to collect data for ergocalciferol (Vitamin D_2). The same crystal was also used to record oscillation data with the synchrotron radiation monochromatic beam. A new molecular structure of (Dinitrato-(N,N ^'-dimethylethylene-diamine)copper(II)) has been determined using Mo Kalpha radiation on a four circle diffractometer. The refinement resulted in an R-factor (on F) of 4.06%.

Invariant 2D object recognition using the wavelet transform and structured neural networks

NASA Astrophysics Data System (ADS)

Khalil, Mahmoud I.; Bayoumi, Mohamed M.

1999-03-01

This paper applies the dyadic wavelet transform and the structured neural networks approach to recognize 2D objects under translation, rotation, and scale transformation. Experimental results are presented and compared with traditional methods. The experimental results showed that this refined technique successfully classified the objects and outperformed some traditional methods especially in the presence of noise.

Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.

PubMed

Pawlak, Tomasz; Potrzebowski, Marek J

2014-03-27

This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.

Crystal structure of the heptamolybdate(VI) (paramolybdate) ion, [Mo7O24]6-, in the ammonium and potassium tetrahydrate salts

USGS Publications Warehouse

Evans, H.T.; Gatehouse, B.M.; Leverett, P.

1975-01-01

The crystal structures of the isomorphous salts MI6 [Mo7O24],4H2O (M = NH4 or K) have been refined by three-dimensional X-ray diffraction methods. Unit cell dimensions of these monoclinic compounds, space group P21/C with Z = 4, are, ammonium salt: a = 8.3934 ?? 0.0008, b = 36.1703 ?? 0.0045, c = 10.4715 ?? 0.0011 A??, ?? = 115.958?? ?? 0.008??; and potassium salt: a = 8.15 ?? 0.02, b = 35.68 ?? 0.1, c = 10.30 ?? 0.02 A??, ?? = 115.2?? ?? 02??. By use of multiple Weissenberg patterns, 8197 intensity data (Mo-K?? radiation) for the ammonium compound and 2178 (Cu-K?? radiation) for the potassium compound were estimated visually and used to test and refine Lindqvist's proposed structure in the space group P21/c. Lindqvist's structure was confirmed and the full matrix least-squares isotropic refinement led to R 0.076 (ammonium) 0.120 (potassium), with direct unambiguous location of the cations and water molecules in the potassium compound.

Solidification Based Grain Refinement in Steels

DTIC Science & Technology

2009-07-24

pearlite (See Figure 1). No evidence of the as-cast austenite dendrite structure was observed. The gating system for this sample resides at the thermal...possible nucleating compounds. 3) Extend grain refinement theory and solidification knowledge through experimental data. 4) Determine structure ...refine the structure of a casting through heat treatment. The energy required for grain refining via thermomechanical processes or heat treatment

On Correspondence of BRST-BFV, Dirac, and Refined Algebraic Quantizations of Constrained Systems

NASA Astrophysics Data System (ADS)

Shvedov, O. Yu.

2002-11-01

The correspondence between BRST-BFV, Dirac, and refined algebraic (group averaging, projection operator) approaches to quantizing constrained systems is analyzed. For the closed-algebra case, it is shown that the component of the BFV wave function corresponding to maximal (minimal) value of number of ghosts and antighosts in the Schrodinger representation may be viewed as a wave function in the refined algebraic (Dirac) quantization approach. The Giulini-Marolf group averaging formula for the inner product in the refined algebraic quantization approach is obtained from the Batalin-Marnelius prescription for the BRST-BFV inner product, which should be generally modified due to topological problems. The considered prescription for the correspondence of states is observed to be applicable to the open-algebra case. The refined algebraic quantization approach is generalized then to the case of nontrivial structure functions. A simple example is discussed. The correspondence of observables for different quantization methods is also investigated.

Tertiary structure prediction and identification of druggable pocket in the cancer biomarker – Osteopontin-c

PubMed Central

2014-01-01

Background Osteopontin (Eta, secreted sialoprotein 1, opn) is secreted from different cell types including cancer cells. Three splice variant forms namely osteopontin-a, osteopontin-b and osteopontin-c have been identified. The main astonishing feature is that osteopontin-c is found to be elevated in almost all types of cancer cells. This was the vital point to consider it for sequence analysis and structure predictions which provide ample chances for prognostic, therapeutic and preventive cancer research. Methods Osteopontin-c gene sequence was determined from Breast Cancer sample and was translated to protein sequence. It was then analyzed using various software and web tools for binding pockets, docking and druggability analysis. Due to the lack of homological templates, tertiary structure was predicted using ab-initio method server – I-TASSER and was evaluated after refinement using web tools. Refined structure was compared with known bone sialoprotein electron microscopic structure and docked with CD44 for binding analysis and binding pockets were identified for drug designing. Results Signal sequence of about sixteen amino acid residues was identified using signal sequence prediction servers. Due to the absence of known structures of similar proteins, three dimensional structure of osteopontin-c was predicted using I-TASSER server. The predicted structure was refined with the help of SUMMA server and was validated using SAVES server. Molecular dynamic analysis was carried out using GROMACS software. The final model was built and was used for docking with CD44. Druggable pockets were identified using pocket energies. Conclusions The tertiary structure of osteopontin-c was predicted successfully using the ab-initio method and the predictions showed that osteopontin-c is of fibrous nature comparable to firbronectin. Docking studies showed the significant similarities of QSAET motif in the interaction of CD44 and osteopontins between the normal and splice variant forms of osteopontins and binding pockets analyses revealed several pockets which paved the way to the identification of a druggable pocket. PMID:24401206

A multistage motion vector processing method for motion-compensated frame interpolation.

PubMed

Huang, Ai- Mei; Nguyen, Truong Q

2008-05-01

In this paper, a novel, low-complexity motion vector processing algorithm at the decoder is proposed for motion-compensated frame interpolation or frame rate up-conversion. We address the problems of having broken edges and deformed structures in an interpolated frame by hierarchically refining motion vectors on different block sizes. Our method explicitly considers the reliability of each received motion vector and has the capability of preserving the structure information. This is achieved by analyzing the distribution of residual energies and effectively merging blocks that have unreliable motion vectors. The motion vector reliability information is also used as a prior knowledge in motion vector refinement using a constrained vector median filter to avoid choosing identical unreliable one. We also propose using chrominance information in our method. Experimental results show that the proposed scheme has better visual quality and is also robust, even in video sequences with complex scenes and fast motion.

Reconstruction of three-dimensional grain structure in polycrystalline iron via an interactive segmentation method

NASA Astrophysics Data System (ADS)

Feng, Min-nan; Wang, Yu-cong; Wang, Hao; Liu, Guo-quan; Xue, Wei-hua

2017-03-01

Using a total of 297 segmented sections, we reconstructed the three-dimensional (3D) structure of pure iron and obtained the largest dataset of 16254 3D complete grains reported to date. The mean values of equivalent sphere radius and face number of pure iron were observed to be consistent with those of Monte Carlo simulated grains, phase-field simulated grains, Ti-alloy grains, and Ni-based super alloy grains. In this work, by finding a balance between automatic methods and manual refinement, we developed an interactive segmentation method to segment serial sections accurately in the reconstruction of the 3D microstructure; this approach can save time as well as substantially eliminate errors. The segmentation process comprises four operations: image preprocessing, breakpoint detection based on mathematical morphology analysis, optimized automatic connection of the breakpoints, and manual refinement by artificial evaluation.

Bayesian ensemble refinement by replica simulations and reweighting.

PubMed

Hummer, Gerhard; Köfinger, Jürgen

2015-12-28

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.

Bayesian ensemble refinement by replica simulations and reweighting

NASA Astrophysics Data System (ADS)

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.

Evaluation of a Didactic Method for the Active Learning of Greedy Algorithms

ERIC Educational Resources Information Center

Esteban-Sánchez, Natalia; Pizarro, Celeste; Velázquez-Iturbide, J. Ángel

2014-01-01

An evaluation of the educational effectiveness of a didactic method for the active learning of greedy algorithms is presented. The didactic method sets students structured-inquiry challenges to be addressed with a specific experimental method, supported by the interactive system GreedEx. This didactic method has been refined over several years of…

Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination.

PubMed

Millán, Claudia; Sammito, Massimo Domenico; McCoy, Airlie J; Nascimento, Andrey F Ziem; Petrillo, Giovanna; Oeffner, Robert D; Domínguez-Gil, Teresa; Hermoso, Juan A; Read, Randy J; Usón, Isabel

2018-04-01

Macromolecular structures can be solved by molecular replacement provided that suitable search models are available. Models from distant homologues may deviate too much from the target structure to succeed, notwithstanding an overall similar fold or even their featuring areas of very close geometry. Successful methods to make the most of such templates usually rely on the degree of conservation to select and improve search models. ARCIMBOLDO_SHREDDER uses fragments derived from distant homologues in a brute-force approach driven by the experimental data, instead of by sequence similarity. The new algorithms implemented in ARCIMBOLDO_SHREDDER are described in detail, illustrating its characteristic aspects in the solution of new and test structures. In an advance from the previously published algorithm, which was based on omitting or extracting contiguous polypeptide spans, model generation now uses three-dimensional volumes respecting structural units. The optimal fragment size is estimated from the expected log-likelihood gain (LLG) values computed assuming that a substructure can be found with a level of accuracy near that required for successful extension of the structure, typically below 0.6 Å root-mean-square deviation (r.m.s.d.) from the target. Better sampling is attempted through model trimming or decomposition into rigid groups and optimization through Phaser's gyre refinement. Also, after model translation, packing filtering and refinement, models are either disassembled into predetermined rigid groups and refined (gimble refinement) or Phaser's LLG-guided pruning is used to trim the model of residues that are not contributing signal to the LLG at the target r.m.s.d. value. Phase combination among consistent partial solutions is performed in reciprocal space with ALIXE. Finally, density modification and main-chain autotracing in SHELXE serve to expand to the full structure and identify successful solutions. The performance on test data and the solution of new structures are described.

Quantitative Analysis of the Morphology of {101} and {001} Faceted Anatase TiO 2 Nanocrystals and Its Implication on Photocatalytic Activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Jue; Olds, Daniel; Peng, Rui

The atomistic structure and morphology (shape and size) of nanomaterials have strong influences on their physical and chemical properties. However, many characterization techniques focus exclusively on one length-scale regime or another when developing quantitative morphology/structural models. In this article, we demonstrate that powder X-ray diffraction and neutron pair distribution function (PDF) can be used to obtain accurate average morphology and atomistic structure of {001} and {101} faceted anatase TiO 2 nanocrystals based on differential evolution refinements using Debye scattering equation calculations. It is also demonstrated that the morphology polydispersity of TiO 2 nanocrystals can be effectively obtained from the diffractionmore » data via a numerical refinement routine. The morphology refinement results are in good agreement with those from transmission electron microscopy and the modeling of small angle neutron scattering data. This method is successfully used to quantify the facet-specified photocatalytic hydrogen evolution activity of anatase TiO 2 nanocrystals with different {001} to {101} ratios. It is found that the sample with an intermediate amount of both {001} and {101} facets shows the best photocatalytic hydrogen evolution reaction (HER) activity. It is expected that the simultaneous structure and morphology refinement technique can be generally used to study the relationship between morphology and functionality of nanomaterials.« less

Quantitative Analysis of the Morphology of {101} and {001} Faceted Anatase TiO 2 Nanocrystals and Its Implication on Photocatalytic Activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Jue; Olds, Daniel; Peng, Rui

The atomistic structure and morphology (shape and size) of nanomaterials have strong influences on their physical and chemical properties. However, many characterization techniques focus exclusively on one length-scale regime or another when developing quantitative morphology/structural models. In this article, we demonstrate that powder X-ray diffraction and neutron pair distribution function (PDF) can be used to obtain accurate average morphology and atomistic structure of {001} and {101} faceted anatase TiO 2 nanocrystals based on differential evolution refinements using Debye scattering equation calculations. It is also demonstrated that the morphology polydispersity of TiO 2 nanocrystals can be effectively obtained from the diffractionmore » data via a numerical refinement routine. The morphology refinement results are in good agreement with those from transmission electron microscopy and the modeling of small angle neutron scattering data. This method is successfully used to quantify the facet-specified photocatalytic hydrogen evolution activity of anatase TiO 2 nanocrystals with different {001} to {101} ratios. It is found that the sample with an intermediate amount of both {001} and {101} facets shows the best photocatalytic hydrogen evolution reaction (HER) activity. As a result, it is expected that the simultaneous structure and morphology refinement technique can be generally used to study the relationship between morphology and functionality of nanomaterials.« less

Quantitative Analysis of the Morphology of {101} and {001} Faceted Anatase TiO 2 Nanocrystals and Its Implication on Photocatalytic Activity

DOE PAGES

Liu, Jue; Olds, Daniel; Peng, Rui; ...

2017-06-14

The atomistic structure and morphology (shape and size) of nanomaterials have strong influences on their physical and chemical properties. However, many characterization techniques focus exclusively on one length-scale regime or another when developing quantitative morphology/structural models. In this article, we demonstrate that powder X-ray diffraction and neutron pair distribution function (PDF) can be used to obtain accurate average morphology and atomistic structure of {001} and {101} faceted anatase TiO 2 nanocrystals based on differential evolution refinements using Debye scattering equation calculations. It is also demonstrated that the morphology polydispersity of TiO 2 nanocrystals can be effectively obtained from the diffractionmore » data via a numerical refinement routine. The morphology refinement results are in good agreement with those from transmission electron microscopy and the modeling of small angle neutron scattering data. This method is successfully used to quantify the facet-specified photocatalytic hydrogen evolution activity of anatase TiO 2 nanocrystals with different {001} to {101} ratios. It is found that the sample with an intermediate amount of both {001} and {101} facets shows the best photocatalytic hydrogen evolution reaction (HER) activity. As a result, it is expected that the simultaneous structure and morphology refinement technique can be generally used to study the relationship between morphology and functionality of nanomaterials.« less

Rietveld analysis of the effect of annealing atmosphere on phase evolution of nanocrystalline TiO2 powders.

PubMed

Salari, M; Rezaee, M; Chidembo, A T; Konstantinov, K; Liu, H K

2012-06-01

The structural evolution of nanocrystalline TiO2 was studied by X-ray diffraction (XRD) and the Rietveld refinement method (RRM). TiO2 powders were prepared by the sol-gel technique. Post annealing of as-synthesized powders in the temperature range from 500 degrees C to 800 degrees C under air and argon atmospheres led to the formation of TiO2 nanoparticles with mean crystallite size in the range of 37-165 nm, based on the Rietveld refinement results. It was found that the phase structure, composition, and crystallite size of the resulting particles were dependent on not only the annealing temperature, but also the annealing atmosphere. Rietveld refinement of the XRD data showed that annealing the powders under argon atmosphere promoted the polymorphic phase transformation from anatase to rutile. Field emission scanning electron microscopy (FESEM) was employed to investigate the morphology and size of the annealed powders.

Figuring Out Gas in Galaxies In Enzo (FOGGIE): Resolving the Inner Circumgalactic Medium

NASA Astrophysics Data System (ADS)

Corlies, Lauren; Peeples, Molly; Tumlinson, Jason; O'Shea, Brian; Smith, Britton

2018-01-01

Cosmological hydrodynamical simulations using every common numerical method have struggled to reproduce the multiphase nature of the circumgalactic medium (CGM) revealed by recent observations. However, to date, resolution in these simulations has been aimed at dense regions — the galactic disk and in-falling satellites — while the diffuse CGM never reaches comparable levels of refinement. Taking advantage of the flexible grid structure of the adaptive mesh refinement code Enzo, we force refinement in a region of the CGM of a Milky Way-like galaxy to the same spatial resolution as that of the disk. In this talk, I will present how the physical and structural distributions of the circumgalactic gas change dramatically as a function of the resolution alone. I will also show the implications these changes have for the observational properties of the gas in the context of the observations.

Iterative feature refinement for accurate undersampled MR image reconstruction

NASA Astrophysics Data System (ADS)

Wang, Shanshan; Liu, Jianbo; Liu, Qiegen; Ying, Leslie; Liu, Xin; Zheng, Hairong; Liang, Dong

2016-05-01

Accelerating MR scan is of great significance for clinical, research and advanced applications, and one main effort to achieve this is the utilization of compressed sensing (CS) theory. Nevertheless, the existing CSMRI approaches still have limitations such as fine structure loss or high computational complexity. This paper proposes a novel iterative feature refinement (IFR) module for accurate MR image reconstruction from undersampled K-space data. Integrating IFR with CSMRI which is equipped with fixed transforms, we develop an IFR-CS method to restore meaningful structures and details that are originally discarded without introducing too much additional complexity. Specifically, the proposed IFR-CS is realized with three iterative steps, namely sparsity-promoting denoising, feature refinement and Tikhonov regularization. Experimental results on both simulated and in vivo MR datasets have shown that the proposed module has a strong capability to capture image details, and that IFR-CS is comparable and even superior to other state-of-the-art reconstruction approaches.

REFMAC5 for the refinement of macromolecular crystal structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murshudov, Garib N., E-mail: garib@ysbl.york.ac.uk; Skubák, Pavol; Lebedev, Andrey A.

The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described. This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement toolsmore » such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, ‘jelly-body’ restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback–Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.« less

Similarity Measures for Protein Ensembles

PubMed Central

Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

2009-01-01

Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformations. However, instead of examining individual conformations it is in many cases more relevant to analyse ensembles of conformations that have been obtained either through experiments or from methods such as molecular dynamics simulations. We here present three approaches that can be used to compare conformational ensembles in the same way as the root mean square deviation is used to compare individual pairs of structures. The methods are based on the estimation of the probability distributions underlying the ensembles and subsequent comparison of these distributions. We first validate the methods using a synthetic example from molecular dynamics simulations. We then apply the algorithms to revisit the problem of ensemble averaging during structure determination of proteins, and find that an ensemble refinement method is able to recover the correct distribution of conformations better than standard single-molecule refinement. PMID:19145244

Crystallographic structure refinement with quadrupolar nuclei: a combined solid-state NMR and GIPAW DFT example using MgBr(2).

PubMed

Widdifield, Cory M; Bryce, David L

2009-09-07

Solid-state NMR spectroscopy and GIPAW DFT calculations reveal the pronounced sensitivity of (79/81)Br and (25)Mg quadrupolar coupling constants to subtle aspects of solid state structure which were not previously detected by pXRD methods.

High Performance, Robust Control of Flexible Space Structures: MSFC Center Director's Discretionary Fund

NASA Technical Reports Server (NTRS)

Whorton, M. S.

1998-01-01

Many spacecraft systems have ambitious objectives that place stringent requirements on control systems. Achievable performance is often limited because of difficulty of obtaining accurate models for flexible space structures. To achieve sufficiently high performance to accomplish mission objectives may require the ability to refine the control design model based on closed-loop test data and tune the controller based on the refined model. A control system design procedure is developed based on mixed H2/H(infinity) optimization to synthesize a set of controllers explicitly trading between nominal performance and robust stability. A homotopy algorithm is presented which generates a trajectory of gains that may be implemented to determine maximum achievable performance for a given model error bound. Examples show that a better balance between robustness and performance is obtained using the mixed H2/H(infinity) design method than either H2 or mu-synthesis control design. A second contribution is a new procedure for closed-loop system identification which refines parameters of a control design model in a canonical realization. Examples demonstrate convergence of the parameter estimation and improved performance realized by using the refined model for controller redesign. These developments result in an effective mechanism for achieving high-performance control of flexible space structures.

X-ray structure determination at low resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brunger, Axel T., E-mail: brunger@stanford.edu; Department of Molecular and Cellular Physiology, Stanford University; Department of Neurology and Neurological Sciences, Stanford University

2009-02-01

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

Molecular dynamics force-field refinement against quasi-elastic neutron scattering data

DOE PAGES

Borreguero Calvo, Jose M.; Lynch, Vickie E.

2015-11-23

Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulationmore » due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.« less

Synthesis and characterization of Y2O3 nano-material: An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Ahmad, Sheeraz; Faizan, Mohd; Ahmad, Shabbir; Ikram, Mohd

2018-04-01

We made an attempt to synthesize pure Y2O3 nanomaterial by using the sol-gel method followed by annealing at 600°C and 900°C. The synthesized Y2O3 nanoparticle was characterized by using XRD, FTIR, and UV-Vis spectroscopy. The structural refinement was performed using FULLPROF software by the Rietveld method. The refinement parameters such as lattice constant, atomic position, occupancy, R-factor and goodness of fit (χ2) were calculated. The nanoparticle has a single phase cubic structure with Ia -3 space group. The main absorption band in FTIR spectra centered at 560 cm-1 is attributed to Y-O vibration while the broadband at 3450 cm-1 arises due to O-H vibration. The band gap was obtained from the reflectance spectra using the K-M function F(R∞). The optimized structural parameters and UV-Vis spectrum were calculated using DFT and TD-DFT/B3LYP methods in bulk phase of Y2O3 and compared with experimental UV-Vis spectra in nanophase.

X-ray and neutron total scattering analysis of Hy·(Bi0.2Ca0.55Sr0.25)(Ag0.25Na0.75)Nb3O10·xH2O perovskite nanosheet booklets with stacking disorder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metz, Peter; Koch, Robert; Cladek, Bernadette

Ion-exchanged Aurivillius materials form perovskite nanosheet booklets wherein well-defined bi-periodic sheets, with ~11.5 Å thickness, exhibit extensive stacking disorder. The perovskite layer contents were defined initially using combined synchrotron X-ray and neutron Rietveld refinement of the parent Aurivillius structure. The structure of the subsequently ion-exchanged material, which is disordered in its stacking sequence, is analyzed using both pair distribution function (PDF) analysis and recursive method simulations of the scattered intensity. Combined X-ray and neutron PDF refinement of supercell stacking models demonstrates sensitivity of the PDF to both perpendicular and transverse stacking vector components. Further, hierarchical ensembles of stacking models weightedmore » by a standard normal distribution are demonstrated to improve PDF fit over 1–25 Å. Recursive method simulations of the X-ray scattering profile demonstrate agreement between the real space stacking analysis and more conventional reciprocal space methods. The local structure of the perovskite sheet is demonstrated to relax only slightly from the Aurivillius structure after ion exchange.« less

Hirshfeld atom refinement for modelling strong hydrogen bonds.

PubMed

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.

Testing MODFLOW-LGR for simulating flow around buried Quaternary valleys - synthetic test cases

NASA Astrophysics Data System (ADS)

Vilhelmsen, T. N.; Christensen, S.

2009-12-01

In this study the Local Grid Refinement (LGR) method developed for MODFLOW-2005 (Mehl and Hill, 2005) is utilized to describe groundwater flow in areas containing buried Quaternary valley structures. The tests are conducted as comparative analysis between simulations run with a globally refined model, a locally refined model, and a globally coarse model, respectively. The models vary from simple one layer models to more complex ones with up to 25 model layers. The comparisons of accuracy are conducted within the locally refined area and focus on water budgets, simulated heads, and simulated particle traces. Simulations made with the globally refined model are used as reference (regarded as “true” values). As expected, for all test cases the application of local grid refinement resulted in more accurate results than when using the globally coarse model. A significant advantage of utilizing MODFLOW-LGR was that it allows increased numbers of model layers to better resolve complex geology within local areas. This resulted in more accurate simulations than when using either a globally coarse model grid or a locally refined model with lower geological resolution. Improved accuracy in the latter case could not be expected beforehand because difference in geological resolution between the coarse parent model and the refined child model contradicts the assumptions of the Darcy weighted interpolation used in MODFLOW-LGR. With respect to model runtimes, it was sometimes found that the runtime for the locally refined model is much longer than for the globally refined model. This was the case even when the closure criteria were relaxed compared to the globally refined model. These results are contradictory to those presented by Mehl and Hill (2005). Furthermore, in the complex cases it took some testing (model runs) to identify the closure criteria and the damping factor that secured convergence, accurate solutions, and reasonable runtimes. For our cases this is judged to be a serious disadvantage of applying MODFLOW-LGR. Another disadvantage in the studied cases was that the MODFLOW-LGR results proved to be somewhat dependent on the correction method used at the parent-child model interface. This indicates that when applying MODFLOW-LGR there is a need for thorough and case-specific considerations regarding choice of correction method. References: Mehl, S. and M. C. Hill (2005). "MODFLOW-2005, THE U.S. GEOLOGICAL SURVEY MODULAR GROUND-WATER MODEL - DOCUMENTATION OF SHARED NODE LOCAL GRID REFINEMENT (LGR) AND THE BOUNDARY FLOW AND HEAD (BFH) PACKAGE " U.S. Geological Survey Techniques and Methods 6-A12

Probabilistic analysis of wind-induced vibration mitigation of structures by fluid viscous dampers

NASA Astrophysics Data System (ADS)

Chen, Jianbing; Zeng, Xiaoshu; Peng, Yongbo

2017-11-01

The high-rise buildings usually suffer from excessively large wind-induced vibrations, and thus vibration control systems might be necessary. Fluid viscous dampers (FVDs) with nonlinear power law against velocity are widely employed. With the transition of design method from traditional frequency domain approaches to more refined direct time domain approaches, the difficulty of time integration of these systems occurs sometimes. In the present paper, firstly the underlying reason of the difficulty is revealed by identifying that the equations of motion of high-rise buildings installed with FVDs are sometimes stiff differential equations. Thus, an approach effective for stiff differential systems, i.e., the backward difference formula (BDF), is then introduced, and verified to be effective for the equation of motion of wind-induced vibration controlled systems. Comparative studies are performed among some methods, including the Newmark method, KR-alpha method, energy-based linearization method and the statistical linearization method. Based on the above results, a 20-story steel frame structure is taken as a practical example. Particularly, the randomness of structural parameters and of wind loading input is emphasized. The extreme values of the responses are examined, showing the effectiveness of the proposed approach, and also necessitating the refined probabilistic analysis in the design of wind-induced vibration mitigation systems.

NASTRAN application for the prediction of aircraft interior noise

NASA Technical Reports Server (NTRS)

Marulo, Francesco; Beyer, Todd B.

1987-01-01

The application of a structural-acoustic analogy within the NASTRAN finite element program for the prediction of aircraft interior noise is presented. Some refinements of the method, which reduce the amount of computation required for large, complex structures, are discussed. Also, further improvements are proposed and preliminary comparisons with structural and acoustic modal data obtained for a large, composite cylinder are presented.

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

NASA Astrophysics Data System (ADS)

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 the potential of the method to simulate turbulent flows past geometrically complex bodies on locally refined meshes. In all the cases, the results are found to be in very good agreement with published data and savings in computational resources are achieved.

Grain Structure Control of Additively Manufactured Metallic Materials

PubMed Central

Faierson, Eric J.

2017-01-01

Grain structure control is challenging for metal additive manufacturing (AM). Grain structure optimization requires the control of grain morphology with grain size refinement, which can improve the mechanical properties of additive manufactured components. This work summarizes methods to promote fine equiaxed grains in both the additive manufacturing process and subsequent heat treatment. Influences of temperature gradient, solidification velocity and alloy composition on grain morphology are discussed. Equiaxed solidification is greatly promoted by introducing a high density of heterogeneous nucleation sites via powder rate control in the direct energy deposition (DED) technique or powder surface treatment for powder-bed techniques. Grain growth/coarsening during post-processing heat treatment can be restricted by presence of nano-scale oxide particles formed in-situ during AM. Grain refinement of martensitic steels can also be achieved by cyclic austenitizing in post-processing heat treatment. Evidently, new alloy powder design is another sustainable method enhancing the capability of AM for high-performance components with desirable microstructures.

Properties of nanocellulose isolated from corncob residue using sulfuric acid, formic acid, oxidative and mechanical methods.

PubMed

Liu, Chao; Li, Bin; Du, Haishun; Lv, Dong; Zhang, Yuedong; Yu, Guang; Mu, Xindong; Peng, Hui

2016-10-20

In this work, nanocellulose was extracted from bleached corncob residue (CCR), an underutilized lignocellulose waste from furfural industry, using four different methods (i.e. sulfuric acid hydrolysis, formic acid (FA) hydrolysis, 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO)-mediated oxidation, and pulp refining, respectively). The self-assembled structure, morphology, dimension, crystallinity, chemical structure and thermal stability of prepared nanocellulose were investigated. FA hydrolysis produced longer cellulose nanocrystals (CNCs) than the one obtained by sulfuric acid hydrolysis, and resulted in high crystallinity and thermal stability due to its preferential degradation of amorphous cellulose and lignin. The cellulose nanofibrils (CNFs) with fine and individualized structure could be isolated by TEMPO-mediated oxidation. In comparison with other nanocellulose products, the intensive pulp refining led to the CNFs with the longest length and the thickest diameter. This comparative study can help to provide an insight into the utilization of CCR as a potential source for nanocellulose production. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cellular Imaging | Center for Cancer Research

Cancer.gov

Innovative imaging methods developed and refined within CCR revealed atomic-level structures of biological molecules and unveiled dynamic views of a cell’s interior that are driving the design of new treatments and diagnostics for cancer.

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment

PubMed Central

2014-01-01

Background Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models. Results MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based methods of predicting both the local and global quality of a single protein model. MULTICOM-CONSTRUCT was a new weighted pairwise model comparison (clustering) method that used the weighted average similarity between models in a pool to measure the global model quality. Our experiments showed that the pairwise model assessment methods worked better when a large portion of models in the pool were of good quality, whereas single-model quality assessment methods performed better on some hard targets when only a small portion of models in the pool were of reasonable quality. Conclusions Since digging out a few good models from a large pool of low-quality models is a major challenge in protein structure prediction, single model quality assessment methods appear to be poised to make important contributions to protein structure modeling. The other interesting finding was that single-model quality assessment scores could be used to weight the models by the consensus pairwise model comparison method to improve its accuracy. PMID:24731387

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment.

PubMed

Cao, Renzhi; Wang, Zheng; Cheng, Jianlin

2014-04-15

Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models. MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based methods of predicting both the local and global quality of a single protein model. MULTICOM-CONSTRUCT was a new weighted pairwise model comparison (clustering) method that used the weighted average similarity between models in a pool to measure the global model quality. Our experiments showed that the pairwise model assessment methods worked better when a large portion of models in the pool were of good quality, whereas single-model quality assessment methods performed better on some hard targets when only a small portion of models in the pool were of reasonable quality. Since digging out a few good models from a large pool of low-quality models is a major challenge in protein structure prediction, single model quality assessment methods appear to be poised to make important contributions to protein structure modeling. The other interesting finding was that single-model quality assessment scores could be used to weight the models by the consensus pairwise model comparison method to improve its accuracy.

Adaptive Finite Element Methods for Continuum Damage Modeling

NASA Technical Reports Server (NTRS)

Min, J. B.; Tworzydlo, W. W.; Xiques, K. E.

1995-01-01

The paper presents an application of adaptive finite element methods to the modeling of low-cycle continuum damage and life prediction of high-temperature components. The major objective is to provide automated and accurate modeling of damaged zones through adaptive mesh refinement and adaptive time-stepping methods. The damage modeling methodology is implemented in an usual way by embedding damage evolution in the transient nonlinear solution of elasto-viscoplastic deformation problems. This nonlinear boundary-value problem is discretized by adaptive finite element methods. The automated h-adaptive mesh refinements are driven by error indicators, based on selected principal variables in the problem (stresses, non-elastic strains, damage, etc.). In the time domain, adaptive time-stepping is used, combined with a predictor-corrector time marching algorithm. The time selection is controlled by required time accuracy. In order to take into account strong temperature dependency of material parameters, the nonlinear structural solution a coupled with thermal analyses (one-way coupling). Several test examples illustrate the importance and benefits of adaptive mesh refinements in accurate prediction of damage levels and failure time.

Semi-experimental equilibrium structure of pyrazinamide from gas-phase electron diffraction. How much experimental is it?

NASA Astrophysics Data System (ADS)

Tikhonov, Denis S.; Vishnevskiy, Yury V.; Rykov, Anatolii N.; Grikina, Olga E.; Khaikin, Leonid S.

2017-03-01

A semi-experimental equilibrium structure of free molecules of pyrazinamide has been determined for the first time using gas electron diffraction method. The refinement was carried using regularization of geometry by calculated quantum chemical parameters. It is discussed to which extent is the final structure experimental. A numerical approach for estimation of the amount of experimental information in the refined parameters is suggested. The following values of selected internuclear distances were determined (values are in Å with 1σ in the parentheses): re(Cpyrazine-Cpyrazine)av = 1.397(2), re(Npyrazine-Cpyrazine)av = 1.332(3), re(Cpyrazine-Camide) = 1.493(1), re(Namide-Camide) = 1.335(2), re(Oamide-Camide) = 1.219(1). The given standard deviations represent pure experimental uncertainties without the influence of regularization.

Discrete size optimization of steel trusses using a refined big bang-big crunch algorithm

NASA Astrophysics Data System (ADS)

Hasançebi, O.; Kazemzadeh Azad, S.

2014-01-01

This article presents a methodology that provides a method for design optimization of steel truss structures based on a refined big bang-big crunch (BB-BC) algorithm. It is shown that a standard formulation of the BB-BC algorithm occasionally falls short of producing acceptable solutions to problems from discrete size optimum design of steel trusses. A reformulation of the algorithm is proposed and implemented for design optimization of various discrete truss structures according to American Institute of Steel Construction Allowable Stress Design (AISC-ASD) specifications. Furthermore, the performance of the proposed BB-BC algorithm is compared to its standard version as well as other well-known metaheuristic techniques. The numerical results confirm the efficiency of the proposed algorithm in practical design optimization of truss structures.

Applying an Empirical Hydropathic Forcefield in Refinement May Improve Low-Resolution Protein X-Ray Crystal Structures

PubMed Central

Koparde, Vishal N.; Scarsdale, J. Neel; Kellogg, Glen E.

2011-01-01

Background The quality of X-ray crystallographic models for biomacromolecules refined from data obtained at high-resolution is assured by the data itself. However, at low-resolution, >3.0 Å, additional information is supplied by a forcefield coupled with an associated refinement protocol. These resulting structures are often of lower quality and thus unsuitable for downstream activities like structure-based drug discovery. Methodology An X-ray crystallography refinement protocol that enhances standard methodology by incorporating energy terms from the HINT (Hydropathic INTeractions) empirical forcefield is described. This protocol was tested by refining synthetic low-resolution structural data derived from 25 diverse high-resolution structures, and referencing the resulting models to these structures. The models were also evaluated with global structural quality metrics, e.g., Ramachandran score and MolProbity clashscore. Three additional structures, for which only low-resolution data are available, were also re-refined with this methodology. Results The enhanced refinement protocol is most beneficial for reflection data at resolutions of 3.0 Å or worse. At the low-resolution limit, ≥4.0 Å, the new protocol generated models with Cα positions that have RMSDs that are 0.18 Å more similar to the reference high-resolution structure, Ramachandran scores improved by 13%, and clashscores improved by 51%, all in comparison to models generated with the standard refinement protocol. The hydropathic forcefield terms are at least as effective as Coulombic electrostatic terms in maintaining polar interaction networks, and significantly more effective in maintaining hydrophobic networks, as synthetic resolution is decremented. Even at resolutions ≥4.0 Å, these latter networks are generally native-like, as measured with a hydropathic interactions scoring tool. PMID:21246043

New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography.

PubMed

McCoy, Airlie J

2002-10-01

Maximum likelihood methods are well known to macromolecular crystallographers as the methods of choice for isomorphous phasing and structure refinement. Recently, the use of maximum likelihood and Bayesian statistics has extended to the areas of molecular replacement and density modification, placing these methods on a stronger statistical foundation and making them more accurate and effective.

Reduced Fragment Diversity for Alpha and Alpha-Beta Protein Structure Prediction using Rosetta.

PubMed

Abbass, Jad; Nebel, Jean-Christophe

2017-01-01

Protein structure prediction is considered a main challenge in computational biology. The biannual international competition, Critical Assessment of protein Structure Prediction (CASP), has shown in its eleventh experiment that free modelling target predictions are still beyond reliable accuracy, therefore, much effort should be made to improve ab initio methods. Arguably, Rosetta is considered as the most competitive method when it comes to targets with no homologues. Relying on fragments of length 9 and 3 from known structures, Rosetta creates putative structures by assembling candidate fragments. Generally, the structure with the lowest energy score, also known as first model, is chosen to be the "predicted one". A thorough study has been conducted on the role and diversity of 3-mers involved in Rosetta's model "refinement" phase. Usage of the standard number of 3-mers - i.e. 200 - has been shown to degrade alpha and alpha-beta protein conformations initially achieved by assembling 9-mers. Therefore, a new prediction pipeline is proposed for Rosetta where the "refinement" phase is customised according to a target's structural class prediction. Over 8% improvement in terms of first model structure accuracy is reported for alpha and alpha-beta classes when decreasing the number of 3- mers. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Block structured adaptive mesh and time refinement for hybrid, hyperbolic + N-body systems

NASA Astrophysics Data System (ADS)

Miniati, Francesco; Colella, Phillip

2007-11-01

We present a new numerical algorithm for the solution of coupled collisional and collisionless systems, based on the block structured adaptive mesh and time refinement strategy (AMR). We describe the issues associated with the discretization of the system equations and the synchronization of the numerical solution on the hierarchy of grid levels. We implement a code based on a higher order, conservative and directionally unsplit Godunov’s method for hydrodynamics; a symmetric, time centered modified symplectic scheme for collisionless component; and a multilevel, multigrid relaxation algorithm for the elliptic equation coupling the two components. Numerical results that illustrate the accuracy of the code and the relative merit of various implemented schemes are also presented.

Hirshfeld atom refinement.

PubMed

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.

Hirshfeld atom refinement

PubMed Central

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

2014-01-01

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 Å2 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. PMID:25295177

Cryo-EM image alignment based on nonuniform fast Fourier transform.

PubMed

Yang, Zhengfan; Penczek, Pawel A

2008-08-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.

Cryo-EM Image Alignment Based on Nonuniform Fast Fourier Transform

PubMed Central

Yang, Zhengfan; Penczek, Pawel A.

2008-01-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform Fast Fourier Transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis. PMID:18499351

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

PubMed

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.

Effect of Various SPD Techniques on Structure and Superplastic Deformation of Two Phase MgLiAl Alloy

NASA Astrophysics Data System (ADS)

Dutkiewicz, Jan; Bobrowski, Piotr; Rusz, Stanislav; Hilser, Ondrej; Tański, Tomasz A.; Borek, Wojciech; Łagoda, Marek; Ostachowski, Paweł; Pałka, Paweł; Boczkal, Grzegorz; Kuc, Dariusz; Mikuszewski, Tomasz

2018-03-01

MgLiAl alloy containing 9 wt% Li and 1.5% Al composed of hexagonal α and bcc β phases was cast under protecting atmosphere and hot extruded. Various methods of severe plastic deformation were applied to study their effect on structure and grain refinement. Rods were subjected to 1-3 passes of Twist Channel Angular Pressing TCAP (with helical component), cyclic compression to total strain ɛ = 5 using MAXStrain Gleeble equipment, both performed at temperature interval 160-200 °C and, as third SPD method, KOBO type extrusion at RT. The TCAP pass resulted in grain refinement of α phase from 30 μm down to about 2 μm and that of β phase from 12 to 5 μm. Maxstrain cycling 10 × up to ɛ = 5 led to much finer grain size of 300 nm. KOBO method performed at RT caused average grain size refinement of α and β phases down to about 1 μm. Hardness of alloy decreased slightly with increasing number of TCAP passes due to increase of small void density. It was higher after MAXStrain cycling and after KOBO extrusion. TEM studies after TCAP passes showed higher dislocation density in the β region than in the α phase. Crystallographic relationship (001) α|| (110) β indicated parallel positioning of slip planes of both phases. Electron diffraction technique confirmed increase of grain misorientation with number of TCAP passes. Stress/strain curves recorded at temperature 200 °C showed superplastic forming after 1st and 3rd TCAP passes with better superplastic properties due to higher elongation with increasing number of passes. Values of strain rate sensitivity coefficient m were calculated at 0.29 after 3rd TCAP pass for strain rate range 10-5 to 5 × 10-3 s-1. Deformation by MAXStrain cycling caused much more effective grain refinement with fine microtwins in α phase. Superplastic deformation was also observed in alloy deformed by KOBO method, however the value of m = 0.21 was obtained at lower temperature of deformation equal to 160 °C and deformation rate in the range 10-5 to 5 × 10-3. Tensile samples deformed superplastically showed grain growth and void formation caused by grain boundary slip. Summarizing, all methods applied resulted in sufficient grain refinement to obtain the effect of superplastic deformation for alloys of two phase α + β structure.

On the release of cppxfel for processing X-ray free-electron laser images.

PubMed

Ginn, Helen Mary; Evans, Gwyndaf; Sauter, Nicholas K; Stuart, David Ian

2016-06-01

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel , a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.

An economic prediction of the finer resolution level wavelet coefficients in electronic structure calculations.

PubMed

Nagy, Szilvia; Pipek, János

2015-12-21

In wavelet based electronic structure calculations, introducing a new, finer resolution level is usually an expensive task, this is why often a two-level approximation is used with very fine starting resolution level. This process results in large matrices to calculate with and a large number of coefficients to be stored. In our previous work we have developed an adaptively refined solution scheme that determines the indices, where the refined basis functions are to be included, and later a method for predicting the next, finer resolution coefficients in a very economic way. In the present contribution, we would like to determine whether the method can be applied for predicting not only the first, but also the other, higher resolution level coefficients. Also the energy expectation values of the predicted wave functions are studied, as well as the scaling behaviour of the coefficients in the fine resolution limit.

On the release of cppxfel for processing X-ray free-electron laser images

DOE PAGES

Ginn, Helen Mary; Evans, Gwyndaf; Sauter, Nicholas K.; ...

2016-05-11

As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Herecppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set.Cppxfelis released with the hope that the unique and useful elements of this package can be repurposed formore » existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.« less

Refined gradient theory of scale-dependent superthin rods

NASA Astrophysics Data System (ADS)

Lurie, S. A.; Kuznetsova, E. L.; Rabinskii, L. N.; Popova, E. I.

2015-03-01

A version of the refined nonclassical theory of thin beams whose thickness is comparable with the scale characteristic of the material structure is constructed on the basis of the gradient theory of elasticity which, in contrast to the classical theory, contains some additional physical characteristics depending on the structure scale parameters and is therefore most appropriate for modeling the strains of scale-dependent systems. The fundamental conditions for the well-posedness of the gradient theories are obtained for the first time, and it is shown that some of the known applied gradient theories do not generally satisfy the well-posedness criterion. A version of the well-posed gradient strain theory which satisfies the symmetry condition is proposed. The well-posed gradient theory is then used to implement the method of kinematic hypotheses for constructing a refined theory of scale-dependent beams. The equilibrium equations of the refined theory of scale-dependent Timoshenko and Bernoulli beams are obtained. It is shown that the scale effects are localized near the beam ends, and therefore, taking the scale effects into account does not give any correction to the bending rigidity of long beams as noted in the previously published papers dealing with the scale-dependent beams.

Verification of fluid-structure-interaction algorithms through the method of manufactured solutions for actuator-line applications

NASA Astrophysics Data System (ADS)

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.

Stochastic and Deterministic Crystal Structure Solution Methods in GSAS-II: Monte Carlo/Simulated Annealing Versus Charge Flipping

DOE PAGES

Von Dreele, Robert

2017-08-29

One of the goals in developing GSAS-II was to expand from the capabilities of the original General Structure Analysis System (GSAS) which largely encompassed just structure refinement and post refinement analysis. GSAS-II has been written almost entirely in Python loaded with graphics, GUI and mathematical packages (matplotlib, pyOpenGL, wxpython, numpy and scipy). Thus, GSAS-II has a fully developed modern GUI as well as extensive graphical display of data and results. However, the structure and operation of Python has required new approaches to many of the algorithms used in crystal structure analysis. The extensions beyond GSAS include image calibration/integration as wellmore » as peak fitting and unit cell indexing for powder data which are precursors for structure solution. Structure solution within GSAS-II begins with either Pawley or LeBail extracted structure factors from powder data or those measured in a single crystal experiment. Both charge flipping and Monte Carlo-Simulated Annealing techniques are available; the former can be applied to (3+1) incommensurate structures as well as conventional 3D structures.« less

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

PubMed

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 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 A, 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.

Calcio-olivine γ-Ca2SiO4: I. Rietveld refinement of the crystal structure

NASA Astrophysics Data System (ADS)

Gobechiya, E. R.; Yamnova, N. A.; Zadov, A. E.; Gazeev, V. M.

2008-05-01

The structure of the natural mineral calcio-olivine (γ-Ca2SiO4) found in skarn xenoliths in the region of the Lakargi Mountain (North Caucasus, Kabardino-Balkaria, Russia) is refined by the Rietveld method [ a = 5.07389(7) Å, b = 11.21128(14) Å, c = 6.75340(9) Å, V = 384.170(5) Å3, Z = 4, ρcalcd = 2.98 g/cm3, space group Pbnm]. The X-ray diffraction pattern of a powdered sample is recorded on a STOE STADI MP diffractometer [λCu K α1; Ge(111) primary monochromator; 6.00° < 2θ < 100.88°; step width, 2.5° in 2θ; number of reflections, 224]. All calculations are performed with the WYRIET (version 3.3) software package. The structural model is refined in the anisotropic approximation to R p = 6.44, R wp = 8.52, R exp = 5.85, R B = 4.98, R F = 6.90, and s = 1.46. It is shown that the sample under investigation is a mixture of several mineral phases, among which calcio-olivine (the natural analogue of the γ-Ca2SiO4 compound) (83%), hillebrandite (13%), and wadalite (4%) are dominant. Only the scale factors and the unit cell parameters are refined for hillebrandite Ca2SiO3(OH)2 [ a = 3.63472(16) Å, b = 16.4140(10) Å, c = 11.7914(8) Å, space group Cmc21, Z = 6] and wadalite Ca6Al5Si2O16Cl3 ( a = 12.0088 Å, space group, I bar 4 3 d Z = 4). The results of the structure refinement of the main component of the sample confirm that the mineral calcio-olivine is isostructural to the synthetic compound γ-Ca2SiO4. The structure of this compound is formed by the heteropolyhedral framework composed of Ca octahedra joined together into olivine-like ribbons and isolated Si tetrahedra.

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

NASA Astrophysics Data System (ADS)

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-Lagrangian approach. This enables us to refine the computational mesh in the vicinity of the droplet parcels and accurately resolve the coupling between the two phases.

Method for producing ultrafine-grained materials using repetitive corrugation and straightening

DOEpatents

Zhu, Yuntian T.; Lowe, Terry C.; Jiang, Honggang; Huang, Jianyu

2001-01-01

A method of refining the grain structure and improving the hardness and strength properties of a metal or metal alloy workpiece is disclosed. The workpiece is subjected to forces that corrugate and then straighten the workpiece. These steps are repeated until an ultrafine-grained product having improved hardness and strength is produced.

Rhombohedrally Distorted γ-Au 5–x Zn 8+y Phases in the Au–Zn System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thimmaiah, Srinivasa; Miller, Gordon J.

2013-02-04

The region of the Au–Zn phase diagram encompassing γ-brass-type phases has been studied experimentally from 45 to 85 atom % Zn. The γ phases were obtained directly from the pure elements by heating to 680 °C in evacuated silica tubes, followed by annealing at 300 °C. Powder X-ray and single-crystal diffraction studies show that γ-“Au5Zn8” phases adopt a rhombohedrally distorted Cr5Al8 structure type rather than the cubic Cu5Zn8 type. The refined compositions from two single crystals extracted from the Zn- and Au-rich loadings are Au4.27(3)Zn8.26(3)γ0.47 (I) and Au4.58(3)Zn8.12(3)γ0.3 (II), respectively (γ = vacancy). These (I and II) refinements indicated bothmore » nonstatistical mixing of Au and Zn atoms as well as partially ordered vacancy distributions. The structures of these γ phases were solved in the acentric space group R3m (No. 160, Z = 6), and the observed lattice parameters from powder patterns were found to be a = 13.1029(6) and 13.1345(8) Å and c = 8.0410(4) and 8.1103(6) Å for crystals I and II, respectively. According to single-crystal refinements, the vacancies were found on the outer tetrahedron (OT) and octahedron (OH) of the 26-atom cluster. Single-crystal structural refinement clearly showed that the vacancy content per unit cell increases with increasing Zn, or valence-electron concentration. Electronic structure calculations, using the tight-binding linear muffin-tin orbital method with the atomic-sphere approximation (TB-LMTO-ASA) method, indicated the presence of a well-pronounced pseudogap at the Fermi level for “Au5Zn8” as the representative composition, an outcome that is consistent with the Hume–Rothery interpretation of γ brass.« less

In Search of Grid Converged Solutions

NASA Technical Reports Server (NTRS)

Lockard, David P.

2010-01-01

Assessing solution error continues to be a formidable task when numerically solving practical flow problems. Currently, grid refinement is the primary method used for error assessment. The minimum grid spacing requirements to achieve design order accuracy for a structured-grid scheme are determined for several simple examples using truncation error evaluations on a sequence of meshes. For certain methods and classes of problems, obtaining design order may not be sufficient to guarantee low error. Furthermore, some schemes can require much finer meshes to obtain design order than would be needed to reduce the error to acceptable levels. Results are then presented from realistic problems that further demonstrate the challenges associated with using grid refinement studies to assess solution accuracy.

Structural simplicity as a restraint on the structure of amorphous silicon

NASA Astrophysics Data System (ADS)

Cliffe, Matthew J.; Bartók, Albert P.; Kerber, Rachel N.; Grey, Clare P.; Csányi, Gábor; Goodwin, Andrew L.

2017-06-01

Understanding the structural origins of the properties of amorphous materials remains one of the most important challenges in structural science. In this study, we demonstrate that local "structural simplicity", embodied by the degree to which atomic environments within a material are similar to each other, is a powerful concept for rationalizing the structure of amorphous silicon (a -Si) a canonical amorphous material. We show, by restraining a reverse Monte Carlo refinement against pair distribution function (PDF) data to be simpler, that the simplest model consistent with the PDF is a continuous random network (CRN). A further effect of producing a simple model of a -Si is the generation of a (pseudo)gap in the electronic density of states, suggesting that structural homogeneity drives electronic homogeneity. That this method produces models of a -Si that approach the state-of-the-art without the need for chemically specific restraints (beyond the assumption of homogeneity) suggests that simplicity-based refinement approaches may allow experiment-driven structural modeling techniques to be developed for the wide variety of amorphous semiconductors with strong local order.

Performance Comparison of Al-Ti Master Alloys with Different Microstructures in Grain Refinement of Commercial Purity Aluminum.

PubMed

Ding, Wanwu; Xia, Tiandong; Zhao, Wenjun

2014-05-07

Three types of Al-5Ti master alloys were synthesized by a method of thermal explosion reaction in pure molten aluminum. Performance comparison of Al-5Ti master alloy in grain refinement of commercial purity Al with different additions (0.6%, 1.0%, 1.6%, 2.0%, and 3.0%) and holding time (10, 30, 60 and 120 min) were investigated. The results show that Al-5Ti master alloy with blocky TiAl₃ particles clearly has better refining efficiency than the master alloy with mixed TiAl₃ particles and the master alloy with needle-like TiAl₃ particles. The structures of master alloys, differing by sizes, morphologies and quantities of TiAl₃ crystals, were found to affect the pattern of the grain refining properties with the holding time. The grain refinement effect was revealed to reduce markedly for master alloys with needle-like TiAl₃ crystals and to show the further significant improvement at a longer holding time for the master alloy containing both larger needle-like and blocky TiAl₃ particles. For the master alloy with finer blocky particles, the grain refining effect did not obviously decrease during the whole studied range of the holding time.

HPHT synthesis, structure and electrical properties of type-I clathrates Ba{sub 8}Al{sub x}Si{sub 46−x}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Binwu; Jia, Xiaopeng; Sun, Hairui

2016-01-15

Clathrate compounds Ba{sub 8}Al{sub x}Si{sub 46−x} were successfully synthesized using the method of high-pressure and high-temperature (HPHT). In this process, we used BaSi{sub 2} as one of the starting materials in place of Ba metals, which reduces the complexity of the program caused by the extremely high chemical reactivity. By using this method, the processing time was reduced from few days to an hour. X-ray diffraction and structural refinement indicated this composition crystallized in type-I clathrate phase. Bond length analysis showed the Ba atoms in small dodecahedron had spherical thermal ellipsoids while those in large tetrakaidecahedron displayed anisotropic thermal ellipsoids.more » The negative Seebeck coefficient indicated transport processes were dominated by electrons as carriers, and increased with the increasing temperature. The electrical properties, including Seebeck coefficient and Power factor, were greatly enhanced by Al substitution. - Graphical abstract: Left: The cavity structure diagram of a China-type large volume cubic high-pressure apparatus, and the Type-I clathrate structure of sample synthesized using HPHT. Middle: X-ray Rietveld refinement profile for Ba{sub 8}Si{sub 46} and element mapping for Ba{sub 8}Al{sub 16}Si{sub 30}. Right: Temperature dependence of Seebeck coefficient for Ba{sub 8}Al{sub x}Si{sub 46−x} prepared by HPHT. - Highlights: • HPHT is a simple and rapid synthetic approach. • We use BaSi{sub 2} as one of the starting materials replacing Ba metals. • The processing time reduces from few days to an hour. • Structure determination is refined by Rietveld analysis of XRD data. • Variable temperature electrical properties are characterized.« less

Total Scattering Analysis of Disordered Nanosheet Materials

NASA Astrophysics Data System (ADS)

Metz, Peter C.

Two dimensional materials are of increasing interest as building blocks for functional coatings, catalysts, and electrochemical devices. While increasingly sophisticated processing routes have been designed to obtain high-quality exfoliated nanosheets and controlled, self-assembled mesostructures, structural characterization of these materials remains challenging. This work presents a novel method of analyzing pair distribution function (PDF) data for disordered nanosheet ensembles, where supercell stacking models are used to infer atom correlations over as much as 50 A. Hierarchical models are used to reduce the parameter space of the refined model and help eliminate strongly correlated parameters. Three data sets for restacked nanosheet assemblies with stacking disorder are analyzed using these methods: simulated data for graphene-like layers, experimental data for 1 nm thick perovskite layers, and experimental data for highly defective delta-MnO2 layers. In each case, the sensitivity of the PDF to the real-space distribution of layer positions is demonstrated by exploring the fit residual as a function of stacking vectors. The refined models demonstrate that nanosheets tend towards local interlayer ordering, which is hypothesized to be driven by the electrostatic potential of the layer surfaces. Correctly accounting for interlayer atom correlations permits more accurate refinement of local structural details including local structure perturbations and defect site occupancies. In the delta-MnO2 nanosheet material, the new modeling approach identified 14% Mn vacancies while application of 3D periodic crystalline models to the < 7 A PDF region suggests a 25% vacancy concentration. In contrast, the perovskite nanosheet material is demonstrated to exhibit almost negligible structural relaxation in contrast with the bulk crystalline material from which it is derived.

The crystal structure of calcite III

NASA Astrophysics Data System (ADS)

Smyth, Joseph R.; Ahrens, Thomas J.

The crystal structure of calcite III has been deduced from existing high pressure powder X-ray diffraction patterns, based on the assumption that it is a displacive modification of the calcite I structure. The structure is monoclinic with space group C2 and a Z of 6. There are two Ca and two C positions, and five O positions, and atom coordinates have been refined by distance-least-squares methods to give reasonable octahedral coordination for Ca and parallel, planar CO3 groups. Unit cell parameters refined from a published powder diffraction pattern at 4.1 GPa are: a = 8.746(8)Å b = 4.685(5)Å c = 8.275(8)Å and β= 94.4°. The structure has a calculated density of 2.949 Mg/m³ at 4.1 GPa which is less than that of aragonite at this pressure and consistent with early piston cylinder studies. This implies that calcite III is indeed a metastable intermediary between calcite I and aragonite.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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.

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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.

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

PubMed Central

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 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. PMID:18094468

Model correlation and damage location for large space truss structures: Secant method development and evaluation

NASA Technical Reports Server (NTRS)

Smith, Suzanne Weaver; Beattie, Christopher A.

1991-01-01

On-orbit testing of a large space structure will be required to complete the certification of any mathematical model for the structure dynamic response. The process of establishing a mathematical model that matches measured structure response is referred to as model correlation. Most model correlation approaches have an identification technique to determine structural characteristics from the measurements of the structure response. This problem is approached with one particular class of identification techniques - matrix adjustment methods - which use measured data to produce an optimal update of the structure property matrix, often the stiffness matrix. New methods were developed for identification to handle problems of the size and complexity expected for large space structures. Further development and refinement of these secant-method identification algorithms were undertaken. Also, evaluation of these techniques is an approach for model correlation and damage location was initiated.

DiffPy-CMI-Python libraries for Complex Modeling Initiative

DOE Office of Scientific and Technical Information (OSTI.GOV)

Billinge, Simon; Juhas, Pavol; Farrow, Christopher

2014-02-01

Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

Macromolecular refinement by model morphing using non-atomic parameterizations.

PubMed

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.

Sensitivity and Limitations of Structures from X-ray and Neutron-Based Diffraction Analyses of Transition Metal Oxide Lithium-Battery Electrodes

DOE PAGES

Liu, Hao; Liu, Haodong; Lapidus, Saul H.; ...

2017-06-21

Lithium transition metal oxides are an important class of electrode materials for lithium-ion batteries. Binary or ternary (transition) metal doping brings about new opportunities to improve the electrode’s performance and often leads to more complex stoichiometries and atomic structures than the archetypal LiCoO 2. Rietveld structural analyses of X-ray and neutron diffraction data is a widely-used approach for structural characterization of crystalline materials. But, different structural models and refinement approaches can lead to differing results, and some parameters can be difficult to quantify due to the inherent limitations of the data. Here, through the example of LiNi 0.8Co 0.15Al 0.05Omore » 2 (NCA), we demonstrated the sensitivity of various structural parameters in Rietveld structural analysis to different refinement approaches and structural models, and proposed an approach to reduce refinement uncertainties due to the inexact X-ray scattering factors of the constituent atoms within the lattice. Furthermore, this refinement approach was implemented for electrochemically-cycled NCA samples and yielded accurate structural parameters using only X-ray diffraction data. The present work provides the best practices for performing structural refinement of lithium transition metal oxides.« less

Sensitivity and Limitations of Structures from X-ray and Neutron-Based Diffraction Analyses of Transition Metal Oxide Lithium-Battery Electrodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Hao; Liu, Haodong; Lapidus, Saul H.

Lithium transition metal oxides are an important class of electrode materials for lithium-ion batteries. Binary or ternary (transition) metal doping brings about new opportunities to improve the electrode’s performance and often leads to more complex stoichiometries and atomic structures than the archetypal LiCoO 2. Rietveld structural analyses of X-ray and neutron diffraction data is a widely-used approach for structural characterization of crystalline materials. But, different structural models and refinement approaches can lead to differing results, and some parameters can be difficult to quantify due to the inherent limitations of the data. Here, through the example of LiNi 0.8Co 0.15Al 0.05Omore » 2 (NCA), we demonstrated the sensitivity of various structural parameters in Rietveld structural analysis to different refinement approaches and structural models, and proposed an approach to reduce refinement uncertainties due to the inexact X-ray scattering factors of the constituent atoms within the lattice. Furthermore, this refinement approach was implemented for electrochemically-cycled NCA samples and yielded accurate structural parameters using only X-ray diffraction data. The present work provides the best practices for performing structural refinement of lithium transition metal oxides.« less

Structure analysis on synthetic emerald crystals

NASA Astrophysics Data System (ADS)

Lee, Pei-Lun; Lee, Jiann-Shing; Huang, Eugene; Liao, Ju-Hsiou

2013-05-01

Single crystals of emerald synthesized by means of the flux method were adopted for crystallographic analyses. Emerald crystals with a wide range of Cr3+-doping content up to 3.16 wt% Cr2O3 were examined by X-ray single crystal diffraction refinement method. The crystal structures of the emerald crystals were refined to R 1 (all data) of 0.019-0.024 and w R 2 (all data) of 0.061-0.073. When Cr3+ substitutes for Al3+, the main adjustment takes place in the Al-octahedron and Be-tetrahedron. The effect of substitution of Cr3+ for Al3+ in the beryl structure results in progressively lengthening of the Al-O distance, while the length of the other bonds remains nearly unchanged. The substitution of Cr3+ for Al3+ may have caused the expansion of a axis, while keeping the c axis unchanged in the emerald lattice. As a consequence, the Al-O-Si and Al-O-Be bonding angles are found to decrease, while the angle of Si-O-Be increases as the Al-O distance increases during the Cr replacement.

Neutron protein crystallography: A complementary tool for locating hydrogens in proteins.

PubMed

O'Dell, William B; Bodenheimer, Annette M; Meilleur, Flora

2016-07-15

Neutron protein crystallography is a powerful tool for investigating protein chemistry because it directly locates hydrogen atom positions in a protein structure. The visibility of hydrogen and deuterium atoms arises from the strong interaction of neutrons with the nuclei of these isotopes. Positions can be unambiguously assigned from diffraction at resolutions typical of protein crystals. Neutrons have the additional benefit to structural biology of not inducing radiation damage in protein crystals. The same crystal could be measured multiple times for parametric studies. Here, we review the basic principles of neutron protein crystallography. The information that can be gained from a neutron structure is presented in balance with practical considerations. Methods to produce isotopically-substituted proteins and to grow large crystals are provided in the context of neutron structures reported in the literature. Available instruments for data collection and software for data processing and structure refinement are described along with technique-specific strategies including joint X-ray/neutron structure refinement. Examples are given to illustrate, ultimately, the unique scientific value of neutron protein crystal structures. Copyright © 2015 Elsevier Inc. All rights reserved.

Study on Separation of Structural Isomer with Magneto-Archimedes method

NASA Astrophysics Data System (ADS)

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.

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

PubMed

Smart, Oliver S; Womack, Thomas O; Flensburg, Claus; Keller, Peter; Paciorek, Włodek; Sharff, Andrew; Vonrhein, Clemens; Bricogne, Gérard

2012-04-01

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 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.

The Collaborative Seismic Earth Model: Generation 1

NASA Astrophysics Data System (ADS)

Fichtner, Andreas; van Herwaarden, Dirk-Philip; Afanasiev, Michael; SimutÄ--, SaulÄ--; Krischer, Lion; ćubuk-Sabuncu, Yeşim; Taymaz, Tuncay; Colli, Lorenzo; Saygin, Erdinc; Villaseñor, Antonio; Trampert, Jeannot; Cupillard, Paul; Bunge, Hans-Peter; Igel, Heiner

2018-05-01

We present a general concept for evolutionary, collaborative, multiscale inversion of geophysical data, specifically applied to the construction of a first-generation Collaborative Seismic Earth Model. This is intended to address the limited resources of individual researchers and the often limited use of previously accumulated knowledge. Model evolution rests on a Bayesian updating scheme, simplified into a deterministic method that honors today's computational restrictions. The scheme is able to harness distributed human and computing power. It furthermore handles conflicting updates, as well as variable parameterizations of different model refinements or different inversion techniques. The first-generation Collaborative Seismic Earth Model comprises 12 refinements from full seismic waveform inversion, ranging from regional crustal- to continental-scale models. A global full-waveform inversion ensures that regional refinements translate into whole-Earth structure.

Refining the threshold of toxicological concern (TTC) for risk prioritization of trace chemicals in food.

PubMed

Felter, Susan; Lane, Richard W; Latulippe, Marie E; Llewellyn, G Craig; Olin, Stephen S; Scimeca, Joseph A; Trautman, Thomas D

2009-09-01

Due to ever-improving analytical capabilities, very low levels of unexpected chemicals can now be detected in foods. Although these may be toxicologically insignificant, such incidents often garner significant attention. The threshold of toxicological concern (TTC) methodology provides a scientifically defensible, transparent approach for putting low-level exposures in the context of potential risk, as a tool to facilitate prioritization of responses, including potential mitigation. The TTC method supports the establishment of tiered, health-protective exposure limits for chemicals lacking a full toxicity database, based on evaluation of the known toxicity of chemicals which share similar structural characteristics. The approach supports the view that prudent actions towards public health protection are based on evaluation of safety as opposed to detection chemistry. This paper builds on the existing TTC literature and recommends refinements that address two key areas. The first describes the inclusion of genotoxicity data as a way to refine the TTC limit for chemicals that have structural alerts for genotoxicity. The second area addresses duration of exposure. Whereas the existing TTC exposure limits assume a lifetime of exposure, human exposure to unintended chemicals in food is often only for a limited time. Recommendations are made to refine the approach for less-than-lifetime exposures.

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

PubMed Central

Zhang, Yang

2014-01-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. PMID:23760925

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

PubMed

Zhang, Yang

2014-02-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

PubMed Central

Jang, Richard; Wang, Yan

2015-01-01

NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement. PMID:25737244

Three-dimensional structure of Erwinia carotovora L-asparaginase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kislitsyn, Yu. A.; Kravchenko, O. V.; Nikonov, S. V.

2006-10-15

Three-dimensional structure of Erwinia carotovora L-asparaginase, which has antitumor activity and is used for the treatment of acute lymphoblastic leukemia, was solved at 3 A resolution and refined to R{sub cryst} = 20% and R{sub free} = 28%. Crystals of recombinant Erwinia carotovora L-asparaginase were grown by the hanging-drop vapor-diffusion method from protein solutions in a HEPES buffer (pH 6.5) and PEG MME 5000 solutions in a cacodylate buffer (pH 6.5) as the precipitant. Three-dimensional X-ray diffraction data were collected up to 3 A resolution from one crystal at room temperature. The structure was solved by the molecular replacement methodmore » using the coordinates of Erwinia chrysanthemi L-asparaginase as the starting model. The coordinates refined with the use of the CNS program package were deposited in the Protein Data Bank (PDB code 1ZCF)« less

Molten Salt Synthesis and Structural Characterization of BaTiO3 Nanocrystal Ceramics

NASA Astrophysics Data System (ADS)

Ahda, S.; Misfadhila, S.; Parikin, P.; Putra, T. Y. S. P.

2017-02-01

A new synthesis route to obtain high-purity barium titanate powder, BaTiO3, using the molten salt method by reacting the raw materials (BaCO3 and TiO2) in an atmosphere of molten NaCl and KCl, has been developed. The synthesized BaTiO3 ceramic particles have been successfully carried out at the sintering temperature 950°C for 4 hours. The Rietveld refinement of the XRD diffraction patterns was employed to characterize the structural information of the nanocrystalline BaTiO3 ceramics. The lattice parameters (a=4.0043 Å, b=4.0308Å with space group P4mm) of tetragonal perovskite structure, as an indication of piezoelectric characteristics, have been successfully determined by the Rietveld refinement. While the crystallitte particle size and strains have been obtained for the values of 110.6 nm and 0.74 % respectively

Parallel Cartesian grid refinement for 3D complex flow simulations

NASA Astrophysics Data System (ADS)

Angelidis, Dionysios; Sotiropoulos, Fotis

2013-11-01

A second order accurate method for discretizing the Navier-Stokes equations on 3D unstructured Cartesian grids is presented. Although the grid generator is based on the oct-tree hierarchical method, fully unstructured data-structure is adopted enabling robust calculations for incompressible flows, avoiding both the need of synchronization of the solution between different levels of refinement and usage of prolongation/restriction operators. The current solver implements a hybrid staggered/non-staggered grid layout, employing the implicit fractional step method to satisfy the continuity equation. The pressure-Poisson equation is discretized by using a novel second order fully implicit scheme for unstructured Cartesian grids and solved using an efficient Krylov subspace solver. The momentum equation is also discretized with second order accuracy and the high performance Newton-Krylov method is used for integrating them in time. Neumann and Dirichlet conditions are used to validate the Poisson solver against analytical functions and grid refinement results to a significant reduction of the solution error. The effectiveness of the fractional step method results in the stability of the overall algorithm and enables the performance of accurate multi-resolution real life simulations. This material is based upon work supported by the Department of Energy under Award Number DE-EE0005482.

Text Extraction from Scene Images by Character Appearance and Structure Modeling

PubMed Central

Yi, Chucai; Tian, Yingli

2012-01-01

In this paper, we propose a novel algorithm to detect text information from natural scene images. Scene text classification and detection are still open research topics. Our proposed algorithm is able to model both character appearance and structure to generate representative and discriminative text descriptors. The contributions of this paper include three aspects: 1) a new character appearance model by a structure correlation algorithm which extracts discriminative appearance features from detected interest points of character samples; 2) a new text descriptor based on structons and correlatons, which model character structure by structure differences among character samples and structure component co-occurrence; and 3) a new text region localization method by combining color decomposition, character contour refinement, and string line alignment to localize character candidates and refine detected text regions. We perform three groups of experiments to evaluate the effectiveness of our proposed algorithm, including text classification, text detection, and character identification. The evaluation results on benchmark datasets demonstrate that our algorithm achieves the state-of-the-art performance on scene text classification and detection, and significantly outperforms the existing algorithms for character identification. PMID:23316111

Water-refined solution structure of the human Grb7-SH2 domain in complex with the erbB2 receptor peptide pY1139.

PubMed

Pias, Sally C; Johnson, Dennis L; Smith, David E; Lyons, Barbara A

2012-08-01

We report a refinement in implicit water of the previously published solution structure of the Grb7-SH2 domain bound to the erbB2 receptor peptide pY1139. Structure quality measures indicate substantial improvement, with residues in the most favored regions of the Ramachandran plot increasing by 14 % and with WHAT IF statistics (Vriend, G. J. Mol. Graph., 1990, 8(1), 52-56) falling closer to expected values for well-refined structures.

Carbohydrate structure: the rocky road to automation.

PubMed

Agirre, Jon; Davies, Gideon J; Wilson, Keith S; Cowtan, Kevin D

2017-06-01

With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to 'protein standards' will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2014-01-21

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.

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome.

PubMed

Lamm, Ayelet T; Stadler, Michael R; Zhang, Huibin; Gent, Jonathan I; Fire, Andrew Z

2011-02-01

We have used a combination of three high-throughput RNA capture and sequencing methods to refine and augment the transcriptome map of a well-studied genetic model, Caenorhabditis elegans. The three methods include a standard (non-directional) library preparation protocol relying on cDNA priming and foldback that has been used in several previous studies for transcriptome characterization in this species, and two directional protocols, one involving direct capture of single-stranded RNA fragments and one involving circular-template PCR (CircLigase). We find that each RNA-seq approach shows specific limitations and biases, with the application of multiple methods providing a more complete map than was obtained from any single method. Of particular note in the analysis were substantial advantages of CircLigase-based and ssRNA-based capture for defining sequences and structures of the precise 5' ends (which were lost using the double-strand cDNA capture method). Of the three methods, ssRNA capture was most effective in defining sequences to the poly(A) junction. Using data sets from a spectrum of C. elegans strains and stages and the UCSC Genome Browser, we provide a series of tools, which facilitate rapid visualization and assignment of gene structures.

Programming new geometry restraints: Parallelity of atomic groups

DOE PAGES

Sobolev, Oleg V.; Afonine, Pavel V.; Adams, Paul D.; ...

2015-08-01

Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use a priori information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they canmore » be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the Computational Crystallography Toolbox( cctbx) are presented.« less

An adaptively refined phase-space element method for cosmological simulations and collisionless dynamics

NASA Astrophysics Data System (ADS)

Hahn, Oliver; Angulo, Raul E.

2016-01-01

N-body simulations are essential for understanding the formation and evolution of structure in the Universe. However, the discrete nature of these simulations affects their accuracy when modelling collisionless systems. We introduce a new approach to simulate the gravitational evolution of cold collisionless fluids by solving the Vlasov-Poisson equations in terms of adaptively refineable `Lagrangian phase-space elements'. These geometrical elements are piecewise smooth maps between Lagrangian space and Eulerian phase-space and approximate the continuum structure of the distribution function. They allow for dynamical adaptive splitting to accurately follow the evolution even in regions of very strong mixing. We discuss in detail various one-, two- and three-dimensional test problems to demonstrate the performance of our method. Its advantages compared to N-body algorithms are: (I) explicit tracking of the fine-grained distribution function, (II) natural representation of caustics, (III) intrinsically smooth gravitational potential fields, thus (IV) eliminating the need for any type of ad hoc force softening. We show the potential of our method by simulating structure formation in a warm dark matter scenario. We discuss how spurious collisionality and large-scale discreteness noise of N-body methods are both strongly suppressed, which eliminates the artificial fragmentation of filaments. Therefore, we argue that our new approach improves on the N-body method when simulating self-gravitating cold and collisionless fluids, and is the first method that allows us to explicitly follow the fine-grained evolution in six-dimensional phase-space.

Optimization of Melt Treatment for Austenitic Steel Grain Refinement

NASA Astrophysics Data System (ADS)

Lekakh, Simon N.; Ge, Jun; Richards, Von; O'Malley, Ron; TerBush, Jessica R.

2017-02-01

Refinement of the as-cast grain structure of austenitic steels requires the presence of active solid nuclei during solidification. These nuclei can be formed in situ in the liquid alloy by promoting reactions between transition metals (Ti, Zr, Nb, and Hf) and metalloid elements (C, S, O, and N) dissolved in the melt. Using thermodynamic simulations, experiments were designed to evaluate the effectiveness of a predicted sequence of reactions targeted to form precipitates that could act as active nuclei for grain refinement in austenitic steel castings. Melt additions performed to promote the sequential precipitation of titanium nitride (TiN) onto previously formed spinel (Al2MgO4) inclusions in the melt resulted in a significant refinement of the as-cast grain structure in heavy section Cr-Ni-Mo stainless steel castings. A refined as-cast structure consisting of an inner fine-equiaxed grain structure and outer columnar dendrite zone structure of limited length was achieved in experimental castings. The sequential of precipitation of TiN onto Al2MgO4 was confirmed using automated SEM/EDX and TEM analyses.

Electrostatic properties of the pyrimethamine-2,4-dihydroxybenzoic acid cocrystal in methanol studied using transferred electron-density parameters.

PubMed

Faroque, Muhammad Umer; Noureen, Sajida; Ahmed, Maqsood; Tahir, Muhammad Nawaz

2018-01-01

The crystal structure of the cocrystal salt form of the antimalarial drug pyrimethamine with 2,4-dihydroxybenzoic acid in methanol [systematic name: 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2,4-dihydroxybenzoate methanol monosolvate, C 12 H 14 ClN 4 + ·C 7 H 5 O 4 - ·CH 3 OH] has been studied using X-ray diffraction data collected at room temperature. The crystal structure was refined using the classical Independent Atom Model (IAM) and the Multipolar Atom Model by transferring electron-density parameters from the ELMAM2 database. The Cl atom was refined anharmonically. The results of both refinement methods have been compared. The intermolecular interactions have been characterized on the basis of Hirshfeld surface analysis and topological analysis using Bader's theory of Atoms in Molecules. The results show that the molecular assembly is built primarily on the basis of charge transfer between 2,4-dihydroxybenzoic acid and pyrimethamine, which results in strong intermolecular hydrogen bonds. This fact is further validated by the calculation of the electrostatic potential based on transferred electron-density parameters.

Calcio-olivine {gamma}-Ca{sub 2}SiO{sub 4}: I. Rietveld refinement of the crystal structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gobechiya, E. R., E-mail: elgob@mail.ru; Yamnova, N. A.; Zadov, A. E.

2008-05-15

The structure of the natural mineral calcio-olivine ({gamma}-Ca{sub 2}SiO{sub 4}) found in skarn xenoliths in the region of the Lakargi Mountain (North Caucasus, Kabardino-Balkaria, Russia) is refined by the Rietveld method [a = 5.07389(7) A, b = 11.21128(14) A, c = 6.75340(9) A, V = 384.170(5) A{sup 3}, Z = 4, {rho}{sub calcd} = 2.98 g/cm{sup 3}, space group Pbnm]. The X-ray diffraction pattern of a powdered sample is recorded on a STOE STADI MP diffractometer [{lambda}CuK{sub {alpha}1}; Ge(111) primary monochromator; 6.00{sup o} < 2{theta} < 100.88{sup o}; step width, 2.5{sup o} in 2{theta}; number of reflections, 224]. All calculationsmore » are performed with the WYRIET (version 3.3) software package. The structural model is refined in the anisotropic approximation to R{sub p} = 6.44, R{sub wp} = 8.52, R{sub exp} = 5.85, R{sub B} = 4.98, R{sub F} = 6.90, and s = 1.46. It is shown that the sample under investigation is a mixture of several mineral phases, among which calcio-olivine (the natural analogue of the {gamma}-Ca{sub 2}SiO{sub 4} compound) (83%), hillebrandite (13%), and wadalite (4%) are dominant. Only the scale factors and the unit cell parameters are refined for hillebrandite Ca{sub 2}SiO{sub 3}(OH){sub 2} [a = 3.63472(16) A, b = 16.4140(10) A, c = 11.7914(8) A, space group Cmc2{sub 1}, Z = 6] and wadalite Ca{sub 6}Al{sub 5}Si{sub 2}O{sub 16}Cl{sub 3} (a = 12.0088 A, space group, I 4 bar 3d, Z = 4). The results of the structure refinement of the main component of the sample confirm that the mineral calcio-olivine is isostructural to the synthetic compound {gamma}-Ca{sub 2}SiO{sub 4}. The structure of this compound is formed by the heteropolyhedral framework composed of Ca octahedra joined together into olivine-like ribbons and isolated Si tetrahedra.« less

A revised partiality model and post-refinement algorithm for X-ray free-electron laser data

DOE PAGES

Ginn, Helen Mary; Brewster, Aaron S.; Hattne, Johan; ...

2015-05-23

Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definitionmore » of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating theR splitvalue) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.« less

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

PubMed Central

Smart, Oliver S.; Womack, Thomas O.; Flensburg, Claus; Keller, Peter; Paciorek, Włodek; Sharff, Andrew; Vonrhein, Clemens; Bricogne, Gérard

2012-01-01

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 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand. PMID:22505257

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

PubMed Central

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; Wall, Michael E.; Jackson, Colin J.; Sauter, Nicholas K.; Adams, Paul D.; Urzhumtsev, Alexandre; Fraser, James S.

2015-01-01

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophos­phodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis. PMID:26249347

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

DOE PAGES

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; ...

2015-07-28

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier'smore » equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. In addition, these methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

Resolution of structural heterogeneity in dynamic crystallography

PubMed Central

Ren, Zhong; Chan, Peter W. Y.; Moffat, Keith; Pai, Emil F.; Royer, William E.; Šrajer, Vukica; Yang, Xiaojing

2013-01-01

Dynamic behavior of proteins is critical to their function. X-­ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic ‘structural changes’ are often indirectly inferred from ‘structural differences’ by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods. PMID:23695239

Resolution of structural heterogeneity in dynamic crystallography.

PubMed

Ren, Zhong; Chan, Peter W Y; Moffat, Keith; Pai, Emil F; Royer, William E; Šrajer, Vukica; Yang, Xiaojing

2013-06-01

Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.

Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

PubMed

Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

2016-02-01

Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

The blind leading the blind: Mutual refinement of approximate theories

NASA Technical Reports Server (NTRS)

Kedar, Smadar T.; Bresina, John L.; Dent, C. Lisa

1991-01-01

The mutual refinement theory, a method for refining world models in a reactive system, is described. The method detects failures, explains their causes, and repairs the approximate models which cause the failures. The approach focuses on using one approximate model to refine another.

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.

PubMed

Olson, Mark A; Feig, Michael; Brooks, Charles L

2008-04-15

This article examines ab initio methods for the prediction of protein loops by a computational strategy of multiscale conformational sampling and physical energy scoring functions. Our approach consists of initial sampling of loop conformations from lattice-based low-resolution models followed by refinement using all-atom simulations. To allow enhanced conformational sampling, the replica exchange method was implemented. Physical energy functions based on CHARMM19 and CHARMM22 parameterizations with generalized Born (GB) solvent models were applied in scoring loop conformations extracted from the lattice simulations and, in the case of all-atom simulations, the ensemble of conformations were generated and scored with these models. Predictions are reported for 25 loop segments, each eight residues long and taken from a diverse set of 22 protein structures. We find that the simulations generally sampled conformations with low global root-mean-square-deviation (RMSD) for loop backbone coordinates from the known structures, whereas clustering conformations in RMSD space and scoring detected less favorable loop structures. Specifically, the lattice simulations sampled basins that exhibited an average global RMSD of 2.21 +/- 1.42 A, whereas clustering and scoring the loop conformations determined an RMSD of 3.72 +/- 1.91 A. Using CHARMM19/GB to refine the lattice conformations improved the sampling RMSD to 1.57 +/- 0.98 A and detection to 2.58 +/- 1.48 A. We found that further improvement could be gained from extending the upper temperature in the all-atom refinement from 400 to 800 K, where the results typically yield a reduction of approximately 1 A or greater in the RMSD of the detected loop. Overall, CHARMM19 with a simple pairwise GB solvent model is more efficient at sampling low-RMSD loop basins than CHARMM22 with a higher-resolution modified analytical GB model; however, the latter simulation method provides a more accurate description of the all-atom energy surface, yet demands a much greater computational cost. (c) 2007 Wiley Periodicals, Inc.

Microstructural characteristics of adiabatic shear localization in a metastable beta titanium alloy deformed at high strain rate and elevated temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhan, Hongyi, E-mail: h.zhan@uq.edu.au; Zeng, Weidong; Wang, Gui

2015-04-15

The microstructural evolution and grain refinement within adiabatic shear bands in the Ti6554 alloy deformed at high strain rates and elevated temperatures have been characterized using transmission electron microscopy. No stress drops were observed in the corresponding stress–strain curve, indicating that the initiation of adiabatic shear bands does not lead to the loss of load capacity for the Ti6554 alloy. The outer region of the shear bands mainly consists of cell structures bounded by dislocation clusters. Equiaxed subgrains in the core area of the shear band can be evolved from the subdivision of cell structures or reconstruction and transverse segmentationmore » of dislocation clusters. It is proposed that dislocation activity dominates the grain refinement process. The rotational recrystallization mechanism may operate as the kinetic requirements for it are fulfilled. The coexistence of different substructures across the shear bands implies that the microstructural evolution inside the shear bands is not homogeneous and different grain refinement mechanisms may operate simultaneously to refine the structure. - Graphical abstract: Display Omitted - Highlights: • The microstructure within the adiabatic shear band was characterized by TEM. • No stress drops were observed in the corresponding stress–strain curve. • Dislocation activity dominated the grain refinement process. • The kinetic requirements for rotational recrystallization mechanism were fulfilled. • Different grain refinement mechanisms operated simultaneously to refine the structure.« less

Designing and benchmarking the MULTICOM protein structure prediction system

PubMed Central

2013-01-01

Background Predicting protein structure from sequence is one of the most significant and challenging problems in bioinformatics. Numerous bioinformatics techniques and tools have been developed to tackle almost every aspect of protein structure prediction ranging from structural feature prediction, template identification and query-template alignment to structure sampling, model quality assessment, and model refinement. How to synergistically select, integrate and improve the strengths of the complementary techniques at each prediction stage and build a high-performance system is becoming a critical issue for constructing a successful, competitive protein structure predictor. Results Over the past several years, we have constructed a standalone protein structure prediction system MULTICOM that combines multiple sources of information and complementary methods at all five stages of the protein structure prediction process including template identification, template combination, model generation, model assessment, and model refinement. The system was blindly tested during the ninth Critical Assessment of Techniques for Protein Structure Prediction (CASP9) in 2010 and yielded very good performance. In addition to studying the overall performance on the CASP9 benchmark, we thoroughly investigated the performance and contributions of each component at each stage of prediction. Conclusions Our comprehensive and comparative study not only provides useful and practical insights about how to select, improve, and integrate complementary methods to build a cutting-edge protein structure prediction system but also identifies a few new sources of information that may help improve the design of a protein structure prediction system. Several components used in the MULTICOM system are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/. PMID:23442819

ADAPTIVE TETRAHEDRAL GRID REFINEMENT AND COARSENING IN MESSAGE-PASSING ENVIRONMENTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hallberg, J.; Stagg, A.

2000-10-01

A grid refinement and coarsening scheme has been developed for tetrahedral and triangular grid-based calculations in message-passing environments. The element adaption scheme is based on an edge bisection of elements marked for refinement by an appropriate error indicator. Hash-table/linked-list data structures are used to store nodal and element formation. The grid along inter-processor boundaries is refined and coarsened consistently with the update of these data structures via MPI calls. The parallel adaption scheme has been applied to the solution of a transient, three-dimensional, nonlinear, groundwater flow problem. Timings indicate efficiency of the grid refinement process relative to the flow solvermore » calculations.« less

MAIN software for density averaging, model building, structure refinement and validation

PubMed Central

Turk, Dušan

2013-01-01

MAIN is software that has been designed to interactively perform the complex tasks of macromolecular crystal structure determination and validation. Using MAIN, it is possible to perform density modification, manual and semi-automated or automated model building and rebuilding, real- and reciprocal-space structure optimization and refinement, map calculations and various types of molecular structure validation. The prompt availability of various analytical tools and the immediate visualization of molecular and map objects allow a user to efficiently progress towards the completed refined structure. The extraordinary depth perception of molecular objects in three dimensions that is provided by MAIN is achieved by the clarity and contrast of colours and the smooth rotation of the displayed objects. MAIN allows simultaneous work on several molecular models and various crystal forms. The strength of MAIN lies in its manipulation of averaged density maps and molecular models when noncrystallographic symmetry (NCS) is present. Using MAIN, it is possible to optimize NCS parameters and envelopes and to refine the structure in single or multiple crystal forms. PMID:23897458

Solving the scalability issue in quantum-based refinement: Q|R#1.

PubMed

Zheng, Min; Moriarty, Nigel W; Xu, Yanting; Reimers, Jeffrey R; Afonine, Pavel V; Waller, Mark P

2017-12-01

Accurately refining biomacromolecules using a quantum-chemical method is challenging because the cost of a quantum-chemical calculation scales approximately as n m , where n is the number of atoms and m (≥3) is based on the quantum method of choice. This fundamental problem means that quantum-chemical calculations become intractable when the size of the system requires more computational resources than are available. In the development of the software package called Q|R, this issue is referred to as Q|R#1. A divide-and-conquer approach has been developed that fragments the atomic model into small manageable pieces in order to solve Q|R#1. Firstly, the atomic model of a crystal structure is analyzed to detect noncovalent interactions between residues, and the results of the analysis are represented as an interaction graph. Secondly, a graph-clustering algorithm is used to partition the interaction graph into a set of clusters in such a way as to minimize disruption to the noncovalent interaction network. Thirdly, the environment surrounding each individual cluster is analyzed and any residue that is interacting with a particular cluster is assigned to the buffer region of that particular cluster. A fragment is defined as a cluster plus its buffer region. The gradients for all atoms from each of the fragments are computed, and only the gradients from each cluster are combined to create the total gradients. A quantum-based refinement is carried out using the total gradients as chemical restraints. In order to validate this interaction graph-based fragmentation approach in Q|R, the entire atomic model of an amyloid cross-β spine crystal structure (PDB entry 2oNA) was refined.

Cross-sectional mapping for refined beam elements with applications to shell-like structures

NASA Astrophysics Data System (ADS)

Pagani, A.; de Miguel, A. G.; Carrera, E.

2017-06-01

This paper discusses the use of higher-order mapping functions for enhancing the physical representation of refined beam theories. Based on the Carrera unified formulation (CUF), advanced one-dimensional models are formulated by expressing the displacement field as a generic expansion of the generalized unknowns. According to CUF, a novel physically/geometrically consistent model is devised by employing Legendre-like polynomial sets to approximate the generalized unknowns at the cross-sectional level, whereas a local mapping technique based on the blending functions method is used to describe the exact physical boundaries of the cross-section domain. Classical and innovative finite element methods, including hierarchical p-elements and locking-free integration schemes, are utilized to solve the governing equations of the unified beam theory. Several numerical applications accounting for small displacements/rotations and strains are discussed, including beam structures with cross-sectional curved edges, cylindrical shells, and thin-walled aeronautical wing structures with reinforcements. The results from the proposed methodology are widely assessed by comparisons with solutions from the literature and commercial finite element software tools. The attention is focussed on the high computational efficiency and the marked capabilities of the present beam model, which can deal with a broad spectrum of structural problems with unveiled accuracy in terms of geometrical representation of the domain boundaries.

Mining the protein data bank with CReF to predict approximate 3-D structures of polypeptides.

PubMed

Dorn, Márcio; de Souza, Osmar Norberto

2010-01-01

n this paper we describe CReF, a Central Residue Fragment-based method to predict approximate 3-D structures of polypeptides by mining the Protein Data Bank (PDB). The approximate predicted structures are good enough to be used as starting conformations in refinement procedures employing state-of-the-art molecular mechanics methods such as molecular dynamics simulations. CReF is very fast and we illustrate its efficacy in three case studies of polypeptides whose sizes vary from 34 to 70 amino acids. As indicated by the RMSD values, our initial results show that the predicted structures adopt the expected fold, similar to the experimental ones.

Weak imposition of frictionless contact constraints on automatically recovered high-order, embedded interfaces using the finite cell method

NASA Astrophysics Data System (ADS)

Bog, Tino; Zander, Nils; Kollmannsberger, Stefan; Rank, Ernst

2018-04-01

The finite cell method (FCM) is a fictitious domain approach that greatly simplifies simulations involving complex structures. Recently, the FCM has been applied to contact problems. The current study continues in this field by extending the concept of weakly enforced boundary conditions to inequality constraints for frictionless contact. Furthermore, it formalizes an approach that automatically recovers high-order contact surfaces of (implicitly defined) embedded geometries by means of an extended Marching Cubes algorithm. To further improve the accuracy of the discretization, irregularities at the boundary of contact zones are treated with multi-level hp-refinements. Numerical results and a systematic study of h-, p- and hp-refinements show that the FCM can efficiently provide accurate results for problems involving contact.

Segmentation of heterogeneous blob objects through voting and level set formulation

PubMed Central

Chang, Hang; Yang, Qing; Parvin, Bahram

2009-01-01

Blob-like structures occur often in nature, where they aid in cueing and the pre-attentive process. These structures often overlap, form perceptual boundaries, and are heterogeneous in shape, size, and intensity. In this paper, voting, Voronoi tessellation, and level set methods are combined to delineate blob-like structures. Voting and subsequent Voronoi tessellation provide the initial condition and the boundary constraints for each blob, while curve evolution through level set formulation provides refined segmentation of each blob within the Voronoi region. The paper concludes with the application of the proposed method to a dataset produced from cell based fluorescence assays and stellar data. PMID:19774202

Iterative refinement of structure-based sequence alignments by Seed Extension

PubMed Central

Kim, Changhoon; Tai, Chin-Hsien; Lee, Byungkook

2009-01-01

Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence alignment procedures still mis-align substantial numbers of residues. In order to correct such errors, we previously explored the possibility of replacing the residue-based dynamic programming algorithm in structure alignment procedures with the Seed Extension algorithm, which does not use a gap penalty. Here, we describe a new procedure called RSE (Refinement with Seed Extension) that iteratively refines a structure-based sequence alignment. Results RSE uses SE (Seed Extension) in its core, which is an algorithm that we reported recently for obtaining a sequence alignment from two superimposed structures. The RSE procedure was evaluated by comparing the correctly aligned fractions of residues before and after the refinement of the structure-based sequence alignments produced by popular programs. CE, DaliLite, FAST, LOCK2, MATRAS, MATT, TM-align, SHEBA and VAST were included in this analysis and the NCBI's CDD root node set was used as the reference alignments. RSE improved the average accuracy of sequence alignments for all programs tested when no shift error was allowed. The amount of improvement varied depending on the program. The average improvements were small for DaliLite and MATRAS but about 5% for CE and VAST. More substantial improvements have been seen in many individual cases. The additional computation times required for the refinements were negligible compared to the times taken by the structure alignment programs. Conclusion RSE is a computationally inexpensive way of improving the accuracy of a structure-based sequence alignment. It can be used as a standalone procedure following a regular structure-based sequence alignment or to replace the traditional iterative refinement procedures based on residue-level dynamic programming algorithm in many structure alignment programs. PMID:19589133

An object-oriented approach for parallel self adaptive mesh refinement on block structured grids

NASA Technical Reports Server (NTRS)

Lemke, Max; Witsch, Kristian; Quinlan, Daniel

1993-01-01

Self-adaptive mesh refinement dynamically matches the computational demands of a solver for partial differential equations to the activity in the application's domain. In this paper we present two C++ class libraries, P++ and AMR++, which significantly simplify the development of sophisticated adaptive mesh refinement codes on (massively) parallel distributed memory architectures. The development is based on our previous research in this area. The C++ class libraries provide abstractions to separate the issues of developing parallel adaptive mesh refinement applications into those of parallelism, abstracted by P++, and adaptive mesh refinement, abstracted by AMR++. P++ is a parallel array class library to permit efficient development of architecture independent codes for structured grid applications, and AMR++ provides support for self-adaptive mesh refinement on block-structured grids of rectangular non-overlapping blocks. Using these libraries, the application programmers' work is greatly simplified to primarily specifying the serial single grid application and obtaining the parallel and self-adaptive mesh refinement code with minimal effort. Initial results for simple singular perturbation problems solved by self-adaptive multilevel techniques (FAC, AFAC), being implemented on the basis of prototypes of the P++/AMR++ environment, are presented. Singular perturbation problems frequently arise in large applications, e.g. in the area of computational fluid dynamics. They usually have solutions with layers which require adaptive mesh refinement and fast basic solvers in order to be resolved efficiently.

Multidataset Refinement Resonant Diffraction, and Magnetic Structures

PubMed Central

Attfield, J. Paul

2004-01-01

The scope of Rietveld and other powder diffraction refinements continues to expand, driven by improvements in instrumentation, methodology and software. This will be illustrated by examples from our research in recent years. Multidataset refinement is now commonplace; the datasets may be from different detectors, e.g., in a time-of-flight experiment, or from separate experiments, such as at several x-ray energies giving resonant information. The complementary use of x rays and neutrons is exemplified by a recent combined refinement of the monoclinic superstructure of magnetite, Fe3O4, below the 122 K Verwey transition, which reveals evidence for Fe2+/Fe3+ charge ordering. Powder neutron diffraction data continue to be used for the solution and Rietveld refinement of magnetic structures. Time-of-flight instruments on cold neutron sources can produce data that have a high intensity and good resolution at high d-spacings. Such profiles have been used to study incommensurate magnetic structures such as FeAsO4 and β–CrPO4. A multiphase, multidataset refinement of the phase-separated perovskite (Pr0.35Y0.07Th0.04Ca0.04Sr0.5)MnO3 has been used to fit three components with different crystal and magnetic structures at low temperatures. PMID:27366599

Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30.

PubMed

Lee, Hasup; Baek, Minkyung; Lee, Gyu Rie; Park, Sangwoo; Seok, Chaok

2017-03-01

Many proteins function as homo- or hetero-oligomers; therefore, attempts to understand and regulate protein functions require knowledge of protein oligomer structures. The number of available experimental protein structures is increasing, and oligomer structures can be predicted using the experimental structures of related proteins as templates. However, template-based models may have errors due to sequence differences between the target and template proteins, which can lead to functional differences. Such structural differences may be predicted by loop modeling of local regions or refinement of the overall structure. In CAPRI (Critical Assessment of PRotein Interactions) round 30, we used recently developed features of the GALAXY protein modeling package, including template-based structure prediction, loop modeling, model refinement, and protein-protein docking to predict protein complex structures from amino acid sequences. Out of the 25 CAPRI targets, medium and acceptable quality models were obtained for 14 and 1 target(s), respectively, for which proper oligomer or monomer templates could be detected. Symmetric interface loop modeling on oligomer model structures successfully improved model quality, while loop modeling on monomer model structures failed. Overall refinement of the predicted oligomer structures consistently improved the model quality, in particular in interface contacts. Proteins 2017; 85:399-407. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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} tomore » 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.« less

Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016

NASA Astrophysics Data System (ADS)

Fradera, Xavier; Verras, Andreas; Hu, Yuan; Wang, Deping; Wang, Hongwu; Fells, James I.; Armacost, Kira A.; Crespo, Alejandro; Sherborne, Brad; Wang, Huijun; Peng, Zhengwei; Gao, Ying-Duo

2018-01-01

We describe the performance of multiple pose prediction methods for the D3R 2016 Grand Challenge. The pose prediction challenge includes 36 ligands, which represent 4 chemotypes and some miscellaneous structures against the FXR ligand binding domain. In this study we use a mix of fully automated methods as well as human-guided methods with considerations of both the challenge data and publicly available data. The methods include ensemble docking, colony entropy pose prediction, target selection by molecular similarity, molecular dynamics guided pose refinement, and pose selection by visual inspection. We evaluated the success of our predictions by method, chemotype, and relevance of publicly available data. For the overall data set, ensemble docking, visual inspection, and molecular dynamics guided pose prediction performed the best with overall mean RMSDs of 2.4, 2.2, and 2.2 Å respectively. For several individual challenge molecules, the best performing method is evaluated in light of that particular ligand. We also describe the protein, ligand, and public information data preparations that are typical of our binding mode prediction workflow.

2D photonic crystal complete band gap search using a cyclic cellular automaton refination

NASA Astrophysics Data System (ADS)

González-García, R.; Castañón, G.; Hernández-Figueroa, H. E.

2014-11-01

We present a refination method based on a cyclic cellular automaton (CCA) that simulates a crystallization-like process, aided with a heuristic evolutionary method called differential evolution (DE) used to perform an ordered search of full photonic band gaps (FPBGs) in a 2D photonic crystal (PC). The solution is proposed as a combinatorial optimization of the elements in a binary array. These elements represent the existence or absence of a dielectric material surrounded by air, thus representing a general geometry whose search space is defined by the number of elements in such array. A block-iterative frequency-domain method was used to compute the FPBGs on a PC, when present. DE has proved to be useful in combinatorial problems and we also present an implementation feature that takes advantage of the periodic nature of PCs to enhance the convergence of this algorithm. Finally, we used this methodology to find a PC structure with a 19% bandgap-to-midgap ratio without requiring previous information of suboptimal configurations and we made a statistical study of how it is affected by disorder in the borders of the structure compared with a previous work that uses a genetic algorithm.

A parallel adaptive mesh refinement algorithm

NASA Technical Reports Server (NTRS)

Quirk, James J.; Hanebutte, Ulf R.

1993-01-01

Over recent years, Adaptive Mesh Refinement (AMR) algorithms which dynamically match the local resolution of the computational grid to the numerical solution being sought have emerged as powerful tools for solving problems that contain disparate length and time scales. In particular, several workers have demonstrated the effectiveness of employing an adaptive, block-structured hierarchical grid system for simulations of complex shock wave phenomena. Unfortunately, from the parallel algorithm developer's viewpoint, this class of scheme is quite involved; these schemes cannot be distilled down to a small kernel upon which various parallelizing strategies may be tested. However, because of their block-structured nature such schemes are inherently parallel, so all is not lost. In this paper we describe the method by which Quirk's AMR algorithm has been parallelized. This method is built upon just a few simple message passing routines and so it may be implemented across a broad class of MIMD machines. Moreover, the method of parallelization is such that the original serial code is left virtually intact, and so we are left with just a single product to support. The importance of this fact should not be underestimated given the size and complexity of the original algorithm.

Crystal structure of low-symmetry rondorfite

NASA Astrophysics Data System (ADS)

Rastsvetaeva, R. K.; Zadov, A. E.; Chukanov, N. V.

2008-03-01

The crystal structure of an aluminum-rich variety of the mineral rondorfite with the composition Ca16[Mg2(Si7Al)(O31OH)]Cl4 from the skarns of the Verkhne-Chegemskoe plateau (the Kabardino-Balkarian Republic, the Northern Caucasus Region, Russia) was solved in the triclinic space group with the unit-cell parameters a = 15.100(2) Å, b = 15.110(2) Å, c = 15.092(2) Å, α = 90.06(1)°, β = 90.01(1)°, γ = 89.93(1)°, Z = 4, sp. gr. P1. The structural model consisting of 248 independent atoms was determined by the phase-correction method and refined to R = 3.8% with anisotropic displacement parameters based on all 7156 independent reflections with 7156 F > 3σ( F). The crystal structure is based on pentamers consisting of four Si tetrahedra linked by the central Mg tetrahedron. The structure can formally be refined in the cubic space group ( a = 15.105 Å, sp. gr. Fd overline 3 , seven independent positions) with anisotropic displacement parameters to R = 2.74% based on 579 reflections with F > 3σ( F) without accounting for more than 1000 observed reflections, which are inconsistent with the cubic symmetry of the crystal structure.

Strategies for carbohydrate model building, refinement and validation

PubMed Central

2017-01-01

Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein–sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade. PMID:28177313

Strategies for carbohydrate model building, refinement and validation.

PubMed

Agirre, Jon

2017-02-01

Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein-sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade.

A template-based approach for parallel hexahedral two-refinement

DOE PAGES

Owen, Steven J.; Shih, Ryan M.; Ernst, Corey D.

2016-10-17

Here, we provide a template-based approach for generating locally refined all-hex meshes. We focus specifically on refinement of initially structured grids utilizing a 2-refinement approach where uniformly refined hexes are subdivided into eight child elements. The refinement algorithm consists of identifying marked nodes that are used as the basis for a set of four simple refinement templates. The target application for 2-refinement is a parallel grid-based all-hex meshing tool for high performance computing in a distributed environment. The result is a parallel consistent locally refined mesh requiring minimal communication and where minimum mesh quality is greater than scaled Jacobian 0.3more » prior to smoothing.« less

A template-based approach for parallel hexahedral two-refinement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Owen, Steven J.; Shih, Ryan M.; Ernst, Corey D.

Here, we provide a template-based approach for generating locally refined all-hex meshes. We focus specifically on refinement of initially structured grids utilizing a 2-refinement approach where uniformly refined hexes are subdivided into eight child elements. The refinement algorithm consists of identifying marked nodes that are used as the basis for a set of four simple refinement templates. The target application for 2-refinement is a parallel grid-based all-hex meshing tool for high performance computing in a distributed environment. The result is a parallel consistent locally refined mesh requiring minimal communication and where minimum mesh quality is greater than scaled Jacobian 0.3more » prior to smoothing.« less

Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.

PubMed

Guillot, Benoît; Jelsch, Christian; Podjarny, Alberto; Lecomte, Claude

2008-05-01

The valence electron density of the protein human aldose reductase was analyzed at 0.66 angstroms resolution. The methodological developments in the software MoPro to adapt standard charge-density techniques from small molecules to macromolecular structures are described. The deformation electron density visible in initial residual Fourier difference maps was significantly enhanced after high-order refinement. The protein structure was refined after transfer of the experimental library multipolar atom model (ELMAM). The effects on the crystallographic statistics, on the atomic thermal displacement parameters and on the structure stereochemistry are analyzed. Constrained refinements of the transferred valence populations Pval and multipoles Plm were performed against the X-ray diffraction data on a selected substructure of the protein with low thermal motion. The resulting charge densities are of good quality, especially for chemical groups with many copies present in the polypeptide chain. To check the effect of the starting point on the result of the constrained multipolar refinement, the same charge-density refinement strategy was applied but using an initial neutral spherical atom model, i.e. without transfer from the ELMAM library. The best starting point for a protein multipolar refinement is the structure with the electron density transferred from the database. This can be assessed by the crystallographic statistical indices, including Rfree, and the quality of the static deformation electron-density maps, notably on the oxygen electron lone pairs. The analysis of the main-chain bond lengths suggests that stereochemical dictionaries would benefit from a revision based on recently determined unrestrained atomic resolution protein structures.

Bulk Nanolaminated Nickel: Preparation, Microstructure, Mechanical Property, and Thermal Stability

NASA Astrophysics Data System (ADS)

Liu, Fan; Yuan, Hao; Goel, Sunkulp; Liu, Ying; Wang, Jing Tao

2018-02-01

A bulk nanolaminated (NL) structure with distinctive fractions of low- and high-angle grain boundaries ( f LAGBs and f HAGBs) is produced in pure nickel, through a two-step process of primary grain refinement by equal-channel angular pressing (ECAP), followed by a secondary geometrical refinement via liquid nitrogen rolling (LNR). The lamellar boundary spacings of 2N and 4N nickel are refined to 40 and 70 nm, respectively, and the yield strength of the NL structure in 2N nickel reaches 1.5 GPa. The impacts of the deformation path, material purity, grain boundary (GB) misorientation, and energy on the microstructure, refinement ability, mechanical strength, and thermal stability are investigated to understand the inherent governing mechanisms. GB migration is the main restoration mechanism limiting the refinement of an NL structure in 4N nickel, while in 2N nickel, shear banding occurs and mediates one-fifth of the total true normal rolling strain at the mesoscale, restricting further refinement. Three typical structures [ultrafine grained (UFG), NL with low f LAGBs, and NL with high f LAGBs] obtained through three different combinations of ECAP and LNR were studied by isochronal annealing for 1 hour at temperatures ranging from 433 K to 973 K (160 °C to 700 °C). Higher thermal stability in the NL structure with high f LAGBs is shown by a 50 K (50 °C) delay in the initiation temperature of recrystallization. Based on calculations and analyses of the stored energies of deformed structures from strain distribution, as characterized by kernel average misorientation (KAM), and from GB misorientations, higher thermal stability is attributed to high f LAGBs in this type of NL structure. This is confirmed by a slower change in the microstructure, as revealed by characterizing its annealing kinetics using KAM maps.

Effect of zirconium addition on welding of aluminum grain refined by titanium plus boron

NASA Astrophysics Data System (ADS)

Zaid, A. I. O.

2014-06-01

Aluminum oxidizes freely in ordinary atmosphere which makes its welding difficult and weak, particularly it solidifies in columnar structure with large grains. Therefore, it is anticipated that the effect of addition of some grain refiners to its melt before solidification is worth while investigating as it may enhance its weldabilty and improve its mechanical strength. In this paper, the effect of addition of zirconium at a weight of 0.1% (which corresponds to the peretictic limit on the aluminum-zirconium base phase diagram) to commercially pure aluminum, grain refined by Ti+B on its weldability, using gas tungsten arc welding, GTAW, method which was formerly known as TIG. A constant current level of 30 AC Ampere was used because it removes the oxides during the welding process. Metallographic examination of the weldments of the different combinations of Al with Al and Al with its microalloys: in the heat affected zone, HAZ, and away from it was carried out and examined for HAZ width, porosity, cracks and microhardness. It was found that grain refining by Ti+B or Zr resulted in enhancement of the weldment.

Development and evaluation of a local grid refinement method for block-centered finite-difference groundwater models using shared nodes

USGS Publications Warehouse

Mehl, S.; Hill, M.C.

2002-01-01

A new method of local grid refinement for two-dimensional block-centered finite-difference meshes is presented in the context of steady-state groundwater-flow modeling. The method uses an iteration-based feedback with shared nodes to couple two separate grids. The new method is evaluated by comparison with results using a uniform fine mesh, a variably spaced mesh, and a traditional method of local grid refinement without a feedback. Results indicate: (1) The new method exhibits quadratic convergence for homogeneous systems and convergence equivalent to uniform-grid refinement for heterogeneous systems. (2) Coupling the coarse grid with the refined grid in a numerically rigorous way allowed for improvement in the coarse-grid results. (3) For heterogeneous systems, commonly used linear interpolation of heads from the large model onto the boundary of the refined model produced heads that are inconsistent with the physics of the flow field. (4) The traditional method works well in situations where the better resolution of the locally refined grid has little influence on the overall flow-system dynamics, but if this is not true, lack of a feedback mechanism produced errors in head up to 3.6% and errors in cell-to-cell flows up to 25%. ?? 2002 Elsevier Science Ltd. All rights reserved.

Knowledge-Building Activity Structures in Japanese Elementary Science Pedagogy

ERIC Educational Resources Information Center

Oshima, Jun; Oshima, Ritsuko; Murayama, Isao; Inagaki, Shigenori; Takenaka, Makiko; Yamamoto, Tomokazu; Yamaguchi, Etsuji; Nakayama, Hayashi

2006-01-01

The purpose of this study is to refine Japanese elementary science activity structures by using a CSCL approach to transform the classroom into a knowledge-building community. We report design studies on two science lessons in two consecutive years and describe the progressive refinement of the activity structures. Through comparisons of student…

Hydrogen bonding in goldichite, KFe(SO4)2ṡ4H2O: structure refinement

NASA Astrophysics Data System (ADS)

Yang, Zhuming; Giester, Gerald

2018-02-01

The crystal structure of goldichite KFe(SO4)2ṡ4H2O was determined on a single crystal from the Baiyinchang copper deposit, Gansu, China. [ P121/ c1, a = 10.395(2), b = 10.475(2), c = 9.0875(18) Å, β = 101.65(3)°, V = 969.1(3) Å3, Z = 4]. All non-H atoms were refined with anisotropic displacement parameters and positions of H-atoms were determined by difference Fourier methods and refined from X-ray diffraction data. The crystal structure of goldichite consists of corrugated sheets parallel to the (100) plane by sharing corners between FeO6 octahedra and SO4 tetrahedra. The interstitial potassium atom exhibits a [KO7(H2O)2] nine-fold coordination, which shares edges to form a column parallel to the c-axis and to build a slab with the corrugated sheet. These slabs are linked in the [100] direction through a network of hydrogen bonds. Three types of hydrogen bonds involve links of slabs: Ow(3)-H(3B)···O(1), Ow(6)-H(6B)···O(11) and Ow(9)-H(9B)···O(11). The FTIR spectrum of goldichite shows a strong absorption between 3384 cm-1 and 3592 cm-1, which is in accordance with the O-H···O distances derived from structure data.

Enrichment of refined olive oil with phenolic compounds: evaluation of their antioxidant activity and their effect on the bitter index.

PubMed

Artajo, Luz S; Romero, María P; Morelló, José R; Motilva, María J

2006-08-09

The study of the antioxidant effects of biophenolic compounds is supported by the current interest in natural products and the ongoing replacement of synthetic antioxidants by natural antioxidants from plant sources. Olives and olive oil, especially extra virgin olive oil, contain a variety of bioactive compounds (phytochemicals) widely considered to be potentially beneficial for health. This research was focused on evaluating the antioxidant activity of the enriched refined olive oil to discover a possible functional food application. Different concentrations of individual and combined phenolic compounds were added to the refined olive oil as lipid matrix, and the antioxidant activity expressed as oxidative stability in hours was determined by using the Rancimat method. Additionally, the bitter index was evaluated to assess the effect of the enrichment in relation to the organoleptic quality. The results showed that the antioxidant activity depends on the concentration of the phenol used for the assay and the chemical structure. In general, the most positive effects were observed in 3,4-dihydroxy and 3,4,5-trihydroxy structures linked to an aromatic ring that conferred to the moiety a higher proton dislocation, thus facilitating the scavenging activity.

Targeting Neuroblastoma Cell Surface Proteins: Recommendations for Homology Modeling of hNET, ALK, and TrkB.

PubMed

Haddad, Yazan; Heger, Zbyněk; Adam, Vojtech

2017-01-01

Targeted therapy is a promising approach for treatment of neuroblastoma as evident from the large number of targeting agents employed in clinical practice today. In the absence of known crystal structures, researchers rely on homology modeling to construct template-based theoretical structures for drug design and testing. Here, we discuss three candidate cell surface proteins that are suitable for homology modeling: human norepinephrine transporter (hNET), anaplastic lymphoma kinase (ALK), and neurotrophic tyrosine kinase receptor 2 (NTRK2 or TrkB). When choosing templates, both sequence identity and structure quality are important for homology modeling and pose the first of many challenges in the modeling process. Homology modeling of hNET can be improved using template models of dopamine and serotonin transporters instead of the leucine transporter (LeuT). The extracellular domains of ALK and TrkB are yet to be exploited by homology modeling. There are several idiosyncrasies that require direct attention throughout the process of model construction, evaluation and refinement. Shifts/gaps in the alignment between the template and target, backbone outliers and side-chain rotamer outliers are among the main sources of physical errors in the structures. Low-conserved regions can be refined with loop modeling method. Residue hydrophobicity, accessibility to bound metals or glycosylation can aid in model refinement. We recommend resolving these idiosyncrasies as part of "good modeling practice" to obtain highest quality model. Decreasing physical errors in protein structures plays major role in the development of targeting agents and understanding of chemical interactions at the molecular level.

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.

PubMed

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.

A Method for Assessing Required Course-Related Skills and Prerequisite Structure

ERIC Educational Resources Information Center

Johnson, Michael D.; Wang, Jyhwen

2015-01-01

Engineering curricula should be dynamic with a goal of constant improvement and refinement. Unfortunately, this is often not the case; courses are developed, altered, and expanded in a piecemeal manner. Namely, as time progresses many programmes end up with courses that are developed and not a developed curriculum. To remedy this shortcoming…

DFT energy optimization of a large carbohydrate: cyclomaltohexaicosaose (CA-26)

USDA-ARS?s Scientific Manuscript database

CA-26 is the largest cyclodextrin (546 atoms) for which refined X-ray structural data is available. Because of its size, 26 D-glucose residues, it is beyond the scope of study of most ab initio or density functional methods, and to date has only been computationally examined using empirical force fi...

Development of advanced acreage estimation methods

NASA Technical Reports Server (NTRS)

Guseman, L. F., Jr. (Principal Investigator)

1982-01-01

The development of an accurate and efficient algorithm for analyzing the structure of MSS data, the application of the Akaiki information criterion to mixture models, and a research plan to delineate some of the technical issues and associated tasks in the area of rice scene radiation characterization are discussed. The AMOEBA clustering algorithm is refined and documented.

Vibration Analysis Of Automotive Structures Using Holographic Interferometry

NASA Astrophysics Data System (ADS)

Brown, G. M.; Wales, R. R.

1983-10-01

Since 1979, Ford Motor Company has been developing holographic interferometry to supplement more conventional test methods to measure vehicle component vibrations. An Apollo PHK-1 Double Pulse Holographic Laser System was employed to visualize a variety of complex vibration modes, primarily on current production and prototype powertrain components. Design improvements to reduce powertrain response to problem excitations have been deter-mined through pulsed laser holography, and have, in several cases, been put into production in Ford vehicles. Whole-field definition of vibration related deflections provide continuity of information missed by accelerometer/modal analysis techniaues. Certain opera-tional problems, common among pulsed ruby holographic lasers, have reauired ongoing hardware and electronics improvements to minimize system downtime. Real-time, time-averaged and stroboscopic C. W. laser holographic techniques are being developed at Ford to complement the double pulse capabilities and provide rapid identification of modal frequencies and nodal lines for analysis of powertrain structures. Methods for mounting and exciting powertrains to minimize rigid body motions are discussed. Work at Ford will continue toward development of C. W. holographic techniques to provide refined test methodology dedicated to noise and vibration diagnostics with particular emphasis on semi-automated methods for quantifying displacement and relative phase using high resolution digitized video and computers. Continued use of refined pulsed and CW laser holographic interferometry for the analysis of complex structure vibrations seems assured.

Report of the Workshop on Geologic Applications of Remote Sensing to the Study of Sedimentary Basins

NASA Technical Reports Server (NTRS)

Lang, H. R. (Editor)

1985-01-01

The Workshop on Geologic Applications of Remote Sensing to the Study of Sedimentary Basins, held January 10 to 11, 1985 in Lakewood, Colorado, involved 43 geologists from industry, government, and academia. Disciplines represented ranged from vertebrate paleontology to geophysical modeling of continents. Deliberations focused on geologic problems related to the formation, stratigraphy, structure, and evolution of foreland basins in general, and to the Wind River/Bighorn Basin area of Wyoming in particular. Geological problems in the Wind River/Bighorn basin area that should be studied using state-of-the-art remote sensing methods were identified. These include: (1) establishing the stratigraphic sequence and mapping, correlating, and analyzing lithofacies of basin-filling strata in order to refine the chronology of basin sedimentation, and (2) mapping volcanic units, fracture patterns in basement rocks, and Tertiary-Holocene landforms in searches for surface manifestations of concealed structures in order to refine models of basin tectonics. Conventional geologic, topographic, geophysical, and borehole data should be utilized in these studies. Remote sensing methods developed in the Wind River/Bighorn Basin area should be applied in other basins.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Kyle K. G., E-mail: kylesmith@utexas.edu; Rossky, Peter J., E-mail: peter.rossky@austin.utexas.edu; Poulsen, Jens Aage, E-mail: jens72@chem.gu.se

The dynamic structure factor of liquid para-hydrogen and ortho-deuterium in corresponding thermodynamic states (T = 20.0 K, n = 21.24 nm{sup −3}) and (T = 23.0 K, n = 24.61 nm{sup −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{sup −1}.more » 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{sup −1} para-hydrogen provides a test case for improved approximations to quantum dynamics.« less

Analysis of biomolecular solvation sites by 3D-RISM theory.

PubMed

Sindhikara, Daniel J; Hirata, Fumio

2013-06-06

We derive, implement, and apply equilibrium solvation site analysis for biomolecules. Our method utilizes 3D-RISM calculations to quickly obtain equilibrium solvent distributions without either necessity of simulation or limits of solvent sampling. Our analysis of these distributions extracts highest likelihood poses of solvent as well as localized entropies, enthalpies, and solvation free energies. We demonstrate our method on a structure of HIV-1 protease where excellent structural and thermodynamic data are available for comparison. Our results, obtained within minutes, show systematic agreement with available experimental data. Further, our results are in good agreement with established simulation-based solvent analysis methods. This method can be used not only for visual analysis of active site solvation but also for virtual screening methods and experimental refinement.

Large-eddy simulation of wind turbine wake interactions on locally refined Cartesian grids

NASA Astrophysics Data System (ADS)

Angelidis, Dionysios; Sotiropoulos, Fotis

2014-11-01

Performing high-fidelity numerical simulations of turbulent flow in wind farms remains a challenging issue mainly because of the large computational resources required to accurately simulate the turbine wakes and turbine/turbine interactions. The discretization of the governing equations on structured grids for mesoscale calculations may not be the most efficient approach for resolving the large disparity of spatial scales. A 3D Cartesian grid refinement method enabling the efficient coupling of the Actuator Line Model (ALM) with locally refined unstructured Cartesian grids adapted to accurately resolve tip vortices and multi-turbine interactions, is presented. Second order schemes are employed for the discretization of the incompressible Navier-Stokes equations in a hybrid staggered/non-staggered formulation coupled with a fractional step method that ensures the satisfaction of local mass conservation to machine zero. The current approach enables multi-resolution LES of turbulent flow in multi-turbine wind farms. The numerical simulations are in good agreement with experimental measurements and are able to resolve the rich dynamics of turbine wakes on grids containing only a small fraction of the grid nodes that would be required in simulations without local mesh refinement. This material is based upon work supported by the Department of Energy under Award Number DE-EE0005482 and the National Science Foundation under Award number NSF PFI:BIC 1318201.

Structure refinement of Zn and Pr-doped Y-Ba-Cu-oxides

NASA Astrophysics Data System (ADS)

Naik, M. S.; Sarode, P. R.; Priolkar, K. R.; Prabhu, R. B.

2018-05-01

Superconducting compounds of composition Y0.9 Pr0.1Ba2 [Cu1-yZny]3O7-δ (0 ≤ y ≤ 0.10) have been synthesized. The structure of these materials has been studied using powder X-ray diffraction technique and refinement has been carried out by using Rietveld refinement procedure. It has been shown that all these compounds crystallize in orthorhombic structure with slight change in c parameter. Increase of parameter O(2) and decrease of parameter O(3)suggest the changes in the Cu-O2 plane of these orthorhombic materials on Zn substitution.

Developments and Validations of Fully Coupled CFD and Practical Vortex Transport Method for High-Fidelity Wake Modeling in Fixed and Rotary Wing Applications

NASA Technical Reports Server (NTRS)

Anusonti-Inthra, Phuriwat

2010-01-01

A novel Computational Fluid Dynamics (CFD) coupling framework using a conventional Reynolds-Averaged Navier-Stokes (BANS) solver to resolve the near-body flow field and a Particle-based Vorticity Transport Method (PVTM) to predict the evolution of the far field wake is developed, refined, and evaluated for fixed and rotary wing cases. For the rotary wing case, the RANS/PVTM modules are loosely coupled to a Computational Structural Dynamics (CSD) module that provides blade motion and vehicle trim information. The PVTM module is refined by the addition of vortex diffusion, stretching, and reorientation models as well as an efficient memory model. Results from the coupled framework are compared with several experimental data sets (a fixed-wing wind tunnel test and a rotary-wing hover test).

A novel non-uniform control vector parameterization approach with time grid refinement for flight level tracking optimal control problems.

PubMed

Liu, Ping; Li, Guodong; Liu, Xinggao; Xiao, Long; Wang, Yalin; Yang, Chunhua; Gui, Weihua

2018-02-01

High quality control method is essential for the implementation of aircraft autopilot system. An optimal control problem model considering the safe aerodynamic envelop is therefore established to improve the control quality of aircraft flight level tracking. A novel non-uniform control vector parameterization (CVP) method with time grid refinement is then proposed for solving the optimal control problem. By introducing the Hilbert-Huang transform (HHT) analysis, an efficient time grid refinement approach is presented and an adaptive time grid is automatically obtained. With this refinement, the proposed method needs fewer optimization parameters to achieve better control quality when compared with uniform refinement CVP method, whereas the computational cost is lower. Two well-known flight level altitude tracking problems and one minimum time cost problem are tested as illustrations and the uniform refinement control vector parameterization method is adopted as the comparative base. Numerical results show that the proposed method achieves better performances in terms of optimization accuracy and computation cost; meanwhile, the control quality is efficiently improved. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Data structures supporting multi-region adaptive isogeometric analysis

NASA Astrophysics Data System (ADS)

Perduta, Anna; Putanowicz, Roman

2018-01-01

Since the first paper published in 2005 Isogeometric Analysis (IGA) has gained strong interest and found applications in many engineering problems. Despite the advancement of the method, there are still far fewer software implementations comparing to Finite Element Method. The paper presents an approach to the development of data structures that can support multi-region IGA with local mesh refinement (patch-based) and possible application in IGA-FEM models. The purpose of this paper is to share original design concepts, that authors have created while developing an IGA package, which other researchers may find beneficial for their own simulation codes.

Simulation of an Isolated Tiltrotor in Hover with an Unstructured Overset-Grid RANS Solver

NASA Technical Reports Server (NTRS)

Lee-Rausch, Elizabeth M.; Biedron, Robert T.

2009-01-01

An unstructured overset-grid Reynolds Averaged Navier-Stokes (RANS) solver, FUN3D, is used to simulate an isolated tiltrotor in hover. An overview of the computational method is presented as well as the details of the overset-grid systems. Steady-state computations within a noninertial reference frame define the performance trends of the rotor across a range of the experimental collective settings. Results are presented to show the effects of off-body grid refinement and blade grid refinement. The computed performance and blade loading trends show good agreement with experimental results and previously published structured overset-grid computations. Off-body flow features indicate a significant improvement in the resolution of the first perpendicular blade vortex interaction with background grid refinement across the collective range. Considering experimental data uncertainty and effects of transition, the prediction of figure of merit on the baseline and refined grid is reasonable at the higher collective range- within 3 percent of the measured values. At the lower collective settings, the computed figure of merit is approximately 6 percent lower than the experimental data. A comparison of steady and unsteady results show that with temporal refinement, the dynamic results closely match the steady-state noninertial results which gives confidence in the accuracy of the dynamic overset-grid approach.

Fast digital zooming system using directionally adaptive image interpolation and restoration.

PubMed

Kang, Wonseok; Jeon, Jaehwan; Yu, Soohwan; Paik, Joonki

2014-01-01

This paper presents a fast digital zooming system for mobile consumer cameras using directionally adaptive image interpolation and restoration methods. The proposed interpolation algorithm performs edge refinement along the initially estimated edge orientation using directionally steerable filters. Either the directionally weighted linear or adaptive cubic-spline interpolation filter is then selectively used according to the refined edge orientation for removing jagged artifacts in the slanted edge region. A novel image restoration algorithm is also presented for removing blurring artifacts caused by the linear or cubic-spline interpolation using the directionally adaptive truncated constrained least squares (TCLS) filter. Both proposed steerable filter-based interpolation and the TCLS-based restoration filters have a finite impulse response (FIR) structure for real time processing in an image signal processing (ISP) chain. Experimental results show that the proposed digital zooming system provides high-quality magnified images with FIR filter-based fast computational structure.

Microgravity

NASA Image and Video Library

1992-06-25

Zeolites are crystalline aluminosilicates that have complex framework structures. However, there are several features of zeolite crystals that make unequivocal structure determinations difficult. The acquisition of reliable structural information on zeolites is greatly facilitated by the availability of high-quality specimens. For structure determinations by conventional diffraction techniques, large single-crystal specimens are essential. Alternatively, structural determinations by powder profile refinement methods relax the constraints on crystal size, but still require materials with a high degree of crystalline perfection. Studies conducted at CAMMP (Center for Advanced Microgravity Materials Processing) have demonstrated that microgravity processing can produce larger crystal sizes and fewer structural defects relative to terrestrial crystal growth. Principal Investigator: Dr. Albert Sacco

Zeolites

NASA Technical Reports Server (NTRS)

1992-01-01

Zeolites are crystalline aluminosilicates that have complex framework structures. However, there are several features of zeolite crystals that make unequivocal structure determinations difficult. The acquisition of reliable structural information on zeolites is greatly facilitated by the availability of high-quality specimens. For structure determinations by conventional diffraction techniques, large single-crystal specimens are essential. Alternatively, structural determinations by powder profile refinement methods relax the constraints on crystal size, but still require materials with a high degree of crystalline perfection. Studies conducted at CAMMP (Center for Advanced Microgravity Materials Processing) have demonstrated that microgravity processing can produce larger crystal sizes and fewer structural defects relative to terrestrial crystal growth. Principal Investigator: Dr. Albert Sacco

Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

DOE PAGES

Timoshenko, J.; Shivhare, A.; Scott, R. W.; ...

2016-06-30

We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

Triclinic lysozyme at 0.65 angstrom resolution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, J.; Dauter, M.; Alkire, R.

The crystal structure of triclinic hen egg-white lysozyme (HEWL) has been refined against diffraction data extending to 0.65 {angstrom} resolution measured at 100 K using synchrotron radiation. Refinement with anisotropic displacement parameters and with the removal of stereochemical restraints for the well ordered parts of the structure converged with a conventional R factor of 8.39% and an R{sub free} of 9.52%. The use of full-matrix refinement provided an estimate of the variances in the derived parameters. In addition to the 129-residue protein, a total of 170 water molecules, nine nitrate ions, one acetate ion and three ethylene glycol molecules weremore » located in the electron-density map. Eight sections of the main chain and many side chains were modeled with alternate conformations. The occupancies of the water sites were refined and this step is meaningful when assessed by use of the free R factor. A detailed description and comparison of the structure are made with reference to the previously reported triclinic HEWL structures refined at 0.925 {angstrom} (at the low temperature of 120 K) and at 0.95 {angstrom} resolution (at room temperature).« less

Polarizable atomic multipole X-ray refinement: application to peptide crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schnieders, Michael J.; Fenn, Timothy D.; Howard Hughes Medical Institute

2009-09-01

A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time. Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussianmore » multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R{sub free} by 20–40% relative to the original spherically symmetric scattering model.« less

Parallel goal-oriented adaptive finite element modeling for 3D electromagnetic exploration

NASA Astrophysics Data System (ADS)

Zhang, Y.; Key, K.; Ovall, J.; Holst, M.

2014-12-01

We present a parallel goal-oriented adaptive finite element method for accurate and efficient electromagnetic (EM) modeling of complex 3D structures. An unstructured tetrahedral mesh allows this approach to accommodate arbitrarily complex 3D conductivity variations and a priori known boundaries. The total electric field is approximated by the lowest order linear curl-conforming shape functions and the discretized finite element equations are solved by a sparse LU factorization. Accuracy of the finite element solution is achieved through adaptive mesh refinement that is performed iteratively until the solution converges to the desired accuracy tolerance. Refinement is guided by a goal-oriented error estimator that uses a dual-weighted residual method to optimize the mesh for accurate EM responses at the locations of the EM receivers. As a result, the mesh refinement is highly efficient since it only targets the elements where the inaccuracy of the solution corrupts the response at the possibly distant locations of the EM receivers. We compare the accuracy and efficiency of two approaches for estimating the primary residual error required at the core of this method: one uses local element and inter-element residuals and the other relies on solving a global residual system using a hierarchical basis. For computational efficiency our method follows the Bank-Holst algorithm for parallelization, where solutions are computed in subdomains of the original model. To resolve the load-balancing problem, this approach applies a spectral bisection method to divide the entire model into subdomains that have approximately equal error and the same number of receivers. The finite element solutions are then computed in parallel with each subdomain carrying out goal-oriented adaptive mesh refinement independently. We validate the newly developed algorithm by comparison with controlled-source EM solutions for 1D layered models and with 2D results from our earlier 2D goal oriented adaptive refinement code named MARE2DEM. We demonstrate the performance and parallel scaling of this algorithm on a medium-scale computing cluster with a marine controlled-source EM example that includes a 3D array of receivers located over a 3D model that includes significant seafloor bathymetry variations and a heterogeneous subsurface.

A semi-implicit level set method for multiphase flows and fluid-structure interaction problems

NASA Astrophysics Data System (ADS)

Cottet, Georges-Henri; Maitre, Emmanuel

2016-06-01

In this paper we present a novel semi-implicit time-discretization of the level set method introduced in [8] for fluid-structure interaction problems. The idea stems from a linear stability analysis derived on a simplified one-dimensional problem. The semi-implicit scheme relies on a simple filter operating as a pre-processing on the level set function. It applies to multiphase flows driven by surface tension as well as to fluid-structure interaction problems. The semi-implicit scheme avoids the stability constraints that explicit scheme need to satisfy and reduces significantly the computational cost. It is validated through comparisons with the original explicit scheme and refinement studies on two-dimensional benchmarks.

Center for Macromolecular Crystallography, University of Alabama in Birmingham

NASA Technical Reports Server (NTRS)

Navia, Manuel A.

1991-01-01

Porcine pancreatic elastase (PPE) crystals grown under microgravity conditions on mission STS-26 of the Space Shuttle Discovery were shown to diffract to considerably higher resolution than the best PPE crystals grown by us on the ground. We have now independently refined both the microgravity and ground-based data. Preliminary results of these refinements are summarized. These results show nearly a doubling of experimental diffraction data for this structure, exceeding 1.3 A resolution. Improved phase information derived from the refined structure of PPE based on this microgravity data has allowed us to interpret previously-uninterpretable electron density obtained from ground-based crystals of a complex of PPE with a chemically-reactive inhibitor. Intermediate stages in the enzyme-inhibitor reaction mechanism in the crystal can now be directly observed. Further refinement of PPE structures is in progress.

Implicit adaptive mesh refinement for 2D reduced resistive magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Philip, Bobby; Chacón, Luis; Pernice, Michael

2008-10-01

An implicit structured adaptive mesh refinement (SAMR) solver for 2D reduced magnetohydrodynamics (MHD) is described. The time-implicit discretization is able to step over fast normal modes, while the spatial adaptivity resolves thin, dynamically evolving features. A Jacobian-free Newton-Krylov method is used for the nonlinear solver engine. For preconditioning, we have extended the optimal "physics-based" approach developed in [L. Chacón, D.A. Knoll, J.M. Finn, An implicit, nonlinear reduced resistive MHD solver, J. Comput. Phys. 178 (2002) 15-36] (which employed multigrid solver technology in the preconditioner for scalability) to SAMR grids using the well-known Fast Adaptive Composite grid (FAC) method [S. McCormick, Multilevel Adaptive Methods for Partial Differential Equations, SIAM, Philadelphia, PA, 1989]. A grid convergence study demonstrates that the solver performance is independent of the number of grid levels and only depends on the finest resolution considered, and that it scales well with grid refinement. The study of error generation and propagation in our SAMR implementation demonstrates that high-order (cubic) interpolation during regridding, combined with a robustly damping second-order temporal scheme such as BDF2, is required to minimize impact of grid errors at coarse-fine interfaces on the overall error of the computation for this MHD application. We also demonstrate that our implementation features the desired property that the overall numerical error is dependent only on the finest resolution level considered, and not on the base-grid resolution or on the number of refinement levels present during the simulation. We demonstrate the effectiveness of the tool on several challenging problems.

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

NASA Astrophysics Data System (ADS)

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.

Extracting physicochemical features to predict protein secondary structure.

PubMed

Huang, Yin-Fu; Chen, Shu-Ying

2013-01-01

We propose a protein secondary structure prediction method based on position-specific scoring matrix (PSSM) profiles and four physicochemical features including conformation parameters, net charges, hydrophobic, and side chain mass. First, the SVM with the optimal window size and the optimal parameters of the kernel function is found. Then, we train the SVM using the PSSM profiles generated from PSI-BLAST and the physicochemical features extracted from the CB513 data set. Finally, we use the filter to refine the predicted results from the trained SVM. For all the performance measures of our method, Q 3 reaches 79.52, SOV94 reaches 86.10, and SOV99 reaches 74.60; all the measures are higher than those of the SVMpsi method and the SVMfreq method. This validates that considering these physicochemical features in predicting protein secondary structure would exhibit better performances.

Extracting Physicochemical Features to Predict Protein Secondary Structure

PubMed Central

Chen, Shu-Ying

2013-01-01

We propose a protein secondary structure prediction method based on position-specific scoring matrix (PSSM) profiles and four physicochemical features including conformation parameters, net charges, hydrophobic, and side chain mass. First, the SVM with the optimal window size and the optimal parameters of the kernel function is found. Then, we train the SVM using the PSSM profiles generated from PSI-BLAST and the physicochemical features extracted from the CB513 data set. Finally, we use the filter to refine the predicted results from the trained SVM. For all the performance measures of our method, Q 3 reaches 79.52, SOV94 reaches 86.10, and SOV99 reaches 74.60; all the measures are higher than those of the SVMpsi method and the SVMfreq method. This validates that considering these physicochemical features in predicting protein secondary structure would exhibit better performances. PMID:23766688

Accelerating Convolutional Sparse Coding for Curvilinear Structures Segmentation by Refining SCIRD-TS Filter Banks.

PubMed

Annunziata, Roberto; Trucco, Emanuele

2016-11-01

Deep learning has shown great potential for curvilinear structure (e.g., retinal blood vessels and neurites) segmentation as demonstrated by a recent auto-context regression architecture based on filter banks learned by convolutional sparse coding. However, learning such filter banks is very time-consuming, thus limiting the amount of filters employed and the adaptation to other data sets (i.e., slow re-training). We address this limitation by proposing a novel acceleration strategy to speed-up convolutional sparse coding filter learning for curvilinear structure segmentation. Our approach is based on a novel initialisation strategy (warm start), and therefore it is different from recent methods improving the optimisation itself. Our warm-start strategy is based on carefully designed hand-crafted filters (SCIRD-TS), modelling appearance properties of curvilinear structures which are then refined by convolutional sparse coding. Experiments on four diverse data sets, including retinal blood vessels and neurites, suggest that the proposed method reduces significantly the time taken to learn convolutional filter banks (i.e., up to -82%) compared to conventional initialisation strategies. Remarkably, this speed-up does not worsen performance; in fact, filters learned with the proposed strategy often achieve a much lower reconstruction error and match or exceed the segmentation performance of random and DCT-based initialisation, when used as input to a random forest classifier.

Structure of catalase determined by MicroED

PubMed Central

Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

2014-01-01

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172

Template-based structure modeling of protein-protein interactions

PubMed Central

Szilagyi, Andras; Zhang, Yang

2014-01-01

The structure of protein-protein complexes can be constructed by using the known structure of other protein complexes as a template. The complex structure templates are generally detected either by homology-based sequence alignments or, given the structure of monomer components, by structure-based comparisons. Critical improvements have been made in recent years by utilizing interface recognition and by recombining monomer and complex template libraries. Encouraging progress has also been witnessed in genome-wide applications of template-based modeling, with modeling accuracy comparable to high-throughput experimental data. Nevertheless, bottlenecks exist due to the incompleteness of the proteinprotein complex structure library and the lack of methods for distant homologous template identification and full-length complex structure refinement. PMID:24721449

Structure and atomic correlations in molecular systems probed by XAS reverse Monte Carlo refinement

NASA Astrophysics Data System (ADS)

Di Cicco, Andrea; Iesari, Fabio; Trapananti, Angela; D'Angelo, Paola; Filipponi, Adriano

2018-03-01

The Reverse Monte Carlo (RMC) algorithm for structure refinement has been applied to x-ray absorption spectroscopy (XAS) multiple-edge data sets for six gas phase molecular systems (SnI2, CdI2, BBr3, GaI3, GeBr4, GeI4). Sets of thousands of molecular replicas were involved in the refinement process, driven by the XAS data and constrained by available electron diffraction results. The equilibrated configurations were analysed to determine the average tridimensional structure and obtain reliable bond and bond-angle distributions. Detectable deviations from Gaussian models were found in some cases. This work shows that a RMC refinement of XAS data is able to provide geometrical models for molecular structures compatible with present experimental evidence. The validation of this approach on simple molecular systems is particularly important in view of its possible simple extension to more complex and extended systems including metal-organic complexes, biomolecules, or nanocrystalline systems.

Homology Modeling of Dopamine D2 and D3 Receptors: Molecular Dynamics Refinement and Docking Evaluation

PubMed Central

Platania, Chiara Bianca Maria; Salomone, Salvatore; Leggio, Gian Marco; Drago, Filippo; Bucolo, Claudio

2012-01-01

Dopamine (DA) receptors, a class of G-protein coupled receptors (GPCRs), have been targeted for drug development for the treatment of neurological, psychiatric and ocular disorders. The lack of structural information about GPCRs and their ligand complexes has prompted the development of homology models of these proteins aimed at structure-based drug design. Crystal structure of human dopamine D3 (hD3) receptor has been recently solved. Based on the hD3 receptor crystal structure we generated dopamine D2 and D3 receptor models and refined them with molecular dynamics (MD) protocol. Refined structures, obtained from the MD simulations in membrane environment, were subsequently used in molecular docking studies in order to investigate potential sites of interaction. The structure of hD3 and hD2L receptors was differentiated by means of MD simulations and D3 selective ligands were discriminated, in terms of binding energy, by docking calculation. Robust correlation of computed and experimental Ki was obtained for hD3 and hD2L receptor ligands. In conclusion, the present computational approach seems suitable to build and refine structure models of homologous dopamine receptors that may be of value for structure-based drug discovery of selective dopaminergic ligands. PMID:22970199

Meteorological regimes for the classification of aerospace air quality predictions for NASA-Kennedy Space Center

NASA Technical Reports Server (NTRS)

Stephens, J. B.; Sloan, J. C.

1976-01-01

A method is described for developing a statistical air quality assessment for the launch of an aerospace vehicle from the Kennedy Space Center in terms of existing climatological data sets. The procedure can be refined as developing meteorological conditions are identified for use with the NASA-Marshall Space Flight Center Rocket Exhaust Effluent Diffusion (REED) description. Classical climatological regimes for the long range analysis can be narrowed as the synoptic and mesoscale structure is identified. Only broad synoptic regimes are identified at this stage of analysis. As the statistical data matrix is developed, synoptic regimes will be refined in terms of the resulting eigenvectors as applicable to aerospace air quality predictions.

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

PubMed

Fenn, Timothy D; Schnieders, Michael J; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S; Brunger, Axel T

2011-04-13

Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

PubMed Central

Fenn, Timothy D.; Schnieders, Michael J.; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S.; Brunger, Axel T.

2011-01-01

Summary Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. PMID:21481775

3-D minimum-structure inversion of magnetotelluric data using the finite-element method and tetrahedral grids

NASA Astrophysics Data System (ADS)

Jahandari, H.; Farquharson, C. G.

2017-11-01

Unstructured grids enable representing arbitrary structures more accurately and with fewer cells compared to regular structured grids. These grids also allow more efficient refinements compared to rectilinear meshes. In this study, tetrahedral grids are used for the inversion of magnetotelluric (MT) data, which allows for the direct inclusion of topography in the model, for constraining an inversion using a wireframe-based geological model and for local refinement at the observation stations. A minimum-structure method with an iterative model-space Gauss-Newton algorithm for optimization is used. An iterative solver is employed for solving the normal system of equations at each Gauss-Newton step and the sensitivity matrix-vector products that are required by this solver are calculated using pseudo-forward problems. This method alleviates the need to explicitly form the Hessian or Jacobian matrices which significantly reduces the required computation memory. Forward problems are formulated using an edge-based finite-element approach and a sparse direct solver is used for the solutions. This solver allows saving and re-using the factorization of matrices for similar pseudo-forward problems within a Gauss-Newton iteration which greatly minimizes the computation time. Two examples are presented to show the capability of the algorithm: the first example uses a benchmark model while the second example represents a realistic geological setting with topography and a sulphide deposit. The data that are inverted are the full-tensor impedance and the magnetic transfer function vector. The inversions sufficiently recovered the models and reproduced the data, which shows the effectiveness of unstructured grids for complex and realistic MT inversion scenarios. The first example is also used to demonstrate the computational efficiency of the presented model-space method by comparison with its data-space counterpart.

Locally refined block-centred finite-difference groundwater models: Evaluation of parameter sensitivity and the consequences for inverse modelling

USGS Publications Warehouse

Mehl, S.; Hill, M.C.

2002-01-01

Models with local grid refinement, as often required in groundwater models, pose special problems for model calibration. This work investigates the calculation of sensitivities and the performance of regression methods using two existing and one new method of grid refinement. The existing local grid refinement methods considered are: (a) a variably spaced grid in which the grid spacing becomes smaller near the area of interest and larger where such detail is not needed, and (b) telescopic mesh refinement (TMR), which uses the hydraulic heads or fluxes of a regional model to provide the boundary conditions for a locally refined model. The new method has a feedback between the regional and local grids using shared nodes, and thereby, unlike the TMR methods, balances heads and fluxes at the interfacing boundary. Results for sensitivities are compared for the three methods and the effect of the accuracy of sensitivity calculations are evaluated by comparing inverse modelling results. For the cases tested, results indicate that the inaccuracies of the sensitivities calculated using the TMR approach can cause the inverse model to converge to an incorrect solution.

Locally refined block-centered finite-difference groundwater models: Evaluation of parameter sensitivity and the consequences for inverse modelling and predictions

USGS Publications Warehouse

Mehl, S.; Hill, M.C.

2002-01-01

Models with local grid refinement, as often required in groundwater models, pose special problems for model calibration. This work investigates the calculation of sensitivities and performance of regression methods using two existing and one new method of grid refinement. The existing local grid refinement methods considered are (1) a variably spaced grid in which the grid spacing becomes smaller near the area of interest and larger where such detail is not needed and (2) telescopic mesh refinement (TMR), which uses the hydraulic heads or fluxes of a regional model to provide the boundary conditions for a locally refined model. The new method has a feedback between the regional and local grids using shared nodes, and thereby, unlike the TMR methods, balances heads and fluxes at the interfacing boundary. Results for sensitivities are compared for the three methods and the effect of the accuracy of sensitivity calculations are evaluated by comparing inverse modelling results. For the cases tested, results indicate that the inaccuracies of the sensitivities calculated using the TMR approach can cause the inverse model to converge to an incorrect solution.

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

PubMed

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.

Role of bismuth on solidification, microstructure and mechanical properties of a near eutectic Al-Si alloys

NASA Astrophysics Data System (ADS)

Farahany, Saeed; Ourdjini, Ali; Bakar, Tuty Asma Abu; Idris, Mohd Hasbullah

2014-09-01

Computer aided thermal analysis and microstructural observation showed that addition of bismuth (Bi) within the range of 0.25 and 2 wt% produced a greater effect on the Al-Si eutectic phase than on primary aluminium and Al2Cu phases. Results showed that with addition of 1 wt% Bi the eutectic silicon structure was refined from flake-like morphology into lamellar. Bi refines rather than modifies the Si structure and increases the Al-Si eutectic fraction solid and more significantly there was no fading even up to 180 min of melt holding. Transmission electron microscopy study showed that the Si twin spacing decreased from 160 to 75 nm which is likely attributed to the refining effect of Bi. It was also found that addition of 1 wt% Bi increased the tensile strength, elongation and the absorbed energy for fracture due to the refined eutectic silicon structure.

Grain Refinement of AZ31 Magnesium Alloy Weldments by AC Pulsing Technique

NASA Astrophysics Data System (ADS)

Kishore Babu, N.; Cross, C. E.

2012-11-01

The current study has investigated the influence of alternating current pulsing on the structure and mechanical properties of AZ31 magnesium alloy gas tungsten arc (GTA) weldments. Autogenous full penetration bead-on-plate GTA welds were made under a variety of conditions including variable polarity (VP), variable polarity mixed (VPM), alternating current (AC), and alternating current pulsing (ACPC). AC pulsing resulted in significant refinement of weld metal when compared with the unpulsed conditions. AC pulsing leads to relatively finer and more equiaxed grain structure in GTA welds. In contrast, VP, VPM, and AC welding resulted in predominantly columnar grain structures. The reason for this grain refinement may be attributed to the periodic variations in temperature gradient and solidification rate associated with pulsing as well as weld pool oscillation observed in the ACPC welds. The observed grain refinement was shown to result in an appreciable increase in fusion zone hardness, tensile strength, and ductility.

An adaptively refined XFEM with virtual node polygonal elements for dynamic crack problems

NASA Astrophysics Data System (ADS)

Teng, Z. H.; Sun, F.; Wu, S. C.; Zhang, Z. B.; Chen, T.; Liao, D. M.

2018-02-01

By introducing the shape functions of virtual node polygonal (VP) elements into the standard extended finite element method (XFEM), a conforming elemental mesh can be created for the cracking process. Moreover, an adaptively refined meshing with the quadtree structure only at a growing crack tip is proposed without inserting hanging nodes into the transition region. A novel dynamic crack growth method termed as VP-XFEM is thus formulated in the framework of fracture mechanics. To verify the newly proposed VP-XFEM, both quasi-static and dynamic cracked problems are investigated in terms of computational accuracy, convergence, and efficiency. The research results show that the present VP-XFEM can achieve good agreement in stress intensity factor and crack growth path with the exact solutions or experiments. Furthermore, better accuracy, convergence, and efficiency of different models can be acquired, in contrast to standard XFEM and mesh-free methods. Therefore, VP-XFEM provides a suitable alternative to XFEM for engineering applications.

Application of Al-2La-1B Grain Refiner to Al-10Si-0.3Mg Casting Alloy

NASA Astrophysics Data System (ADS)

Jing, Lijun; Pan, Ye; Lu, Tao; Li, Chenlin; Pi, Jinhong; Sheng, Ningyue

2018-05-01

This paper reports the application and microstructure refining effect of an Al-2La-1B grain refiner in Al-10Si-0.3Mg casting alloy. Compared with the traditional Al-5Ti-1B refiner, Al-2La-1B refiner shows better performances on the grain refinement of Al-10Si-0.3Mg alloy. Transmission electron microscopy analysis suggests that the crystallite structure features of LaB6 are beneficial to the heterogeneous nucleation of α-Al grains. Regarding the mechanical performances, tensile properties of Al-10Si-0.3Mg casting alloy are prominently improved, due to the refined microstructures.

Synchrotron Powder X-ray Diffraction Study of the Structure and Dehydration Behavior of Sepiolite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Post,J.; Bish, D.; Heaney, P.

2007-01-01

Rietveld refinements using synchrotron powder X-ray diffraction data were used to study the crystal structure and dehydration behavior of sepiolite from Durango, Mexico. The room-temperature (RT) sepiolite structure in air compares well with previous models but reveals an additional zeolitic H{sub 2}O site. The RT structure under vacuum retained only {approx}1/8 of the zeolitic H{sub 2}O and the volume decreased by 1.3%. Real-time, temperature-resolved synchrotron powder X-ray diffraction data and Rietveld refinements were used to investigate the behavior of the sepiolite structure from 300 to 925 K. Rietveld refinements revealed that most of the zeolitic H{sub 2}O is lost bymore » {approx}390 K, accompanied by a decrease in the a and c unit-cell parameters. Above {approx}600 K the sepiolite structure folds as one-half of the crystallographically bound H{sub 2}O is lost. Rietveld refinements of the 'anhydrous' sepiolite structure reveal that, in general, unit-cell parameters a and b and volume steadily decrease with increasing temperature; there is an obvious change in slope at {approx}820 K suggesting a phase transformation coinciding with the loss of the remaining bound H{sub 2}O molecule.« less

An efficicient data structure for three-dimensional vertex based finite volume method

NASA Astrophysics Data System (ADS)

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.

Iterative tensor voting for perceptual grouping of ill-defined curvilinear structures.

PubMed

Loss, Leandro A; Bebis, George; Parvin, Bahram

2011-08-01

In this paper, a novel approach is proposed for perceptual grouping and localization of ill-defined curvilinear structures. Our approach builds upon the tensor voting and the iterative voting frameworks. Its efficacy lies on iterative refinements of curvilinear structures by gradually shifting from an exploratory to an exploitative mode. Such a mode shifting is achieved by reducing the aperture of the tensor voting fields, which is shown to improve curve grouping and inference by enhancing the concentration of the votes over promising, salient structures. The proposed technique is validated on delineating adherens junctions that are imaged through fluorescence microscopy. However, the method is also applicable for screening other organisms based on characteristics of their cell wall structures. Adherens junctions maintain tissue structural integrity and cell-cell interactions. Visually, they exhibit fibrous patterns that may be diffused, heterogeneous in fluorescence intensity, or punctate and frequently perceptual. Besides the application to real data, the proposed method is compared to prior methods on synthetic and annotated real data, showing high precision rates.

Profex: a graphical user interface for the Rietveld refinement program BGMN.

PubMed

Doebelin, Nicola; Kleeberg, Reinhard

2015-10-01

Profex is a graphical user interface for the Rietveld refinement program BGMN . Its interface focuses on preserving BGMN 's powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems.

Profex: a graphical user interface for the Rietveld refinement program BGMN

PubMed Central

Doebelin, Nicola; Kleeberg, Reinhard

2015-01-01

Profex is a graphical user interface for the Rietveld refinement program BGMN. Its interface focuses on preserving BGMN’s powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems. PMID:26500466

Swarm: robust and fast clustering method for amplicon-based studies.

PubMed

Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2014-01-01

Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters' internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.

Swarm: robust and fast clustering method for amplicon-based studies

PubMed Central

Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2014-01-01

Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units. PMID:25276506

Synchrotron-based XAS on structure investigation of La0.99-xSrx(Na, K, Ba)0.01MnO3 nanoparticles: Evidence of magnetic properties

NASA Astrophysics Data System (ADS)

Daengsakul, Sujittra; Saengplot, Saowalak; Kidkhunthod, Pinit; Pimsawat, Adulphan; Maensiri, Santi

2018-04-01

This work presents the structural study of La0.99-xSrx(Na, K, Ba)0.01MnO3 or LSAM nanoparticles synthesized using thermal-hydro decomposition method where A denotes Na, K, Sr and Ba, respectively. The effect of ionic radii size of A dopants or rA from the substitution of A for La and Sr on the MnO6 octrahedral structure, where the average size of the cations occupying in A-site or 〈rA〉 is fixed at ∼ 1.24 Å, is focused. The LSAM nanoparticles are carefully studied using X-ray diffraction (XRD) including Rietveld refinement and X-ray Absorption Spectroscopy (XAS) including X-ray Absorption Near edge Structure (XANES) and X-ray Absorption Fine Structure (EXAFS). The Rietveld refinement shows all nano-powder samples have rhombohedral structure. By XANES technique we found that the effect of A substitutions at A-site causes a slight change of mean oxidation state of Mn between 3.54 and 3.60. Furthermore, the structural distortion of MnO6 octrahedral in samples is analysed and obtained from EXAFS. The observed trend of ferromagnetism for all LSAM samples can be clearly explained by evidences of A-site doping, structural distortion around Mn atoms and mixing Mn3+/Mn4+ valence states.

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.

PubMed

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.

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

PubMed Central

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

2012-01-01

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. PMID:22505259

Teaching macromolecular modeling.

PubMed Central

Harvey, S C; Tan, R K

1992-01-01

Training newcomers to the field of macromolecular modeling is as difficult as is training beginners in x-ray crystallography, nuclear magnetic resonance, or other methods in structural biology. In one or two lectures, the most that can be conveyed is a general sense of the relationship between modeling and other structural methods. If a full semester is available, then students can be taught how molecular structures are built, manipulated, refined, and analyzed on a computer. Here we describe a one-semester modeling course that combines lectures, discussions, and a laboratory using a commercial modeling package. In the laboratory, students carry out prescribed exercises that are coordinated to the lectures, and they complete a term project on a modeling problem of their choice. The goal is to give students an understanding of what kinds of problems can be attacked by molecular modeling methods and which problems are beyond the current capabilities of those methods. PMID:1489919

2010 Diffraction Methods in Structural Biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 oralmore » 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.« less

Correcting pervasive errors in RNA crystallography through enumerative structure prediction.

PubMed

Chou, Fang-Chieh; Sripakdeevong, Parin; Dibrov, Sergey M; Hermann, Thomas; Das, Rhiju

2013-01-01

Three-dimensional RNA models fitted into crystallographic density maps exhibit pervasive conformational ambiguities, geometric errors and steric clashes. To address these problems, we present enumerative real-space refinement assisted by electron density under Rosetta (ERRASER), coupled to Python-based hierarchical environment for integrated 'xtallography' (PHENIX) diffraction-based refinement. On 24 data sets, ERRASER automatically corrects the majority of MolProbity-assessed errors, improves the average R(free) factor, resolves functionally important discrepancies in noncanonical structure and refines low-resolution models to better match higher-resolution models.

The structural and Raman spectral studies on Ni0.5Cu0.5Fe2O4 ferrite

NASA Astrophysics Data System (ADS)

Somani, M.; Saleem, M.

2018-05-01

Spinel ferrite Ni0.5Cu0.5Fe2O4 has been successfully prepared via solid state reaction. The crystal structure studies using XRD technique revealed cubic structure of the sample. The XRD spectra was further refined via Retvield Refinement and all the parameters regarding structure were obtained which confirmed cubic structure. The assigned space group was found to be Fd-3m. Particle size was calculated to be 56 nm. The Raman Spectra revealed five active Raman modes which confirmed spinel structure.

Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis

PubMed Central

Cole, Jason C.

2017-01-01

The Cambridge Structural Database (CSD) is the worldwide resource for the dissemination of all published three-dimensional structures of small-molecule organic and metal–organic compounds. This paper briefly describes how this collection of crystal structures can be used en masse in the context of macromolecular crystallography. Examples highlight how the CSD and associated software aid protein–ligand complex validation, and show how the CSD could be further used in the generation of geometrical restraints for protein structure refinement. PMID:28291758

Confocal microscopy refines generic concept of a problematic taxon: rediagnosis of the genus Neoprothrix and remarks on female anatomy of eriophyoids (Acari: Eriophyoidea).

PubMed

Chetverikov, Philipp E; Desnitskiy, Alexey G; Navia, Denise

2015-02-16

Due to the higher resolution, confocal microscopy (CLSM) can be applied to refine the origin of tiny structures of the autofluorescent exoskeletons of microarthropods (mites in particular) which are hard to visualize using traditional differential interference contract light microscopy (DIC LM) and phase contrast light microscopy (PC LM). Three-dimensional (3D) reconstructions of the prodorsal shield topography of eriophyoid mites using Neoprothrix hibiscus Reis and Navia as a model, suggest that the structures originally treated as paired setae vi are two internal rod-like apodemes. Based on this, the genus Neoprothrix is excluded from the subfamily Prothricinae Amrine and transferred to the subfamily Sierraphytoptinae Keifer. Observations on partially cleared specimens of N. hibiscus showed that remnants of the central nervous system, paired glands and developing oocytes can be visualized using DIC LM and CLSM methods. New high quality microscope images are provided of recently described "flower-shaped" structures and two main components of yolk inclusions of the mature eggs inside the oviduct.

Impact of uncertainties in the uranium 235 cross section resonance structure on characteristics measured in the BFS-79 critical assemblies

NASA Astrophysics Data System (ADS)

Andrianova, Olga; Lomakov, Gleb; Manturov, Gennady

2017-09-01

The report presents the results of an analysis of benchmark experiments form the international ICSBEP Handbook (HEU-MET-INTER-005) carried out at the the SSC RF - IPPE in cooperation with the Idaho National Laboratory (INL, USA) applicable to the verification of calculations of a wide range of tasks related to safe storage of vitrified radioactive waste. Experiments on the BFS assemblies make it possible to perform a large series of studies needed for neutron data refinement, including measurements of reactivity effects which allow testing the neutron cross section resonance structure. This series of studies is considered as a sample joint analysis framework for differential and integral experiments required to correct nuclea data files of the ROSFOND evaluated neutron data library. Thus, it is shown that despite the wide range of available experimental data, in so far as it relates to the resonance region refinement, the experiments on reactivity measurement make it possible to more subtly reflect the resonance structure peculiarities in addition to the time-of-flight measurement method.

Refinement of atomic and magnetic structures using neutron diffraction for synthesized bulk and nano-nickel zinc gallate ferrite

NASA Astrophysics Data System (ADS)

Ata-Allah, S. S.; Balagurov, A. M.; Hashhash, A.; Bobrikov, I. A.; Hamdy, Sh.

2016-01-01

The parent NiFe2O4 and Zn/Ga substituted spinel ferrite powders have been prepared by solid state reaction technique. As a typical example, the Ni0.7Zn0.3Fe1.5Ga0.5O4 sample has been prepared by sol-gel auto combustion method with the nano-scale crystallites size. X-ray and Mössbauer studies were carried out for the prepared samples. Structure and microstructure properties were investigated using the time-of-flight HRFD instrument at the IBR-2 pulsed reactor, at a temperatures range 15-473 K. The Rietveld refinement of the neutron diffraction data revealed that all samples possess cubic symmetry corresponding to the space group Fd3m. Cations distribution show that Ni2+ is a complete inverse spinel ion, while Ga3+ equally distributed between the two A and B-sublattices. The level of microstrains in bulk samples was estimated as very small while the size of coherently scattered domains is quite large. For nano-structured sample the domain size is around 120 Å.

Synchrotron Powder X-ray Diffraction Study of the Structure and Dehydration Behavior of Sepiolite

NASA Astrophysics Data System (ADS)

Post, J. E.; Bish, D. L.; Heaney, P. J.

2006-05-01

Sepiolite is a hydrous Mg-silicate clay mineral with fibrous morphology that typically occurs as fine-grained, poorly crystalline masses. It occurs in a wide variety of geological environments and has been mined for centuries because of its many uses, e.g. in the pharmaceutical, fertilizer, and pesticide industries. Its versatile functionality derives from the large surface area and microporosity that are characteristic of the material. In recent years, sepiolite has received considerable attention with regard to the adsorption of organics, for use as a support for catalysts, as a molecular sieve, and as an inorganic membrane for ultrafiltration. Because of its fine-grained and poorly crystalline nature, it has not been possible to study sepiolite's crystal structure using single-crystal X-ray diffraction methods, and consequently many details of the structure are still not well known. In this study, Rietveld refinements using synchrotron powder X-ray diffraction data were used to investigate the crystal structure and dehydration behavior of sepiolite from Durango, Mexico. The room- temperature (RT) sepiolite structure in air compares well with previous models but reveals an additional zeolitic water site. The RT structure under vacuum retained only ~1/8 of the zeolitic water and the volume decreased 1.3%. Real-time, temperature-resolved synchrotron powder X-ray diffraction data and Rietveld refinements were used to investigate the behavior of the sepiolite structure from 300 to 925 K. Rietveld refinements revealed that most of the zeolitic water is lost by ~390 K, accompanied by a decrease in the a and c unit-cell parameters. Above ~600 K the sepiolite structure folds as one-half of the crystallographically bound water is lost. Rietveld refinements of the "anhydrous" sepiolite structure reveal that, in general, unit-cell parameters a, b, â and volume steadily decrease with increasing temperature; there is an obvious change in slope at ~820 K suggesting a phase transformation coinciding with the loss of the remaining bound water molecule. These temperature-resolved real-time powder X-ray diffraction studies provide the first comprehensive description of the sepiolite structure and the complex changes it undergoes as it dehydrates. Additional heating and cooling in situ powder X-ray diffraction experiments are underway in order to investigate the relative stabilities and rehydration behaviors of the partially-hydrated sepiolite phases. The results of these studies should provide a more robust model for predicting and modifying the properties and applications of this critical industrial material and environmentally important mineral.

Methods for evaluating the predictive accuracy of structural dynamic models

NASA Technical Reports Server (NTRS)

Hasselman, T. K.; Chrostowski, Jon D.

1990-01-01

Uncertainty of frequency response using the fuzzy set method and on-orbit response prediction using laboratory test data to refine an analytical model are emphasized with respect to large space structures. Two aspects of the fuzzy set approach were investigated relative to its application to large structural dynamics problems: (1) minimizing the number of parameters involved in computing possible intervals; and (2) the treatment of extrema which may occur in the parameter space enclosed by all possible combinations of the important parameters of the model. Extensive printer graphics were added to the SSID code to help facilitate model verification, and an application of this code to the LaRC Ten Bay Truss is included in the appendix to illustrate this graphics capability.

Crystallographic changes in lead zirconate titanate due to neutron irradiation

DOE PAGES

Henriques, Alexandra; Graham, Joseph T.; Landsberger, Sheldon; ...

2014-11-17

Piezoelectric and ferroelectric materials are useful as the active element in non-destructive monitoring devices for high-radiation areas. Here, crystallographic structural refinement (i.e., the Rietveld method) is used to quantify the type and extent of structural changes in PbZr 0 .5Ti 0 .5O 3 after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 10 15 neutrons/cm 2. The results show a measurable decrease in the occupancy of Pb and O due to irradiation, with O vacancies in the tetragonal phase being created preferentially on one of the two O sites. The results demonstrate a method by which themore » effects of radiation on crystallographic structure may be investigated.« less

Meshfree truncated hierarchical refinement for isogeometric analysis

NASA Astrophysics Data System (ADS)

Atri, H. R.; Shojaee, S.

2018-05-01

In this paper truncated hierarchical B-spline (THB-spline) is coupled with reproducing kernel particle method (RKPM) to blend advantages of the isogeometric analysis and meshfree methods. Since under certain conditions, the isogeometric B-spline and NURBS basis functions are exactly represented by reproducing kernel meshfree shape functions, recursive process of producing isogeometric bases can be omitted. More importantly, a seamless link between meshfree methods and isogeometric analysis can be easily defined which provide an authentic meshfree approach to refine the model locally in isogeometric analysis. This procedure can be accomplished using truncated hierarchical B-splines to construct new bases and adaptively refine them. It is also shown that the THB-RKPM method can provide efficient approximation schemes for numerical simulations and represent a promising performance in adaptive refinement of partial differential equations via isogeometric analysis. The proposed approach for adaptive locally refinement is presented in detail and its effectiveness is investigated through well-known benchmark examples.

COMET-AR User's Manual: COmputational MEchanics Testbed with Adaptive Refinement

NASA Technical Reports Server (NTRS)

Moas, E. (Editor)

1997-01-01

The COMET-AR User's Manual provides a reference manual for the Computational Structural Mechanics Testbed with Adaptive Refinement (COMET-AR), a software system developed jointly by Lockheed Palo Alto Research Laboratory and NASA Langley Research Center under contract NAS1-18444. The COMET-AR system is an extended version of an earlier finite element based structural analysis system called COMET, also developed by Lockheed and NASA. The primary extensions are the adaptive mesh refinement capabilities and a new "object-like" database interface that makes COMET-AR easier to extend further. This User's Manual provides a detailed description of the user interface to COMET-AR from the viewpoint of a structural analyst.

Wind Farm LES Simulations Using an Overset Methodology

NASA Astrophysics Data System (ADS)

Ananthan, Shreyas; Yellapantula, Shashank

2017-11-01

Accurate simulation of wind farm wakes under realistic atmospheric inflow conditions and complex terrain requires modeling a wide range of length and time scales. The computational domain can span several kilometers while requiring mesh resolutions in O(10-6) to adequately resolve the boundary layer on the blade surface. Overset mesh methodology offers an attractive option to address the disparate range of length scales; it allows embedding body-confirming meshes around turbine geomtries within nested wake capturing meshes of varying resolutions necessary to accurately model the inflow turbulence and the resulting wake structures. Dynamic overset hole-cutting algorithms permit relative mesh motion that allow this nested mesh structure to track unsteady inflow direction changes, turbine control changes (yaw and pitch), and wake propagation. An LES model with overset mesh for localized mesh refinement is used to analyze wind farm wakes and performance and compared with local mesh refinements using non-conformal (hanging node) unstructured meshes. Turbine structures will be modeled using both actuator line approaches and fully-resolved structures to test the efficacy of overset methods for wind farm applications. Exascale Computing Project (ECP), Project Number: 17-SC-20-SC, a collaborative effort of two DOE organizations - the Office of Science and the National Nuclear Security Administration.

The 3D Structure of the Binding Pocket of the Human Oxytocin Receptor for Benzoxazine Antagonists, Determined by Molecular Docking, Scoring Functions and 3D-QSAR Methods

NASA Astrophysics Data System (ADS)

Jójárt, Balázs; Martinek, Tamás A.; Márki, Árpád

2005-05-01

Molecular docking and 3D-QSAR studies were performed to determine the binding mode for a series of benzoxazine oxytocin antagonists taken from the literature. Structural hypotheses were generated by docking the most active molecule to the rigid receptor by means of AutoDock 3.05. The cluster analysis yielded seven possible binding conformations. These structures were refined by using constrained simulated annealing, and the further ligands were aligned in the refined receptor by molecular docking. A good correlation was found between the estimated Δ G bind and the p K i values for complex F. The Connolly-surface analysis, CoMFA and CoMSIA models q CoMFA 2 = 0.653, q CoMSA 2 = 0.630 and r pred,CoMFA 2 = 0.852 , r pred,CoMSIA 2 = 0.815) confirmed the scoring function results. The structural features of the receptor-ligand complex and the CoMFA and CoMSIA fields are in closely connected. These results suggest that receptor-ligand complex F is the most likely binding hypothesis for the studied benzoxazine analogs.

Array-based, parallel hierarchical mesh refinement algorithms for unstructured meshes

DOE PAGES

Ray, Navamita; Grindeanu, Iulian; Zhao, Xinglin; ...

2016-08-18

In this paper, we describe an array-based hierarchical mesh refinement capability through uniform refinement of unstructured meshes for efficient solution of PDE's using finite element methods and multigrid solvers. A multi-degree, multi-dimensional and multi-level framework is designed to generate the nested hierarchies from an initial coarse mesh that can be used for a variety of purposes such as in multigrid solvers/preconditioners, to do solution convergence and verification studies and to improve overall parallel efficiency by decreasing I/O bandwidth requirements (by loading smaller meshes and in memory refinement). We also describe a high-order boundary reconstruction capability that can be used tomore » project the new points after refinement using high-order approximations instead of linear projection in order to minimize and provide more control on geometrical errors introduced by curved boundaries.The capability is developed under the parallel unstructured mesh framework "Mesh Oriented dAtaBase" (MOAB Tautges et al. (2004)). We describe the underlying data structures and algorithms to generate such hierarchies in parallel and present numerical results for computational efficiency and effect on mesh quality. Furthermore, we also present results to demonstrate the applicability of the developed capability to study convergence properties of different point projection schemes for various mesh hierarchies and to a multigrid finite-element solver for elliptic problems.« less

A feature refinement approach for statistical interior CT reconstruction

NASA Astrophysics Data System (ADS)

Hu, Zhanli; Zhang, Yunwan; Liu, Jianbo; Ma, Jianhua; Zheng, Hairong; Liang, Dong

2016-07-01

Interior tomography is clinically desired to reduce the radiation dose rendered to patients. In this work, a new statistical interior tomography approach for computed tomography is proposed. The developed design focuses on taking into account the statistical nature of local projection data and recovering fine structures which are lost in the conventional total-variation (TV)—minimization reconstruction. The proposed method falls within the compressed sensing framework of TV minimization, which only assumes that the interior ROI is piecewise constant or polynomial and does not need any additional prior knowledge. To integrate the statistical distribution property of projection data, the objective function is built under the criteria of penalized weighed least-square (PWLS-TV). In the implementation of the proposed method, the interior projection extrapolation based FBP reconstruction is first used as the initial guess to mitigate truncation artifacts and also provide an extended field-of-view. Moreover, an interior feature refinement step, as an important processing operation is performed after each iteration of PWLS-TV to recover the desired structure information which is lost during the TV minimization. Here, a feature descriptor is specifically designed and employed to distinguish structure from noise and noise-like artifacts. A modified steepest descent algorithm is adopted to minimize the associated objective function. The proposed method is applied to both digital phantom and in vivo Micro-CT datasets, and compared to FBP, ART-TV and PWLS-TV. The reconstruction results demonstrate that the proposed method performs better than other conventional methods in suppressing noise, reducing truncated and streak artifacts, and preserving features. The proposed approach demonstrates its potential usefulness for feature preservation of interior tomography under truncated projection measurements.

A feature refinement approach for statistical interior CT reconstruction.

PubMed

Hu, Zhanli; Zhang, Yunwan; Liu, Jianbo; Ma, Jianhua; Zheng, Hairong; Liang, Dong

2016-07-21

Interior tomography is clinically desired to reduce the radiation dose rendered to patients. In this work, a new statistical interior tomography approach for computed tomography is proposed. The developed design focuses on taking into account the statistical nature of local projection data and recovering fine structures which are lost in the conventional total-variation (TV)-minimization reconstruction. The proposed method falls within the compressed sensing framework of TV minimization, which only assumes that the interior ROI is piecewise constant or polynomial and does not need any additional prior knowledge. To integrate the statistical distribution property of projection data, the objective function is built under the criteria of penalized weighed least-square (PWLS-TV). In the implementation of the proposed method, the interior projection extrapolation based FBP reconstruction is first used as the initial guess to mitigate truncation artifacts and also provide an extended field-of-view. Moreover, an interior feature refinement step, as an important processing operation is performed after each iteration of PWLS-TV to recover the desired structure information which is lost during the TV minimization. Here, a feature descriptor is specifically designed and employed to distinguish structure from noise and noise-like artifacts. A modified steepest descent algorithm is adopted to minimize the associated objective function. The proposed method is applied to both digital phantom and in vivo Micro-CT datasets, and compared to FBP, ART-TV and PWLS-TV. The reconstruction results demonstrate that the proposed method performs better than other conventional methods in suppressing noise, reducing truncated and streak artifacts, and preserving features. The proposed approach demonstrates its potential usefulness for feature preservation of interior tomography under truncated projection measurements.

Evaluation of the dermal carcinogenicity of lubricant base oils by the mouse skin painting bioassay and other proposed methods.

PubMed

Chasey, K L; McKee, R H

1993-01-01

Lubricant base oils are petroleum products that are predominantly derived from the vacuum distillation of crude oil. Various types of refinement can be employed during the manufacturing process, and evidence suggests that certain of the associated process streams produce skin cancer. Polycyclic aromatic compounds (PACs), some of which are considered as the causative agents, are removed, concentrated or chemically converted during the refinement process. In order to understand the effects of various types of refinement processes on carcinogenic potential, 94 oils were evaluated in the mouse epidermal cancer bioassay. This Exxon database is unique, because of the wide range of crude oils and processing histories represented. Seven processing history classifications are described, and conclusions concerning the impacts of each refinement process on dermal carcinogenicity are discussed. This research also included an evaluation of selected biological and chemical test methods for predicting carcinogenic potential. These included a modified version of the Ames test for mutagenicity, as well as analytical characterizations of the polycyclic aromatic structures in the oils. For classification purposes, a sample was considered to be carcinogenic if it resulted in the production of two or more tumor-bearing animals (in test groups of either 40 or 50 animals). The modified Ames test was considered to be positive if the mutagenicity index was > or = 2.0, and PAC analyses were similarly designated as positive or negative according to proposed guidelines. All of the alternative test methods showed similar agreement with dermal carcinogenicity bioassay data; concordance values were > or = 80%. However, each test was incorrect in ca. 10%-20% of the cases evaluated.(ABSTRACT TRUNCATED AT 250 WORDS)

Significance of structural changes in proteins: expected errors in refined protein structures.

PubMed Central

Stroud, R. M.; Fauman, E. B.

1995-01-01

A quantitative expression key to evaluating significant structural differences or induced shifts between any two protein structures is derived. Because crystallography leads to reports of a single (or sometimes dual) position for each atom, the significance of any structural change based on comparison of two structures depends critically on knowing the expected precision of each median atomic position reported, and on extracting it for each atom, from the information provided in the Protein Data Bank and in the publication. The differences between structures of protein molecules that should be identical, and that are normally distributed, indicating that they are not affected by crystal contacts, were analyzed with respect to many potential indicators of structure precision, so as to extract, essentially by "machine learning" principles, a generally applicable expression involving the highest correlates. Eighteen refined crystal structures from the Protein Data Bank, in which there are multiple molecules in the crystallographic asymmetric unit, were selected and compared. The thermal B factor, the connectivity of the atom, and the ratio of the number of reflections to the number of atoms used in refinement correlate best with the magnitude of the positional differences between regions of the structures that otherwise would be expected to be the same. These results are embodied in a six-parameter equation that can be applied to any crystallographically refined structure to estimate the expected uncertainty in position of each atom. Structure change in a macromolecule can thus be referenced to the expected uncertainty in atomic position as reflected in the variance between otherwise identical structures with the observed values of correlated parameters. PMID:8563637

Hydrothermal synthesis, characterization, and thermal properties of alumino silicate azide sodalite, Na8[AlSiO4]6(N3)2

NASA Astrophysics Data System (ADS)

Borhade, A. V.; Wakchaure, S. G.; Dholi, A. G.; Kshirsagar, T. A.

2017-07-01

First time we report the synthesis, structural characterization and thermal behavior of an unusual N3 - containing alumino-silicate sodalite mineral. Azide sodalite, Na8[AlSiO4]6(N3)2 has been synthesized under hydrothermal conditions at 433 K in steel lined Teflon autoclave. The structural and microstructural properties of azide sodalite mineral was characterized by various methods including FT-IR, XRD, SEM, TGA, and MAS NMR. Crystal structure have been refined by Rietveld method in P\\bar 43n space group, indicating that the N3 - sodalite has cubic in lattice. High temperature study was carried out to see the effect of thermal expansion on cell dimension ( a o) of azide sodalite. Thermal behavior of sodalite was also assessed by thermogravimetric method.

Integrated Conceptual Design of Joined-Wing SensorCraft Using Response Surface Models

DTIC Science & Technology

2006-11-01

vi Acknowledgements I would like to express my sincere appreciation to my thesis advisor, Dr. Robert Canfield for his guidance and...55 Raymer Approximate and Group Weights Sizing Methods....................................... 57 Finite Element Model Structural Weight...Empty Weight Fraction Equation ............................... 54 Figure 29 Response of Refined Weight to T/W and W/S Inputs for Model (2) Raymer ASW

Parallel three-dimensional magnetotelluric inversion using adaptive finite-element method. Part I: theory and synthetic study

NASA Astrophysics Data System (ADS)

Grayver, Alexander V.

2015-07-01

This paper presents a distributed magnetotelluric inversion scheme based on adaptive finite-element method (FEM). The key novel aspect of the introduced algorithm is the use of automatic mesh refinement techniques for both forward and inverse modelling. These techniques alleviate tedious and subjective procedure of choosing a suitable model parametrization. To avoid overparametrization, meshes for forward and inverse problems were decoupled. For calculation of accurate electromagnetic (EM) responses, automatic mesh refinement algorithm based on a goal-oriented error estimator has been adopted. For further efficiency gain, EM fields for each frequency were calculated using independent meshes in order to account for substantially different spatial behaviour of the fields over a wide range of frequencies. An automatic approach for efficient initial mesh design in inverse problems based on linearized model resolution matrix was developed. To make this algorithm suitable for large-scale problems, it was proposed to use a low-rank approximation of the linearized model resolution matrix. In order to fill a gap between initial and true model complexities and resolve emerging 3-D structures better, an algorithm for adaptive inverse mesh refinement was derived. Within this algorithm, spatial variations of the imaged parameter are calculated and mesh is refined in the neighborhoods of points with the largest variations. A series of numerical tests were performed to demonstrate the utility of the presented algorithms. Adaptive mesh refinement based on the model resolution estimates provides an efficient tool to derive initial meshes which account for arbitrary survey layouts, data types, frequency content and measurement uncertainties. Furthermore, the algorithm is capable to deliver meshes suitable to resolve features on multiple scales while keeping number of unknowns low. However, such meshes exhibit dependency on an initial model guess. Additionally, it is demonstrated that the adaptive mesh refinement can be particularly efficient in resolving complex shapes. The implemented inversion scheme was able to resolve a hemisphere object with sufficient resolution starting from a coarse discretization and refining mesh adaptively in a fully automatic process. The code is able to harness the computational power of modern distributed platforms and is shown to work with models consisting of millions of degrees of freedom. Significant computational savings were achieved by using locally refined decoupled meshes.

Carpet: Adaptive Mesh Refinement for the Cactus Framework

NASA Astrophysics Data System (ADS)

Schnetter, Erik; Hawley, Scott; Hawke, Ian

2016-11-01

Carpet is an adaptive mesh refinement and multi-patch driver for the Cactus Framework (ascl:1102.013). Cactus is a software framework for solving time-dependent partial differential equations on block-structured grids, and Carpet acts as driver layer providing adaptive mesh refinement, multi-patch capability, as well as parallelization and efficient I/O.

Development of Multidisciplinary, Multifidelity Analysis, Integration, and Optimization of Aerospace Vehicles

DTIC Science & Technology

2010-02-27

investigated in more detail. The intermediate level of fidelity, though more expensive, is then used to refine the analysis , add geometric detail, and...design stage is used to further refine the analysis , narrowing the design to a handful of options. Figure 1. Integrated Hierarchical Framework. In...computational structural and computational fluid modeling. For the structural analysis tool we used McIntosh Structural Dynamics’ finite element code CNEVAL

Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

PubMed

Paluch, Piotr; Pawlak, Tomasz; Oszajca, Marcin; Lasocha, Wieslaw; Potrzebowski, Marek J

2015-02-01

We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924. Copyright © 2014 Elsevier Inc. All rights reserved.

Three-dimensional local grid refinement for block-centered finite-difference groundwater models using iteratively coupled shared nodes: A new method of interpolation and analysis of errors

USGS Publications Warehouse

Mehl, S.; Hill, M.C.

2004-01-01

This paper describes work that extends to three dimensions the two-dimensional local-grid refinement method for block-centered finite-difference groundwater models of Mehl and Hill [Development and evaluation of a local grid refinement method for block-centered finite-difference groundwater models using shared nodes. Adv Water Resour 2002;25(5):497-511]. In this approach, the (parent) finite-difference grid is discretized more finely within a (child) sub-region. The grid refinement method sequentially solves each grid and uses specified flux (parent) and specified head (child) boundary conditions to couple the grids. Iteration achieves convergence between heads and fluxes of both grids. Of most concern is how to interpolate heads onto the boundary of the child grid such that the physics of the parent-grid flow is retained in three dimensions. We develop a new two-step, "cage-shell" interpolation method based on the solution of the flow equation on the boundary of the child between nodes shared with the parent grid. Error analysis using a test case indicates that the shared-node local grid refinement method with cage-shell boundary head interpolation is accurate and robust, and the resulting code is used to investigate three-dimensional local grid refinement of stream-aquifer interactions. Results reveal that (1) the parent and child grids interact to shift the true head and flux solution to a different solution where the heads and fluxes of both grids are in equilibrium, (2) the locally refined model provided a solution for both heads and fluxes in the region of the refinement that was more accurate than a model without refinement only if iterations are performed so that both heads and fluxes are in equilibrium, and (3) the accuracy of the coupling is limited by the parent-grid size - A coarse parent grid limits correct representation of the hydraulics in the feedback from the child grid.

The PDB_REDO server for macromolecular structure model optimization.

PubMed

Joosten, Robbie P; Long, Fei; Murshudov, Garib N; Perrakis, Anastassis

2014-07-01

The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011 ▶), Structure, 19, 1395-1412]. The PDB_REDO procedure aims for 'constructive validation', aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallo-graphers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB.

The PDB_REDO server for macromolecular structure model optimization

PubMed Central

Joosten, Robbie P.; Long, Fei; Murshudov, Garib N.; Perrakis, Anastassis

2014-01-01

The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011 ▶), Structure, 19, 1395–1412]. The PDB_REDO procedure aims for ‘constructive validation’, aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallo­graphers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB. PMID:25075342

Compact cell-centered discretization stencils at fine-coarse block structured grid interfaces

NASA Astrophysics Data System (ADS)

Pletzer, Alexander; Jamroz, Ben; Crockett, Robert; Sides, Scott

2014-03-01

Different strategies for coupling fine-coarse grid patches are explored in the context of the adaptive mesh refinement (AMR) method. We show that applying linear interpolation to fill in the fine grid ghost values can produce a finite volume stencil of comparable accuracy to quadratic interpolation provided the cell volumes are adjusted. The volume of fine cells expands whereas the volume of neighboring coarse cells contracts. The amount by which the cells contract/expand depends on whether the interface is a face, an edge, or a corner. It is shown that quadratic or better interpolation is required when the conductivity is spatially varying, anisotropic, the refinement ratio is other than two, or when the fine-coarse interface is concave.

3D Reconstruction of Space Objects from Multi-Views by a Visible Sensor

PubMed Central

Zhang, Haopeng; Wei, Quanmao; Jiang, Zhiguo

2017-01-01

In this paper, a novel 3D reconstruction framework is proposed to recover the 3D structural model of a space object from its multi-view images captured by a visible sensor. Given an image sequence, this framework first estimates the relative camera poses and recovers the depths of the surface points by the structure from motion (SFM) method, then the patch-based multi-view stereo (PMVS) algorithm is utilized to generate a dense 3D point cloud. To resolve the wrong matches arising from the symmetric structure and repeated textures of space objects, a new strategy is introduced, in which images are added to SFM in imaging order. Meanwhile, a refining process exploiting the structural prior knowledge that most sub-components of artificial space objects are composed of basic geometric shapes is proposed and applied to the recovered point cloud. The proposed reconstruction framework is tested on both simulated image datasets and real image datasets. Experimental results illustrate that the recovered point cloud models of space objects are accurate and have a complete coverage of the surface. Moreover, outliers and points with severe noise are effectively filtered out by the refinement, resulting in an distinct improvement of the structure and visualization of the recovered points. PMID:28737675

GRID: a high-resolution protein structure refinement algorithm.

PubMed

Chitsaz, Mohsen; Mayo, Stephen L

2013-03-05

The energy-based refinement of protein structures generated by fold prediction algorithms to atomic-level accuracy remains a major challenge in structural biology. Energy-based refinement is mainly dependent on two components: (1) sufficiently accurate force fields, and (2) efficient conformational space search algorithms. Focusing on the latter, we developed a high-resolution refinement algorithm called GRID. It takes a three-dimensional protein structure as input and, using an all-atom force field, attempts to improve the energy of the structure by systematically perturbing backbone dihedrals and side-chain rotamer conformations. We compare GRID to Backrub, a stochastic algorithm that has been shown to predict a significant fraction of the conformational changes that occur with point mutations. We applied GRID and Backrub to 10 high-resolution (≤ 2.8 Å) crystal structures from the Protein Data Bank and measured the energy improvements obtained and the computation times required to achieve them. GRID resulted in energy improvements that were significantly better than those attained by Backrub while expending about the same amount of computational resources. GRID resulted in relaxed structures that had slightly higher backbone RMSDs compared to Backrub relative to the starting crystal structures. The average RMSD was 0.25 ± 0.02 Å for GRID versus 0.14 ± 0.04 Å for Backrub. These relatively minor deviations indicate that both algorithms generate structures that retain their original topologies, as expected given the nature of the algorithms. Copyright © 2012 Wiley Periodicals, Inc.

An adaptive embedded mesh procedure for leading-edge vortex flows

NASA Technical Reports Server (NTRS)

Powell, Kenneth G.; Beer, Michael A.; Law, Glenn W.

1989-01-01

A procedure for solving the conical Euler equations on an adaptively refined mesh is presented, along with a method for determining which cells to refine. The solution procedure is a central-difference cell-vertex scheme. The adaptation procedure is made up of a parameter on which the refinement decision is based, and a method for choosing a threshold value of the parameter. The refinement parameter is a measure of mesh-convergence, constructed by comparison of locally coarse- and fine-grid solutions. The threshold for the refinement parameter is based on the curvature of the curve relating the number of cells flagged for refinement to the value of the refinement threshold. Results for three test cases are presented. The test problem is that of a delta wing at angle of attack in a supersonic free-stream. The resulting vortices and shocks are captured efficiently by the adaptive code.

Numerical simulation of h-adaptive immersed boundary method for freely falling disks

NASA Astrophysics Data System (ADS)

Zhang, Pan; Xia, Zhenhua; Cai, Qingdong

2018-05-01

In this work, a freely falling disk with aspect ratio 1/10 is directly simulated by using an adaptive numerical model implemented on a parallel computation framework JASMIN. The adaptive numerical model is a combination of the h-adaptive mesh refinement technique and the implicit immersed boundary method (IBM). Our numerical results agree well with the experimental results in all of the six degrees of freedom of the disk. Furthermore, very similar vortex structures observed in the experiment were also obtained.

Combining global and local approximations

NASA Technical Reports Server (NTRS)

Haftka, Raphael T.

1991-01-01

A method based on a linear approximation to a scaling factor, designated the 'global-local approximation' (GLA) method, is presented and shown capable of extending the range of usefulness of derivative-based approximations to a more refined model. The GLA approach refines the conventional scaling factor by means of a linearly varying, rather than constant, scaling factor. The capabilities of the method are demonstrated for a simple beam example with a crude and more refined FEM model.

Cluster Analysis of Time-Dependent Crystallographic Data: Direct Identification of Time-Independent Structural Intermediates

PubMed Central

Kostov, Konstantin S.; Moffat, Keith

2011-01-01

The initial output of a time-resolved macromolecular crystallography experiment is a time-dependent series of difference electron density maps that displays the time-dependent changes in underlying structure as a reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which these intermediates interconvert; and thereby to elucidate a chemical kinetic mechanism. One strategy toward achieving this goal is to use cluster analysis, a statistical method that groups objects based on their similarity. If the difference electron density at a particular voxel in the time-dependent difference electron density (TDED) maps is sensitive to the presence of one and only one intermediate, then its temporal evolution will exactly parallel the concentration profile of that intermediate with time. The rationale is therefore to cluster voxels with respect to the shapes of their TDEDs, so that each group or cluster of voxels corresponds to one structural intermediate. Clusters of voxels whose TDEDs reflect the presence of two or more specific intermediates can also be identified. From such groupings one can then infer the number of intermediates, obtain their time-independent difference density characteristics, and refine the structure of each intermediate. We review the principles of cluster analysis and clustering algorithms in a crystallographic context, and describe the application of the method to simulated and experimental time-resolved crystallographic data for the photocycle of photoactive yellow protein. PMID:21244840

Solution adaptive grids applied to low Reynolds number flow

NASA Astrophysics Data System (ADS)

de With, G.; Holdø, A. E.; Huld, T. A.

2003-08-01

A numerical study has been undertaken to investigate the use of a solution adaptive grid for flow around a cylinder in the laminar flow regime. The main purpose of this work is twofold. The first aim is to investigate the suitability of a grid adaptation algorithm and the reduction in mesh size that can be obtained. Secondly, the uniform asymmetric flow structures are ideal to validate the mesh structures due to mesh refinement and consequently the selected refinement criteria. The refinement variable used in this work is a product of the rate of strain and the mesh cell size, and contains two variables Cm and Cstr which determine the order of each term. By altering the order of either one of these terms the refinement behaviour can be modified.

The structure of denisovite, a fibrous nanocrystalline polytypic disordered ‘very complex’ silicate, studied by a synergistic multi-disciplinary approach employing methods of electron crystallography and X-ray powder diffraction

PubMed Central

Schowalter, Marco; Schmidt, Martin U.; Czank, Michael; Depmeier, Wulf; Rosenauer, Andreas

2017-01-01

Denisovite is a rare mineral occurring as aggregates of fibres typically 200–500 nm diameter. It was confirmed as a new mineral in 1984, but important facts about its chemical formula, lattice parameters, symmetry and structure have remained incompletely known since then. Recently obtained results from studies using microprobe analysis, X-ray powder diffraction (XRPD), electron crystallography, modelling and Rietveld refinement will be reported. The electron crystallography methods include transmission electron microscopy (TEM), selected-area electron diffraction (SAED), high-angle annular dark-field imaging (HAADF), high-resolution transmission electron microscopy (HRTEM), precession electron diffraction (PED) and electron diffraction tomography (EDT). A structural model of denisovite was developed from HAADF images and later completed on the basis of quasi-kinematic EDT data by ab initio structure solution using direct methods and least-squares refinement. The model was confirmed by Rietveld refinement. The lattice parameters are a = 31.024 (1), b = 19.554 (1) and c = 7.1441 (5) Å, β = 95.99 (3)°, V = 4310.1 (5) Å3 and space group P12/a1. The structure consists of three topologically distinct dreier silicate chains, viz. two xonotlite-like dreier double chains, [Si6O17]10−, and a tubular loop-branched dreier triple chain, [Si12O30]12−. The silicate chains occur between three walls of edge-sharing (Ca,Na) octahedra. The chains of silicate tetrahedra and the octahedra walls extend parallel to the z axis and form a layer parallel to (100). Water molecules and K+ cations are located at the centre of the tubular silicate chain. The latter also occupy positions close to the centres of eight-membered rings in the silicate chains. The silicate chains are geometrically constrained by neighbouring octahedra walls and present an ambiguity with respect to their z position along these walls, with displacements between neighbouring layers being either Δz = c/4 or −c/4. Such behaviour is typical for polytypic sequences and leads to disorder along [100]. In fact, the diffraction pattern does not show any sharp reflections with l odd, but continuous diffuse streaks parallel to a* instead. Only reflections with l even are sharp. The diffuse scattering is caused by (100) nano­lamellae separated by stacking faults and twin boundaries. The structure can be described according to the order–disorder (OD) theory as a stacking of layers parallel to (100). PMID:28512570

Structure-From-Motion in 3D Space Using 2D Lidars

PubMed Central

Choi, Dong-Geol; Bok, Yunsu; Kim, Jun-Sik; Shim, Inwook; Kweon, In So

2017-01-01

This paper presents a novel structure-from-motion methodology using 2D lidars (Light Detection And Ranging). In 3D space, 2D lidars do not provide sufficient information for pose estimation. For this reason, additional sensors have been used along with the lidar measurement. In this paper, we use a sensor system that consists of only 2D lidars, without any additional sensors. We propose a new method of estimating both the 6D pose of the system and the surrounding 3D structures. We compute the pose of the system using line segments of scan data and their corresponding planes. After discarding the outliers, both the pose and the 3D structures are refined via nonlinear optimization. Experiments with both synthetic and real data show the accuracy and robustness of the proposed method. PMID:28165372

Refining mass formulas for astrophysical applications: A Bayesian neural network approach

NASA Astrophysics Data System (ADS)

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.

Iterative Tensor Voting for Perceptual Grouping of Ill-Defined Curvilinear Structures: Application to Adherens Junctions

PubMed Central

Loss, Leandro A.; Bebis, George; Parvin, Bahram

2012-01-01

In this paper, a novel approach is proposed for perceptual grouping and localization of ill-defined curvilinear structures. Our approach builds upon the tensor voting and the iterative voting frameworks. Its efficacy lies on iterative refinements of curvilinear structures by gradually shifting from an exploratory to an exploitative mode. Such a mode shifting is achieved by reducing the aperture of the tensor voting fields, which is shown to improve curve grouping and inference by enhancing the concentration of the votes over promising, salient structures. The proposed technique is applied to delineation of adherens junctions imaged through fluorescence microscopy. This class of membrane-bound macromolecules maintains tissue structural integrity and cell-cell interactions. Visually, it exhibits fibrous patterns that may be diffused, punctate and frequently perceptual. Besides the application to real data, the proposed method is compared to prior methods on synthetic and annotated real data, showing high precision rates. PMID:21421432

Advanced thermally stable jet fuels. Technical progress report, January 1995--March 1995

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schobert, H.H.; Eser, S.; Song, C.

Quantitative structure-property relationships have been applied to study the thermal stability of pure hydrocarbons typical of jet fuel components. A simple method of chemical structure description in terms of Benson groups was tested in searching for structure-property relationships for the hydrocarbons tested experimentally in this program. Molecular connectivity as a structure-based approach to chemical structure-property relationship analysis was also tested. Further development of both the experimental data base and computational methods will be necessary. Thermal decomposition studies, using glass tube reactors, were extended to two additional model compounds: n-decane and n-dodecane. Efforts on refining the deposit growth measurement and characterizationmore » of suspended matter in stressed fuels have lead to improvements in the analysis of stressed fuels. Catalytic hydrogenation and dehydrogenation studies utilizing a molybdenum sulfide catalyst are also described.« less

Fiberboards from loblolly pine refiner groundwood: effects of gross wood characteristics and board density

Treesearch

Charles W. McMillin

1968-01-01

Boards for insulation and and structural uses are being manufactured in increasing quantities. The coarse fiber required for these products can be disk-refined from untreated wood chips. Since such fiber is produced in essentially one mechanical operation, continuous control is required of the raw material as well as the refining process.

PDB_REDO: constructive validation, more than just looking for errors.

PubMed

Joosten, Robbie P; Joosten, Krista; Murshudov, Garib N; Perrakis, Anastassis

2012-04-01

Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R(free) and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise `static' structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets.

PDB_REDO: constructive validation, more than just looking for errors

PubMed Central

Joosten, Robbie P.; Joosten, Krista; Murshudov, Garib N.; Perrakis, Anastassis

2012-01-01

Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R free and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise ‘static’ structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets. PMID:22505269

Advanced techniques in placental biology -- workshop report.

PubMed

Nelson, D M; Sadovsky, Y; Robinson, J M; Croy, B A; Rice, G; Kniss, D A

2006-04-01

Major advances in placental biology have been realized as new technologies have been developed and existing methods have been refined in many areas of biological research. Classical anatomy and whole-organ physiology tools once used to analyze placental structure and function have been supplanted by more sophisticated techniques adapted from molecular biology, proteomics, and computational biology and bioinformatics. In addition, significant refinements in morphological study of the placenta and its constituent cell types have improved our ability to assess form and function in highly integrated manner. To offer an overview of modern technologies used by investigators to study the placenta, this workshop: Advanced techniques in placental biology, assembled experts who discussed fundamental principles and real time examples of four separate methodologies. Y. Sadovsky presented the principles of microRNA function as an endogenous mechanism of gene regulation. J. Robinson demonstrated the utility of correlative microscopy in which light-level and transmission electron microscopy are combined to provide cellular and subcellular views of placental cells. A. Croy provided a lecture on the use of microdissection techniques which are invaluable for isolating very small subsets of cell types for molecular analysis. Finally, G. Rice presented an overview methods on profiling of complex protein mixtures within tissue and/or fluid samples that, when refined, will offer databases that will underpin a systems approach to modern trophoblast biology.

Electron Beam Melting and Refining of Metals: Computational Modeling and Optimization

PubMed Central

Vutova, Katia; Donchev, Veliko

2013-01-01

Computational modeling offers an opportunity for a better understanding and investigation of thermal transfer mechanisms. It can be used for the optimization of the electron beam melting process and for obtaining new materials with improved characteristics that have many applications in the power industry, medicine, instrument engineering, electronics, etc. A time-dependent 3D axis-symmetrical heat model for simulation of thermal transfer in metal ingots solidified in a water-cooled crucible at electron beam melting and refining (EBMR) is developed. The model predicts the change in the temperature field in the casting ingot during the interaction of the beam with the material. A modified Pismen-Rekford numerical scheme to discretize the analytical model is developed. These equation systems, describing the thermal processes and main characteristics of the developed numerical method, are presented. In order to optimize the technological regimes, different criteria for better refinement and obtaining dendrite crystal structures are proposed. Analytical problems of mathematical optimization are formulated, discretized and heuristically solved by cluster methods. Using important for the practice simulation results, suggestions can be made for EBMR technology optimization. The proposed tool is important and useful for studying, control, optimization of EBMR process parameters and improving of the quality of the newly produced materials. PMID:28788351

Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement.

PubMed

Cui, Feng; Jernigan, Robert; Wu, Zhijun

2008-04-01

Nuclear Overhauser effects (NOE) distance constraints and torsion angle constraints are major conformational constraints for nuclear magnetic resonance (NMR) structure refinement. In particular, the number of NOE constraints has been considered as an important determinant for the quality of NMR structures. Of course, the availability of torsion angle constraints is also critical for the formation of correct local conformations. In our recent work, we have shown how a set of knowledge-based short-range distance constraints can also be utilized for NMR structure refinement, as a complementary set of conformational constraints to the NOE and torsion angle constraints. In this paper, we show the results from a series of structure refinement experiments by using different types of conformational constraints--NOE, torsion angle, or knowledge-based constraints--or their combinations, and make a quantitative assessment on how the experimentally acquired constraints contribute to the quality of structural models and whether or not they can be combined with or substituted by the knowledge-based constraints. We have carried out the experiments on a small set of NMR structures. Our preliminary calculations have revealed that the torsion angle constraints contribute substantially to the quality of the structures, but require to be combined with the NOE constraints to be fully effective. The knowledge-based constraints can be functionally as crucial as the torsion angle constraints, although they are statistical constraints after all and are not meant to be able to replace the latter.

Real-space refinement in PHENIX for cryo-EM and crystallography

DOE PAGES

Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.; ...

2018-06-01

This work describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement ofmore » 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.« less

Real-space refinement in PHENIX for cryo-EM and crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.

This work describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement ofmore » 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.« less

Auto-adaptive finite element meshes

NASA Technical Reports Server (NTRS)

Richter, Roland; Leyland, Penelope

1995-01-01

Accurate capturing of discontinuities within compressible flow computations is achieved by coupling a suitable solver with an automatic adaptive mesh algorithm for unstructured triangular meshes. The mesh adaptation procedures developed rely on non-hierarchical dynamical local refinement/derefinement techniques, which hence enable structural optimization as well as geometrical optimization. The methods described are applied for a number of the ICASE test cases are particularly interesting for unsteady flow simulations.

Crystallite size strain analysis of nanocrystalline La0.7Sr0.3MnO3 perovskite by Williamson-Hall plot method

NASA Astrophysics Data System (ADS)

Kumar, Dinesh; Verma, Narendra Kumar; Singh, Chandra Bhal; Singh, Akhilesh Kumar

2018-04-01

The nanocrystalline Sr-doped LaMnO3 (La0.7Sr0.3MnO3 = LSMO) perovskite manganites having different crystallite size were synthesized using the nitrate-glycine auto-combustion method. The phase purity of the manganites was checked by X-ray diffraction (XRD) measurement. The XRD patterns of the sample reveal that La0.7S0.3MnO3 crystallizes into rhombohedral crystal structure with space group R-3c. The size-dependence of structural lattice parameters have been investigated with the help of Rietveld refinement. The structural parameters increase as a function of crystallite size. The crystallite-size and internal strain as a function of crystallite-size have been calculated using Williamson-Hall plot.

Supersonic cruise research aircraft structural studies: Methods and results

NASA Technical Reports Server (NTRS)

Sobieszczanski-Sobieski, J.; Gross, D.; Kurtze, W.; Newsom, J.; Wrenn, G.; Greene, W.

1981-01-01

NASA Langley Research Center SCAR in-house structural studies are reviewed. In methods development, advances include a new system of integrated computer programs called ISSYS, progress in determining aerodynamic loads and aerodynamically induced structural loads (including those due to gusts), flutter optimization for composite and metal airframe configurations using refined and simplified mathematical models, and synthesis of active controls. Results given address several aspects of various SCR configurations. These results include flutter penalties on composite wing, flutter suppression using active controls, roll control effectiveness, wing tip ground clearance, tail size effect on flutter, engine weight and mass distribution influence on flutter, and strength and flutter optimization of new configurations. The ISSYS system of integrated programs performed well in all the applications illustrated by the results, the diversity of which attests to ISSYS' versatility.

Active damping of modal vibrations by force apportioning

NASA Technical Reports Server (NTRS)

Hallauer, W. L., Jr.

1980-01-01

Force apportioning, a method of active structural damping based on that used in modal vibration testing of isolating modes by multiple shaker excitation, was analyzed and numerically simulated. A distribution of as few forces as possible on the structure is chosen so as to maximally affect selected vibration modes while minimally exciting all other modes. The accuracy of numerical simulations of active damping, active damping of higher-frequency modes, and studies of imperfection sensitivity are discussed. The computer programs developed are described and possible refinements of the research are examined.

SRB attrition rate study of the aft skirt due to water impact cavity collapse loading

NASA Technical Reports Server (NTRS)

Crockett, C. D.

1976-01-01

A methodology was presented so that realistic attrition prediction could aid in selecting an optimum design option for minimizing the effects of updated loads on the Space Shuttle Solid Rocket Booster (SRB) aft skirt. The updated loads resulted in water impact attrition rates greater than 10 percent for the aft skirt structure. Adding weight to reinforce the aft skirt was undesirable. The refined method treats the occurrences of the load distribution probabilistically, radially and longitudinally, with respect to the critical structural response.

Scaling of strength and lifetime probability distributions of quasibrittle structures based on atomistic fracture mechanics

PubMed Central

Bažant, Zdeněk P.; Le, Jia-Liang; Bazant, Martin Z.

2009-01-01

The failure probability of engineering structures such as aircraft, bridges, dams, nuclear structures, and ships, as well as microelectronic components and medical implants, must be kept extremely low, typically <10−6. The safety factors needed to ensure it have so far been assessed empirically. For perfectly ductile and perfectly brittle structures, the empirical approach is sufficient because the cumulative distribution function (cdf) of random material strength is known and fixed. However, such an approach is insufficient for structures consisting of quasibrittle materials, which are brittle materials with inhomogeneities that are not negligible compared with the structure size. The reason is that the strength cdf of quasibrittle structure varies from Gaussian to Weibullian as the structure size increases. In this article, a recently proposed theory for the strength cdf of quasibrittle structure is refined by deriving it from fracture mechanics of nanocracks propagating by small, activation-energy-controlled, random jumps through the atomic lattice. This refinement also provides a plausible physical justification of the power law for subcritical creep crack growth, hitherto considered empirical. The theory is further extended to predict the cdf of structural lifetime at constant load, which is shown to be size- and geometry-dependent. The size effects on structure strength and lifetime are shown to be related and the latter to be much stronger. The theory fits previously unexplained deviations of experimental strength and lifetime histograms from the Weibull distribution. Finally, a boundary layer method for numerical calculation of the cdf of structural strength and lifetime is outlined. PMID:19561294

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

NASA Technical Reports Server (NTRS)

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.

X-ray diffraction studies of enkephalins. Crystal structure of [(4'-bromo) Phe4,Leu5]enkephalin.

PubMed Central

Ishida, T; Kenmotsu, M; Mino, Y; Inoue, M; Fujiwara, T; Tomita, K; Kimura, T; Sakakibara, S

1984-01-01

In order to investigate the structure-activity relationship of [Leu5]- and [Met5]enkephalins, [(4'-bromo)Phe4, Leu5]-, [(4'-bromo)Phe4, Met5]- and [Met5] enkephalins were synthesized and crystallized. The crystal structure of [(4'-bromo) Phe4, Leu5]- enkephalin was determined by X-ray diffraction method using the heavy atom method and refined to R = 0.092 by the least-squares method. The molecule in this crystal took essentially the same type I' beta-turn conformation found in [Leu5]enkephalin [Smith & Griffin (1978) Science 199, 1214-1216). On the other hand, the preliminary three-dimensional Patterson analyses showed that the most probable conformations of [(4'-bromo)Phe4,Met5]- and [Met5]enkephalins are both the dimeric extended forms. Based on these insights, the biologically active conformation of enkephalin was discussed in relation to the mu- and delta-receptors. PMID:6721829

Segmentation of the pectoral muscle in breast MR images using structure tensor and deformable model

NASA Astrophysics Data System (ADS)

Lee, Myungeun; Kim, Jong Hyo

2012-02-01

Recently, breast MR images have been used in wider clinical area including diagnosis, treatment planning, and treatment response evaluation, which requests quantitative analysis and breast tissue segmentation. Although several methods have been proposed for segmenting MR images, segmenting out breast tissues robustly from surrounding structures in a wide range of anatomical diversity still remains challenging. Therefore, in this paper, we propose a practical and general-purpose approach for segmenting the pectoral muscle boundary based on the structure tensor and deformable model. The segmentation work flow comprises four key steps: preprocessing, detection of the region of interest (ROI) within the breast region, segmenting the pectoral muscle and finally extracting and refining the pectoral muscle boundary. From experimental results we show that the proposed method can segment the pectoral muscle robustly in diverse patient cases. In addition, the proposed method will allow the application of the quantification research for various breast images.

Nano sized La2Co2O6 double perovskite synthesized by sol gel method

NASA Astrophysics Data System (ADS)

Solanki, Neha; Lodhi, Pavitra Devi; Choudhary, K. K.; Kaurav, Netram

2018-05-01

We report here the synthesis of double perovskite La2Co2O6 (LCO) compound by a sol gel route method. The double perovskite structure of LCO system was confirmed via X-ray diffraction (XRD) analysis. Further, the lattice parameter, unit cell volume and bond length were refined by means of rietveld analysis using the full proof software. Debye Scherer formula was used to determine the particle size. The compound crystallized in triclinic structure with space group P-1 in ambient condition. We also obtained Raman modes from XRD spectra of poly-crystalline LCO sample. These results were interpreted for the observation of phonon excitations in this compound.

Grid-size dependence of Cauchy boundary conditions used to simulate stream-aquifer interactions

USGS Publications Warehouse

Mehl, S.; Hill, M.C.

2010-01-01

This work examines the simulation of stream–aquifer interactions as grids are refined vertically and horizontally and suggests that traditional methods for calculating conductance can produce inappropriate values when the grid size is changed. Instead, different grid resolutions require different estimated values. Grid refinement strategies considered include global refinement of the entire model and local refinement of part of the stream. Three methods of calculating the conductance of the Cauchy boundary conditions are investigated. Single- and multi-layer models with narrow and wide streams produced stream leakages that differ by as much as 122% as the grid is refined. Similar results occur for globally and locally refined grids, but the latter required as little as one-quarter the computer execution time and memory and thus are useful for addressing some scale issues of stream–aquifer interactions. Results suggest that existing grid-size criteria for simulating stream–aquifer interactions are useful for one-layer models, but inadequate for three-dimensional models. The grid dependence of the conductance terms suggests that values for refined models using, for example, finite difference or finite-element methods, cannot be determined from previous coarse-grid models or field measurements. Our examples demonstrate the need for a method of obtaining conductances that can be translated to different grid resolutions and provide definitive test cases for investigating alternative conductance formulations.

Nonlinear Multiobjective MPC-Based Optimal Operation of a High Consistency Refining System in Papermaking

DOE PAGES

Li, Mingjie; Zhou, Ping; Wang, Hong; ...

2017-09-19

As one of the most important unit in the papermaking industry, the high consistency (HC) refining system is confronted with challenges such as improving pulp quality, energy saving, and emissions reduction in its operation processes. Here in this correspondence, an optimal operation of HC refining system is presented using nonlinear multiobjective model predictive control strategies that aim at set-point tracking objective of pulp quality, economic objective, and specific energy (SE) consumption objective, respectively. First, a set of input and output data at different times are employed to construct the subprocess model of the state process model for the HC refiningmore » system, and then the Wiener-type model can be obtained through combining the mechanism model of Canadian Standard Freeness and the state process model that determines their structures based on Akaike information criterion. Second, the multiobjective optimization strategy that optimizes both the set-point tracking objective of pulp quality and SE consumption is proposed simultaneously, which uses NSGA-II approach to obtain the Pareto optimal set. Furthermore, targeting at the set-point tracking objective of pulp quality, economic objective, and SE consumption objective, the sequential quadratic programming method is utilized to produce the optimal predictive controllers. In conclusion, the simulation results demonstrate that the proposed methods can make the HC refining system provide a better performance of set-point tracking of pulp quality when these predictive controllers are employed. In addition, while the optimal predictive controllers orienting with comprehensive economic objective and SE consumption objective, it has been shown that they have significantly reduced the energy consumption.« less

Nonlinear Multiobjective MPC-Based Optimal Operation of a High Consistency Refining System in Papermaking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Mingjie; Zhou, Ping; Wang, Hong

As one of the most important unit in the papermaking industry, the high consistency (HC) refining system is confronted with challenges such as improving pulp quality, energy saving, and emissions reduction in its operation processes. Here in this correspondence, an optimal operation of HC refining system is presented using nonlinear multiobjective model predictive control strategies that aim at set-point tracking objective of pulp quality, economic objective, and specific energy (SE) consumption objective, respectively. First, a set of input and output data at different times are employed to construct the subprocess model of the state process model for the HC refiningmore » system, and then the Wiener-type model can be obtained through combining the mechanism model of Canadian Standard Freeness and the state process model that determines their structures based on Akaike information criterion. Second, the multiobjective optimization strategy that optimizes both the set-point tracking objective of pulp quality and SE consumption is proposed simultaneously, which uses NSGA-II approach to obtain the Pareto optimal set. Furthermore, targeting at the set-point tracking objective of pulp quality, economic objective, and SE consumption objective, the sequential quadratic programming method is utilized to produce the optimal predictive controllers. In conclusion, the simulation results demonstrate that the proposed methods can make the HC refining system provide a better performance of set-point tracking of pulp quality when these predictive controllers are employed. In addition, while the optimal predictive controllers orienting with comprehensive economic objective and SE consumption objective, it has been shown that they have significantly reduced the energy consumption.« less

Effect of Solutes on Grain Refinement of As-Cast Fe-4Si Alloy

NASA Astrophysics Data System (ADS)

Li, Ming; Li, Jian-Min; Zheng, Qing; Wang, Geoff; Zhang, Ming-Xing

2018-06-01

Grain size is one of the key microstructural factors that control the mechanical properties of steels. The present work aims to extend the theories of grain refinement which were established for cast light alloys to steel systems. Using a designed Fe-4 wt pct Si alloy (all-ferrite structure during whole solidification process), the solute effect on grain refinement/grain coarsening in ferritic systems was comprehensively investigated. Experimental results showed that boron (B), which is associated with the highest Q value (growth restriction factor) in ferrite, significantly refined the as-cast structure of the Fe-4 wt pct Si alloy. Cu and Mo with low Q values had no effect on grain refinement. However, although Y and Zr have relatively high Q values, addition of these two solutes led to grain coarsening in the Fe-4Si alloy. Understanding the results in regards to the growth restriction factor and the driving force for the solidification led to the conclusion that in addition to the grain growth restriction effect, the changes of thermodynamic driving force for solidification due to the solute addition also played a key role in grain refinement in ferritic alloys.

Effect of Solutes on Grain Refinement of As-Cast Fe-4Si Alloy

NASA Astrophysics Data System (ADS)

Li, Ming; Li, Jian-Min; Zheng, Qing; Wang, Geoff; Zhang, Ming-Xing

2018-03-01

Grain size is one of the key microstructural factors that control the mechanical properties of steels. The present work aims to extend the theories of grain refinement which were established for cast light alloys to steel systems. Using a designed Fe-4 wt pct Si alloy (all-ferrite structure during whole solidification process), the solute effect on grain refinement/grain coarsening in ferritic systems was comprehensively investigated. Experimental results showed that boron (B), which is associated with the highest Q value (growth restriction factor) in ferrite, significantly refined the as-cast structure of the Fe-4 wt pct Si alloy. Cu and Mo with low Q values had no effect on grain refinement. However, although Y and Zr have relatively high Q values, addition of these two solutes led to grain coarsening in the Fe-4Si alloy. Understanding the results in regards to the growth restriction factor and the driving force for the solidification led to the conclusion that in addition to the grain growth restriction effect, the changes of thermodynamic driving force for solidification due to the solute addition also played a key role in grain refinement in ferritic alloys.

Refined structures of three crystal forms of toxic shock syndrome toxin-1 and of a tetramutant with reduced activity.

PubMed Central

Prasad, G. S.; Radhakrishnan, R.; Mitchell, D. T.; Earhart, C. A.; Dinges, M. M.; Cook, W. J.; Schlievert, P. M.; Ohlendorf, D. H.

1997-01-01

The structure of toxic shock syndrome toxin-1 (TSST-1), the causative agent in toxic shock syndrome, has been determined in three crystal forms. The three structural models have been refined to R-factors of 0.154, 0.150, and 0.198 at resolutions of 2.05 A, 2.90 A, and 2.75 A, respectively. One crystal form of TSST-1 contains a zinc ion bound between two symmetry-related molecules. Although not required for biological activity, zinc dramatically potentiates the mitogenicity of TSST-1 at very low concentrations. In addition, the structure of the tetramutant TSST-1H [T69I, Y80W, E132K, I140T], which is nonmitogenic and does not amplify endotoxin shock, has been determined and refined in a fourth crystal form (R-factor = 0.173 to 1.9 A resolution). PMID:9194182

Computations of Unsteady Viscous Compressible Flows Using Adaptive Mesh Refinement in Curvilinear Body-fitted Grid Systems

NASA Technical Reports Server (NTRS)

Steinthorsson, E.; Modiano, David; Colella, Phillip

1994-01-01

A methodology for accurate and efficient simulation of unsteady, compressible flows is presented. The cornerstones of the methodology are a special discretization of the Navier-Stokes equations on structured body-fitted grid systems and an efficient solution-adaptive mesh refinement technique for structured grids. The discretization employs an explicit multidimensional upwind scheme for the inviscid fluxes and an implicit treatment of the viscous terms. The mesh refinement technique is based on the AMR algorithm of Berger and Colella. In this approach, cells on each level of refinement are organized into a small number of topologically rectangular blocks, each containing several thousand cells. The small number of blocks leads to small overhead in managing data, while their size and regular topology means that a high degree of optimization can be achieved on computers with vector processors.

Vibration Testing of Electrical Cables to Quantify Loads at Tie-Down Locations

NASA Technical Reports Server (NTRS)

Dutson, Joseph D.

2013-01-01

The standard method for defining static equivalent structural load factors for components is based on Mile s equation. Unless test data is available, 5% critical damping is assumed for all components when calculating loads. Application of this method to electrical cable tie-down hardware often results in high loads, which often exceed the capability of typical tie-down options such as cable ties and P-clamps. Random vibration testing of electrical cables was used to better understand the factors that influence component loads: natural frequency, damping, and mass participation. An initial round of vibration testing successfully identified variables of interest, checked out the test fixture and instrumentation, and provided justification for removing some conservatism in the standard method. Additional testing is planned that will include a larger range of cable sizes for the most significant contributors to load as variables to further refine loads at cable tie-down points. Completed testing has provided justification to reduce loads at cable tie-downs by 45% with additional refinement based on measured cable natural frequencies.

The Long-Term Conditions Questionnaire: conceptual framework and item development

PubMed Central

Peters, Michele; Potter, Caroline M; Kelly, Laura; Hunter, Cheryl; Gibbons, Elizabeth; Jenkinson, Crispin; Coulter, Angela; Forder, Julien; Towers, Ann-Marie; A’Court, Christine; Fitzpatrick, Ray

2016-01-01

Purpose To identify the main issues of importance when living with long-term conditions to refine a conceptual framework for informing the item development of a patient-reported outcome measure for long-term conditions. Materials and methods Semi-structured qualitative interviews (n=48) were conducted with people living with at least one long-term condition. Participants were recruited through primary care. The interviews were transcribed verbatim and analyzed by thematic analysis. The analysis served to refine the conceptual framework, based on reviews of the literature and stakeholder consultations, for developing candidate items for a new measure for long-term conditions. Results Three main organizing concepts were identified: impact of long-term conditions, experience of services and support, and self-care. The findings helped to refine a conceptual framework, leading to the development of 23 items that represent issues of importance in long-term conditions. The 23 candidate items formed the first draft of the measure, currently named the Long-Term Conditions Questionnaire. Conclusion The aim of this study was to refine the conceptual framework and develop items for a patient-reported outcome measure for long-term conditions, including single and multiple morbidities and physical and mental health conditions. Qualitative interviews identified the key themes for assessing outcomes in long-term conditions, and these underpinned the development of the initial draft of the measure. These initial items will undergo cognitive testing to refine the items prior to further validation in a survey. PMID:27621678

Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pražnikar, Jure; University of Primorska,; Turk, Dušan, E-mail: dusan.turk@ijs.si

2014-12-01

The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model. The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. Theymore » utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of R{sub free} or may leave it out completely.« less

Grain Refinement Efficiency in Commercial-Purity Aluminum Influenced by the Addition of Al-4Ti Master Alloys with Varying TiAl3 Particles

PubMed Central

Zhao, Jianhua; He, Jiansheng; Tang, Qi; Wang, Tao; Chen, Jing

2016-01-01

A series of Al-4Ti master alloys with various TiAl3 particles were prepared via pouring the pure aluminum added with K2TiF6 or sponge titanium into three different molds made of graphite, copper, and sand. The microstructure and morphology of TiAl3 particles were characterized and analyzed by scanning electron microscope (SEM) with energy dispersive spectroscopy (EDS). The microstructure of TiAl3 particles in Al-4Ti master alloys and their grain refinement efficiency in commercial-purity aluminum were investigated in this study. Results show that there were three different morphologies of TiAl3 particles in Al-4Ti master alloys: petal-like structures, blocky structures, and flaky structures. The Al-4Ti master alloy with blocky TiAl3 particles had better and more stable grain refinement efficiency than the master alloys with petal-like and flaky TiAl3 particles. The average grain size of the refined commercial-purity aluminum always hereditarily followed the size of the original TiAl3 particles. In addition, the grain refinement efficiency of Al-4Ti master alloys with the same morphology, size, and distribution of TiAl3 particles prepared through different processes was almost identical. PMID:28773987

Grain Refinement Efficiency in Commercial-Purity Aluminum Influenced by the Addition of Al-4Ti Master Alloys with Varying TiAl₃ Particles.

PubMed

Zhao, Jianhua; He, Jiansheng; Tang, Qi; Wang, Tao; Chen, Jing

2016-10-26

A series of Al-4Ti master alloys with various TiAl₃ particles were prepared via pouring the pure aluminum added with K₂TiF₆ or sponge titanium into three different molds made of graphite, copper, and sand. The microstructure and morphology of TiAl₃ particles were characterized and analyzed by scanning electron microscope (SEM) with energy dispersive spectroscopy (EDS). The microstructure of TiAl₃ particles in Al-4Ti master alloys and their grain refinement efficiency in commercial-purity aluminum were investigated in this study. Results show that there were three different morphologies of TiAl₃ particles in Al-4Ti master alloys: petal-like structures, blocky structures, and flaky structures. The Al-4Ti master alloy with blocky TiAl₃ particles had better and more stable grain refinement efficiency than the master alloys with petal-like and flaky TiAl₃ particles. The average grain size of the refined commercial-purity aluminum always hereditarily followed the size of the original TiAl₃ particles. In addition, the grain refinement efficiency of Al-4Ti master alloys with the same morphology, size, and distribution of TiAl₃ particles prepared through different processes was almost identical.

Adaptive Mesh Refinement for Microelectronic Device Design

NASA Technical Reports Server (NTRS)

Cwik, Tom; Lou, John; Norton, Charles

1999-01-01

Finite element and finite volume methods are used in a variety of design simulations when it is necessary to compute fields throughout regions that contain varying materials or geometry. Convergence of the simulation can be assessed by uniformly increasing the mesh density until an observable quantity stabilizes. Depending on the electrical size of the problem, uniform refinement of the mesh may be computationally infeasible due to memory limitations. Similarly, depending on the geometric complexity of the object being modeled, uniform refinement can be inefficient since regions that do not need refinement add to the computational expense. In either case, convergence to the correct (measured) solution is not guaranteed. Adaptive mesh refinement methods attempt to selectively refine the region of the mesh that is estimated to contain proportionally higher solution errors. The refinement may be obtained by decreasing the element size (h-refinement), by increasing the order of the element (p-refinement) or by a combination of the two (h-p refinement). A successful adaptive strategy refines the mesh to produce an accurate solution measured against the correct fields without undue computational expense. This is accomplished by the use of a) reliable a posteriori error estimates, b) hierarchal elements, and c) automatic adaptive mesh generation. Adaptive methods are also useful when problems with multi-scale field variations are encountered. These occur in active electronic devices that have thin doped layers and also when mixed physics is used in the calculation. The mesh needs to be fine at and near the thin layer to capture rapid field or charge variations, but can coarsen away from these layers where field variations smoothen and charge densities are uniform. This poster will present an adaptive mesh refinement package that runs on parallel computers and is applied to specific microelectronic device simulations. Passive sensors that operate in the infrared portion of the spectrum as well as active device simulations that model charge transport and Maxwell's equations will be presented.

Synthesis and crystal structure determination of yttrium ultraphosphate YP 5O 14

NASA Astrophysics Data System (ADS)

Mbarek, A.; Graia, M.; Chadeyron, G.; Zambon, D.; Bouaziz, J.; Fourati, M.

2009-03-01

The crystal structure of monoclinic YP 5O 14 (space group C2/ c, a=12.919(2) Å, b=12.796(4) Å, c=12.457(2) Å, β=91.30(1)°, Z=8) has been refined from single-crystal X-ray diffraction data. Full-matrix least-squares refinement on F2 using 2249 independent reflections for 183 refinable parameters results in a final R value of 0.027 ( ωR=0.069). The structure is isotypic with HoP 5O 14. This structure is built up from infinite layers of PO 4 tetrahedra linked through isolated YO 8 polyhedra. The three-dimensional cohesion of the framework results from Y-O-P bridges. This crystal structure refinement leads to the calculated X-ray diffraction powder pattern of this monoclinic polymorph, which has been the starting point of a thorough study of the solid-state synthesis of this ultraphosphate. This investigation further leads to a better outstanding of features observed during the synthesis of powdered samples. The thermal behavior of this ultraphosphate has been studied by DTA and TGA analyses. The infrared and Raman spectroscopic characterizations have been carried out on polycrystalline samples. The luminescence properties of the Eu 3+ ion incorporated in the monoclinic C2/ c polymorph of YP 5O 14 as local structural probe show that in YP 5O 14: 5% Eu 3+ sample, the Eu 3+ ions are distributed over the two Y 3+ crystallographic sites of C 2 symmetry of this structure.

Ion-pairing in aqueous CaCl 2 and RbBr solutions. Simultaneous structural refinement of XAFS and XRD data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, Thai V.; Fulton, John L.

2013-01-22

We present a new methodology involving the simultaneous refinement of both x-ray absorption and x-ray diffraction spectra (X-ray Absorption/Diffraction Structural Refinement,XADSR), to study hydration and ion pair structure of CaCl 2 and RbBr salts in concentrated aqueous solutions. The XADSR analysis includes the XAFS spectra analysis of both the cation and anion as a probe of their short-range structure with an XRD spectral analysis as a probe of the global structural. Together they deliver a comprehensive picture of the cation and anion hydration, the contact ion pair (CIP) structure and the solvent-separated ion pair (SSIP) structure. XADSR analysis of 6.0more » m aqueous CaCl 2 reveals that there are an insignificant number of Ca 2+-Cl- CIP’s, but there are approximately 3.4 SSIP’s separated by about 4.99 Å. In contrast XADSR analysis of aqueous RbBr yields about 0.7 pair CIP at a bond length 3.51 Å. The present work demonstrates a new approach for a direct co-refinement of XRD and XAFS spectra in a simple and reliable fashion, opening new opportunities for analysis in various disordered and crystalline systems. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated for the U.S. Department of Energy by Battelle.« less

GeneSilico protein structure prediction meta-server.

PubMed

Kurowski, Michal A; Bujnicki, Janusz M

2003-07-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta.

GeneSilico protein structure prediction meta-server

PubMed Central

Kurowski, Michal A.; Bujnicki, Janusz M.

2003-01-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta. PMID:12824313

Econometrics of inventory holding and shortage costs: the case of refined gasoline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krane, S.D.

1985-01-01

This thesis estimates a model of a firm's optimal inventory and production behavior in order to investigate the link between the role of inventories in the business cycle and the microeconomic incentives for holding stocks of finished goods. The goal is to estimate a set of structural cost function parameters that can be used to infer the optimal cyclical response of inventories and production to shocks in demand. To avoid problems associated with the use of value based aggregate inventory data, an industry level physical unit data set for refined motor gasoline is examined. The Euler equations for a refiner'smore » multiperiod decision problem are estimated using restrictions imposed by the rational expectations hypothesis. The model also embodies the fact that, in most periods, the level of shortages will be zero, and even when positive, the shortages are not directly observable in the data set. These two concerns lead us to use a generalized method of moments estimation technique on a functional form that resembles the formulation of a Tobit problem. The estimation results are disappointing; the model and data yield coefficient estimates incongruous with the cost function interpretations of the structural parameters. These is only some superficial evidence that production smoothing is significant and that marginal inventory shortage costs increase at a faster rate than do marginal holding costs.« less

Structural analysis of zeolite NaA synthesized by a cost-effective hydrothermal method using kaolin and its use as water softener.

PubMed

Loiola, A R; Andrade, J C R A; Sasaki, J M; da Silva, L R D

2012-02-01

Zeolite 4A (LTA) has been successfully synthesized by a hydrothermal method, where kaolin was used as silica and alumina source. The synthesized zeolite was characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), laser granulometry, and FTIR spectroscopy. XRD data from the Rietveld refinement method confirmed only one crystallographic phase. Zeolite A morphology was observed by SEM analysis, and it showed well-defined crystals with slightly different sizes but with the same cubic shape. Particle size distribution of the crystals was confirmed by laser granulometry, whereas FTIR spectroscopy revealed significant structural differences between the starting material and the final zeolite product used as water softener. Copyright © 2010 Elsevier Inc. All rights reserved.

Experimental and first principle study of the structure, electronic, optical and luminescence properties of M-type GdNbO4 phosphor

NASA Astrophysics Data System (ADS)

Ding, Shoujun; Zhang, Haotian; Zhang, Qingli; Chen, Yuanzhi; Dou, Renqin; Peng, Fang; Liu, Wenpeng; Sun, Dunlu

2018-06-01

In this work, GdNbO4 polycrystalline with monoclinic phase was prepared by traditional high-temperature solid-state reaction. Its structure was determined by X-ray diffraction and its unit cell parameters were obtained with Rietveld refinement method. Its luminescence properties (including absorbance, emission and luminescence lifetime) were investigated with experiment method and the CIE chromaticity coordinate was presented. Furthermore, a systematic theoretical calculation (including band gap, density of states and optical properties) based on the density function theory methods was performed on GdNbO4. Lastly, a comparison between experiment and calculated results was conducted. The calculated and experiment results obtained in this work can provide an essential understanding of GdNbO4 material.

CASTRO: A NEW COMPRESSIBLE ASTROPHYSICAL SOLVER. II. GRAY RADIATION HYDRODYNAMICS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, W.; Almgren, A.; Bell, J.

We describe the development of a flux-limited gray radiation solver for the compressible astrophysics code, CASTRO. CASTRO uses an Eulerian grid with block-structured adaptive mesh refinement based on a nested hierarchy of logically rectangular variable-sized grids with simultaneous refinement in both space and time. The gray radiation solver is based on a mixed-frame formulation of radiation hydrodynamics. In our approach, the system is split into two parts, one part that couples the radiation and fluid in a hyperbolic subsystem, and another parabolic part that evolves radiation diffusion and source-sink terms. The hyperbolic subsystem is solved explicitly with a high-order Godunovmore » scheme, whereas the parabolic part is solved implicitly with a first-order backward Euler method.« less

X-ray diffraction study of Penicillium Vitale catalase in the complex with aminotriazole

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borovik, A. A.; Grebenko, A. I.; Melik-Adamyan, V. R., E-mail: mawr@ns.crys.ras.ru

2011-07-15

The three-dimensional structure of the enzyme catalase from Penicillium vitale in a complex with the inhibitor aminotriazole was solved and refined by protein X-ray crystallography methods. An analysis of the three-dimensional structure of the complex showed that the inhibition of the enzyme occurs as a result of the covalent binding of aminotriazole to the amino-acid residue His64 in the active site of the enzyme. An investigation of the three-dimensional structure of the complex resulted in the amino-acid residues being more precisely identified. The binding sites of saccharide residues and calcium ions in the protein molecule were found.

Synthesis and X-ray structural investigation of (5R*,6S*)-1-benzoyl-5-methylthio-6-methoxy-1-azapenam

NASA Astrophysics Data System (ADS)

Krajewski, J. W.; Gluziński, P.; Grochowski, E.; Pupek, K.; Mishnyov, A.; Kemme, A.

1992-08-01

The compound (5R*,6S*)-1-benzoyl-5-methylthio-6-methoxy-1-azapenam ( 3) has been synthesized and its structure investigated by X-ray diffraction. The compound crystallizes in a monoclinic system, space group Cc, Z = 4, a = 12.01(1), b = 16.51(1), c = 8.048(6) Å, β = 115.87(6)°. The structure was solved by direct methods and refined by a full-matrix, least-squares procedure to give R = 0.070, Rw = 0.046, w = 1.34/(σ 2F). The expected cis configuration around the β-lactam ring was fully confirmed.

Combinative application of pH-zone-refining and conventional high-speed counter-current chromatography for preparative separation of caged polyprenylated xanthones from gamboge.

PubMed

Xu, Min; Fu, Wenwei; Zhang, Baojun; Tan, Hongsheng; Xiu, Yanfeng; Xu, Hongxi

2016-02-01

An efficient method for the preparative separation of four structurally similar caged xanthones from the crude extracts of gamboge was established, which involves the combination of pH-zone-refining counter-current chromatography and conventional high-speed counter-current chromatography for the first time. pH-zone-refining counter-current chromatography was performed with the solvent system composed of n-hexane/ethyl acetate/methanol/water (7:3:8:2, v/v/v/v), where 0.1% trifluoroacetic acid was added to the upper organic stationary phase as a retainer and 0.03% triethylamine was added to the aqueous mobile phase as an eluter. From 3.157 g of the crude extract, 1.134 g of gambogic acid, 180.5 mg of gambogenic acid and 572.9 mg of a mixture of two other caged polyprenylated xanthones were obtained. The mixture was further separated by conventional high-speed counter-current chromatography with a solvent system composed of n-hexane/ethyl acetate/methanol/water (5:5:10:5, v/v/v/v) and n-hexane/methyl tert-butyl ether/acetonitrile/water (8:2:6:4,v/v/v/v), yielding 11.6 mg of isogambogenic acid and 10.4 mg of β-morellic acid from 218.0 mg of the mixture, respectively. The purities of all four of the compounds were over 95%, as determined by high-performance liquid chromatography, and the chemical structures of the four compounds were confirmed by electrospray ionization mass spectrometry and NMR spectroscopy. The combinative application of pH-zone-refining counter-current chromatography and conventional high-speed counter-current chromatography shows great advantages in isolating and enriching the caged polyprenylated xanthones. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Overlapping communities from dense disjoint and high total degree clusters

NASA Astrophysics Data System (ADS)

Zhang, Hongli; Gao, Yang; Zhang, Yue

2018-04-01

Community plays an important role in the field of sociology, biology and especially in domains of computer science, where systems are often represented as networks. And community detection is of great importance in the domains. A community is a dense subgraph of the whole graph with more links between its members than between its members to the outside nodes, and nodes in the same community probably share common properties or play similar roles in the graph. Communities overlap when nodes in a graph belong to multiple communities. A vast variety of overlapping community detection methods have been proposed in the literature, and the local expansion method is one of the most successful techniques dealing with large networks. The paper presents a density-based seeding method, in which dense disjoint local clusters are searched and selected as seeds. The proposed method selects a seed by the total degree and density of local clusters utilizing merely local structures of the network. Furthermore, this paper proposes a novel community refining phase via minimizing the conductance of each community, through which the quality of identified communities is largely improved in linear time. Experimental results in synthetic networks show that the proposed seeding method outperforms other seeding methods in the state of the art and the proposed refining method largely enhances the quality of the identified communities. Experimental results in real graphs with ground-truth communities show that the proposed approach outperforms other state of the art overlapping community detection algorithms, in particular, it is more than two orders of magnitude faster than the existing global algorithms with higher quality, and it obtains much more accurate community structure than the current local algorithms without any priori information.

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

DOE PAGES

Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; ...

2015-03-17

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. In conclusion, these developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

DOE PAGES

Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; ...

2015-03-17

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

PubMed Central

Uervirojnangkoorn, Monarin; Zeldin, Oliver B; Lyubimov, Artem Y; Hattne, Johan; Brewster, Aaron S; Sauter, Nicholas K; Brunger, Axel T; Weis, William I

2015-01-01

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited. DOI: http://dx.doi.org/10.7554/eLife.05421.001 PMID:25781634

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

NASA Astrophysics Data System (ADS)

Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; Kathuria, Sagar V.; Bilsel, Osman; Matthews, C. Robert; Lane, T. J.; Pande, Vijay S.

2017-03-01

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. Here, 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. This 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. Using these results, we then predict incisive single molecule FRET experiments as a means of model validation. This 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.

Structure-based coarse-graining for inhomogeneous liquid polymer systems.

PubMed

Fukuda, Motoo; Zhang, Hedong; Ishiguro, Takahiro; Fukuzawa, Kenji; Itoh, Shintaro

2013-08-07

The iterative Boltzmann inversion (IBI) method is used to derive interaction potentials for coarse-grained (CG) systems by matching structural properties of a reference atomistic system. However, because it depends on such thermodynamic conditions as density and pressure of the reference system, the derived CG nonbonded potential is probably not applicable to inhomogeneous systems containing different density regimes. In this paper, we propose a structure-based coarse-graining scheme to devise CG nonbonded potentials that are applicable to different density bulk systems and inhomogeneous systems with interfaces. Similar to the IBI, the radial distribution function (RDF) of a reference atomistic bulk system is used for iteratively refining the CG nonbonded potential. In contrast to the IBI, however, our scheme employs an appropriately estimated initial guess and a small amount of refinement to suppress transfer of the many-body interaction effects included in the reference RDF into the CG nonbonded potential. To demonstrate the application of our approach to inhomogeneous systems, we perform coarse-graining for a liquid perfluoropolyether (PFPE) film coated on a carbon surface. The constructed CG PFPE model favorably reproduces structural and density distribution functions, not only for bulk systems, but also at the liquid-vacuum and liquid-solid interfaces, demonstrating that our CG scheme offers an easy and practical way to accurately determine nonbonded potentials for inhomogeneous systems.

Analysis of rapidly synthesized guest-filled porous complexes with synchrotron radiation: Practical guidelines for the crystalline sponge method

DOE PAGES

Ramadhar, Timothy R.; Zheng, Shao -Liang; Chen, Yu -Sheng; ...

2015-01-01

A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported. The procedure for the synthesis of the zinc-based metal–organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collectionmore » times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination.« less

Rietveld Refinement on X-Ray Diffraction Patterns of Bioapatite in Human Fetal Bones

PubMed Central

Meneghini, Carlo; Dalconi, Maria Chiara; Nuzzo, Stefania; Mobilio, Settimio; Wenk, Rudy H.

2003-01-01

Bioapatite, the main constituent of mineralized tissue in mammalian bones, is a calcium-phosphate-based mineral that is similar in structure and composition to hydroxyapatite. In this work, the crystallographic structure of bioapatite in human fetuses was investigated by synchrotron radiation x-ray diffraction (XRD) and microdiffraction (μ-XRD) techniques. Rietveld refinement analyses of XRD and μ-XRD data allow for quantitative probing of the structural modifications of bioapatite as functions of the mineralization process and gestational age. PMID:12609904

In-situ crystal structure determination of seifertite SiO 2 at 129 GPa: Studying a minor phase near Earth’s core–mantle boundary

DOE PAGES

Zhang, Li; Popov, Dmitry; Meng, Yue; ...

2016-01-01

Seifertite SiO₂ likely exists as a minor phase near the core–mantle boundary. By simulating the pressure and temperature conditions near the core–mantle boundary, seifertite was synthesized as a minor phase in a coarse-grained, polycrystalline sample coexisting with the (Mg,Fe)SiO₃ post-perovskite (pPv) phase at 129 GPa and 2500 K. Here we report the first in situ single-crystal structure determination and refinement of seifertite at high pressure and after a temperature quench from laser heating. We improved the data coverage of a minor phase from a diamond-anvil cell (DAC) by merging single-crystal data of seifertite from six selected grains that had differentmore » orientations. Observed systematic absences of reflections from the six individual grains allowed only one space group: Pbcn. The refined results of seifertite are in good agreement with the predictions from previous first-principles calculations at high pressure. This approach provides a method for structure determination of a minor phase in a mineral assemblage synthesized under P-T conditions representative of the deep Earth.« less

In-situ crystal structure determination of seifertite SiO 2 at 129 GPa: Studying a minor phase near Earth’s core–mantle boundary

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Li; Popov, Dmitry; Meng, Yue

Seifertite SiO₂ likely exists as a minor phase near the core–mantle boundary. By simulating the pressure and temperature conditions near the core–mantle boundary, seifertite was synthesized as a minor phase in a coarse-grained, polycrystalline sample coexisting with the (Mg,Fe)SiO₃ post-perovskite (pPv) phase at 129 GPa and 2500 K. Here we report the first in situ single-crystal structure determination and refinement of seifertite at high pressure and after a temperature quench from laser heating. We improved the data coverage of a minor phase from a diamond-anvil cell (DAC) by merging single-crystal data of seifertite from six selected grains that had differentmore » orientations. Observed systematic absences of reflections from the six individual grains allowed only one space group: Pbcn. The refined results of seifertite are in good agreement with the predictions from previous first-principles calculations at high pressure. This approach provides a method for structure determination of a minor phase in a mineral assemblage synthesized under P-T conditions representative of the deep Earth.« less

Nonconforming mortar element methods: Application to spectral discretizations

NASA Technical Reports Server (NTRS)

Maday, Yvon; Mavriplis, Cathy; Patera, Anthony

1988-01-01

Spectral element methods are p-type weighted residual techniques for partial differential equations that combine the generality of finite element methods with the accuracy of spectral methods. Presented here is a new nonconforming discretization which greatly improves the flexibility of the spectral element approach as regards automatic mesh generation and non-propagating local mesh refinement. The method is based on the introduction of an auxiliary mortar trace space, and constitutes a new approach to discretization-driven domain decomposition characterized by a clean decoupling of the local, structure-preserving residual evaluations and the transmission of boundary and continuity conditions. The flexibility of the mortar method is illustrated by several nonconforming adaptive Navier-Stokes calculations in complex geometry.

Synthesis and structural study of 4-(2-chlorophenyl)-2-ethoxy-5,6,7,8,9,10-hexahydrocycloocta[B]pyridine-3-carbonitrile

NASA Astrophysics Data System (ADS)

Fathima, K. Saiadali; Vasumathi, M.; Anitha, K.

2016-05-01

The novel organic material C20H21ClN2O was synthesized by One-Pot synthesis method and the single crystals were grown by slow evaporation solution growth technique. The crystal structure was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R=0.039 for 2746 reflections. Crystal system of the grown crystal was found to be monoclinic with the space group P21/a and a=9.196(4) Å, b=13.449(4) Å, c=14.818(4) Å, β= 101.542(3)°, V=1795.6(11) Å3 and Z=4. In this crystal structure, cyclooctanone prefers to reside in a chair-boat conformation. The structure is stabilized by attractive molecular force such as CH/π interaction called hydrophobic interaction.

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

DOE PAGES

Janowski, Pawel A.; Moriarty, Nigel W.; Kelley, Brian P.; ...

2016-08-31

Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows.PHENIX–AFITTrefinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentiallymore » difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows.PHENIX–AFITTrefinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combiningAFITTand thePHENIXsoftware suite on a data set of 189 protein–ligand PDB structures are presented. Refinements usingPHENIX–AFITTsignificantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. Finally, for the data presented,PHENIX–AFITTrefinements result in more chemically accurate models for small-molecule ligands.« less

PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

PubMed

Lee, Woonghee; Stark, Jaime L; Markley, John L

2014-11-01

Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

Microstructural modification of pure Mg for improving mechanical and biocorrosion properties.

PubMed

Ahmadkhaniha, D; Järvenpää, A; Jaskari, M; Sohi, M Heydarzadeh; Zarei-Hanzaki, A; Fedel, M; Deflorian, F; Karjalainen, L P

2016-08-01

In this study, the effect of microstructural modification on mechanical properties and biocorrosion resistance of pure Mg was investigated for tailoring a load-bearing orthopedic biodegradable implant material. This was performed utilizing the friction stir processing (FSP) in 1-3 passes to refine the grain size. Microstructure was examined in an optical microscope and scanning electron microscope with an electron backscatter diffraction unit. X-ray diffraction method was used to identify the texture. Mechanical properties were measured by microhardness and tensile testing. Electrochemical impedance spectroscopy was applied to evaluate corrosion behavior. The results indicate that even applying a single pass of FSP refined the grain size significantly. Increasing the number of FSP passes further refined the structure, increased the mechanical strength and intensified the dominating basal texture. The best combination of mechanical properties and corrosion resistance were achieved after three FSP passes. In this case, the yield strength was about six times higher than that of the as-cast Mg and the corrosion resistance was also improved compared to that in the as-cast condition. Copyright © 2016 Elsevier Ltd. All rights reserved.

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling

NASA Astrophysics Data System (ADS)

Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

2018-01-01

Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structures to model the backbone flexibility and molecular dynamics simulations to model the sidechain and ligand flexibility. The methods are tested for the binding of 35 ligands to FXR as part of the first stage of the Drug Design Data Resource (D3R) Grand Challenge 2 blind challenge. The results show that the multiple-target docking protocol performs surprisingly well, with correct poses found for 21 of the ligands. MD simulations started on the docked structures are remarkably stable, but show almost no tendency of refining the structure closer to the experimentally found binding pose. Reconnaissance metadynamics enhances the exploration of new binding poses, but additional collective variables involving the protein are needed to exploit the full potential of the method.

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.

PubMed

Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

2018-01-01

Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structures to model the backbone flexibility and molecular dynamics simulations to model the sidechain and ligand flexibility. The methods are tested for the binding of 35 ligands to FXR as part of the first stage of the Drug Design Data Resource (D3R) Grand Challenge 2 blind challenge. The results show that the multiple-target docking protocol performs surprisingly well, with correct poses found for 21 of the ligands. MD simulations started on the docked structures are remarkably stable, but show almost no tendency of refining the structure closer to the experimentally found binding pose. Reconnaissance metadynamics enhances the exploration of new binding poses, but additional collective variables involving the protein are needed to exploit the full potential of the method.

Refining glass structure in two dimensions

NASA Astrophysics Data System (ADS)

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.

Object-based change detection method using refined Markov random field

NASA Astrophysics Data System (ADS)

Peng, Daifeng; Zhang, Yongjun

2017-01-01

In order to fully consider the local spatial constraints between neighboring objects in object-based change detection (OBCD), an OBCD approach is presented by introducing a refined Markov random field (MRF). First, two periods of images are stacked and segmented to produce image objects. Second, object spectral and textual histogram features are extracted and G-statistic is implemented to measure the distance among different histogram distributions. Meanwhile, object heterogeneity is calculated by combining spectral and textual histogram distance using adaptive weight. Third, an expectation-maximization algorithm is applied for determining the change category of each object and the initial change map is then generated. Finally, a refined change map is produced by employing the proposed refined object-based MRF method. Three experiments were conducted and compared with some state-of-the-art unsupervised OBCD methods to evaluate the effectiveness of the proposed method. Experimental results demonstrate that the proposed method obtains the highest accuracy among the methods used in this paper, which confirms its validness and effectiveness in OBCD.

Refining historical limits method to improve disease cluster detection, New York City, New York, USA.

PubMed

Levin-Rector, Alison; Wilson, Elisha L; Fine, Annie D; Greene, Sharon K

2015-02-01

Since the early 2000s, the Bureau of Communicable Disease of the New York City Department of Health and Mental Hygiene has analyzed reportable infectious disease data weekly by using the historical limits method to detect unusual clusters that could represent outbreaks. This method typically produced too many signals for each to be investigated with available resources while possibly failing to signal during true disease outbreaks. We made method refinements that improved the consistency of case inclusion criteria and accounted for data lags and trends and aberrations in historical data. During a 12-week period in 2013, we prospectively assessed these refinements using actual surveillance data. The refined method yielded 74 signals, a 45% decrease from what the original method would have produced. Fewer and less biased signals included a true citywide increase in legionellosis and a localized campylobacteriosis cluster subsequently linked to live-poultry markets. Future evaluations using simulated data could complement this descriptive assessment.

USSR Report, International Affairs

DTIC Science & Technology

1986-10-07

the comprehensive utilization of coal and devel- opment of improved methods assuring a more effective use of low-quality coals, low- calory lignites...promising trend of the joint activity in this sphere. Thus, cyclone furnaces for burning low-quality fuel and fuel wastes save up to 10-20 per cent of...structure of the developing countries should be refined and made concrete and we should move from studying particular classes and strata to a comprehensive

Bragg projection ptychography on niobium phase domain

DOE PAGES

Burdet, Nicolas; Shi, Xiaowen; Huang, Xiaojing; ...

2016-08-10

Here, we demonstrate that the highly sensitive phase-contrast properties of Bragg coherent diffraction measurements combined with the translational diversity of ptychography can provide a Bragg “dark field” imaging method capable of revealing the finger print of domain structure in metallic thin films. Experimental diffraction data was taken from a epitaxially grown niobium metallic thin film on sapphire; and analyzed with the help of a careful combination of implemented refinement mechanisms.

Density Functional Theory Calculations of the Dissociation of H[2] on (100) 2H-MoS[2] Surfaces: A Key Step in the Hydroprocessing of Crude Oil

ERIC Educational Resources Information Center

Todorova, Teodora; Alexiev, Valentin; Weber, Thomas

2006-01-01

Hydrogen activation on the (100) surface of MoS[2] structures was investigated by means of density functional theory calculations. Linear and quadratic synchronous transit methods with a conjugate gradient refinement of the saddle point were used to localize transition states. The calculations include heterolytic and homolytic dissociation of…

Improved Estimates of Thermodynamic Parameters

NASA Technical Reports Server (NTRS)

Lawson, D. D.

1982-01-01

Techniques refined for estimating heat of vaporization and other parameters from molecular structure. Using parabolic equation with three adjustable parameters, heat of vaporization can be used to estimate boiling point, and vice versa. Boiling points and vapor pressures for some nonpolar liquids were estimated by improved method and compared with previously reported values. Technique for estimating thermodynamic parameters should make it easier for engineers to choose among candidate heat-exchange fluids for thermochemical cycles.

PaFlexPepDock: parallel ab-initio docking of peptides onto their receptors with full flexibility based on Rosetta.

PubMed

Li, Haiou; Lu, Liyao; Chen, Rong; Quan, Lijun; Xia, Xiaoyan; Lü, Qiang

2014-01-01

Structural information related to protein-peptide complexes can be very useful for novel drug discovery and design. The computational docking of protein and peptide can supplement the structural information available on protein-peptide interactions explored by experimental ways. Protein-peptide docking of this paper can be described as three processes that occur in parallel: ab-initio peptide folding, peptide docking with its receptor, and refinement of some flexible areas of the receptor as the peptide is approaching. Several existing methods have been used to sample the degrees of freedom in the three processes, which are usually triggered in an organized sequential scheme. In this paper, we proposed a parallel approach that combines all the three processes during the docking of a folding peptide with a flexible receptor. This approach mimics the actual protein-peptide docking process in parallel way, and is expected to deliver better performance than sequential approaches. We used 22 unbound protein-peptide docking examples to evaluate our method. Our analysis of the results showed that the explicit refinement of the flexible areas of the receptor facilitated more accurate modeling of the interfaces of the complexes, while combining all of the moves in parallel helped the constructing of energy funnels for predictions.

Chiral pathways in DNA dinucleotides using gradient optimized refinement along metastable borders

NASA Astrophysics Data System (ADS)

Romano, Pablo; Guenza, Marina

We present a study of DNA breathing fluctuations using Markov state models (MSM) with our novel refinement procedure. MSM have become a favored method of building kinetic models, however their accuracy has always depended on using a significant number of microstates, making the method costly. We present a method which optimizes macrostates by refining borders with respect to the gradient along the free energy surface. As the separation between macrostates contains highest discretization errors, this method corrects for any errors produced by limited microstate sampling. Using our refined MSM methods, we investigate DNA breathing fluctuations, thermally induced conformational changes in native B-form DNA. Running several microsecond MD simulations of DNA dinucleotides of varying sequences, to include sequence and polarity effects, we've analyzed using our refined MSM to investigate conformational pathways inherent in the unstacking of DNA bases. Our kinetic analysis has shown preferential chirality in unstacking pathways that may be critical in how proteins interact with single stranded regions of DNA. These breathing dynamics can help elucidate the connection between conformational changes and key mechanisms within protein-DNA recognition. NSF Chemistry Division (Theoretical Chemistry), the Division of Physics (Condensed Matter: Material Theory), XSEDE.

40 CFR 80.330 - What are the sampling and testing requirements for refiners and importers?

Code of Federal Regulations, 2010 CFR

2010-07-01

... an exemption under this section, upon notification from EPA, the refiner's exemption will be void ab initio. (b) Sampling methods. For purposes of paragraph (a) of this section, refiners and importers shall...

40 CFR 80.330 - What are the sampling and testing requirements for refiners and importers?

Code of Federal Regulations, 2013 CFR

2013-07-01

... an exemption under this section, upon notification from EPA, the refiner's exemption will be void ab initio. (b) Sampling methods. For purposes of paragraph (a) of this section, refiners and importers shall...

40 CFR 80.330 - What are the sampling and testing requirements for refiners and importers?

Code of Federal Regulations, 2011 CFR

2011-07-01

... an exemption under this section, upon notification from EPA, the refiner's exemption will be void ab initio. (b) Sampling methods. For purposes of paragraph (a) of this section, refiners and importers shall...

40 CFR 80.330 - What are the sampling and testing requirements for refiners and importers?

Code of Federal Regulations, 2012 CFR

2012-07-01

... an exemption under this section, upon notification from EPA, the refiner's exemption will be void ab initio. (b) Sampling methods. For purposes of paragraph (a) of this section, refiners and importers shall...

40 CFR 80.330 - What are the sampling and testing requirements for refiners and importers?

Code of Federal Regulations, 2014 CFR

2014-07-01

... an exemption under this section, upon notification from EPA, the refiner's exemption will be void ab initio. (b) Sampling methods. For purposes of paragraph (a) of this section, refiners and importers shall...

Structural, magnetic, and Mössbauer spectroscopy of Cu substituted M-type hexaferrites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Awadallah, Ahmad, E-mail: ahmadmoh@yahoo.co; Mahmood, Sami H., E-mail: s.mahmood@ju.edu.jo; Maswadeh, Yazan, E-mail: nawabra251@gmail.com

2016-02-15

Highlights: • Single BaM hexaferrite structural phases with Cu substations were prepared. • The magnetocrystalline anisotropy decreased with Cu substitution. • The coercivity was significantly modified while the magnetization remained high. • Hexaferrites with 0.2–0.4 Cu possess properties suitable for magnetic recording. • Ionic distributions from structural refinement agreed with Mössbauer spectroscopy. - Abstract: BaFe{sub 12−x}Cu{sub x}O{sub 19} hexaferrites were prepared using ball milling and sintering at 1100 °C. Refinement of the X-ray diffraction patterns was carried out to determine the structural parameters and the ionic distribution over the crystallographic sites. The preferential site occupation and valence state of Cumore » was consistent with the results obtained from the analysis of Mössbauer spectra. Further, the magnetic parameters of the samples were discussed in light of the structural and Mössbauer analyses. The magnetic phase transition temperature was found to decrease with the level of Cu substitution, in accordance with the reduction of the superexchange interactions. Further, the magnetic softening of the hexaferrite and the significant reduction in magnetocrystalline anisotropy with Cu substitution was consistent with the ionic distribution in the lattice. This study clearly demonstrated the feasibility of using a simple method to fabricate hexaferrites with a modified coercivity, while maintain the saturation magnetization high enough for practical applications.« less

On the Daubechies-based wavelet differentiation matrix

NASA Technical Reports Server (NTRS)

Jameson, Leland

1993-01-01

The differentiation matrix for a Daubechies-based wavelet basis is constructed and superconvergence is proven. That is, it will be proven that under the assumption of periodic boundary conditions that the differentiation matrix is accurate of order 2M, even though the approximation subspace can represent exactly only polynomials up to degree M-1, where M is the number of vanishing moments of the associated wavelet. It is illustrated that Daubechies-based wavelet methods are equivalent to finite difference methods with grid refinement in regions of the domain where small-scale structure is present.

Grain refinement control in TIG arc welding

NASA Technical Reports Server (NTRS)

Iceland, W. F.; Whiffen, E. L. (Inventor)

1975-01-01

A method for controlling grain size and weld puddle agitation in a tungsten electrode inert gas welding system to produce fine, even grain size and distribution is disclosed. In the method the frequency of dc welding voltage pulses supplied to the welding electrode is varied over a preselected frequency range and the arc gas voltage is monitored. At some frequency in the preselected range the arc gas voltage will pass through a maximum. By maintaining the operating frequency of the system at this value, maximum weld puddle agitation and fine grain structure are produced.

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

PubMed

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

Indigenous lunar construction materials

NASA Technical Reports Server (NTRS)

Rogers, Wayne P.; Sture, Stein

1991-01-01

The utilization of local resources for the construction and operation of a lunar base can significantly reduce the cost of transporting materials and supplies from Earth. The feasibility of processing lunar regolith to form construction materials and structural components is investigated. A preliminary review of potential processing methods such as sintering, hot-pressing, liquification, and cast basalt techniques, was completed. The processing method proposed is a variation on the cast basalt technique. It involves liquification of the regolith at 1200-1300 C, casting the liquid into a form, and controlled cooling. While the process temperature is higher than that for sintering or hot-pressing (1000-1100 C), this method is expected to yield a true engineering material with low variability in properties, high strength, and the potential to form large structural components. A scenario for this processing method was integrated with a design for a representative lunar base structure and potential construction techniques. The lunar shelter design is for a modular, segmented, pressurized, hemispherical dome which could serve as habitation and laboratory space. Based on this design, estimates of requirements for power, processing equipment, and construction equipment were made. This proposed combination of material processing method, structural design, and support requirements will help to establish the feasibility of lunar base construction using indigenous materials. Future work will refine the steps of the processing method. Specific areas where more information is needed are: furnace characteristics in vacuum; heat transfer during liquification; viscosity, pouring and forming behavior of molten regolith; design of high temperature forms; heat transfer during cooling; recrystallization of basalt; and refinement of estimates of elastic moduli, compressive and tensile strength, thermal expansion coefficient, thermal conductivity, and heat capacity. The preliminary design of the lunar shelter showed us that joining is a critical technology needed for building a structure from large segments. The problem of joining is important to the design of any structure that is not completely prefabricated. It is especially important when the structure is subjected to tensile loading by an internal pressure. For a lunar shelter constructed from large segments the joints between these large segments must be strong, and they must permit automated construction. With a cast basalt building material which is brittle, there is the additional problem of connecting the joint with the material and avoiding stress concentration that would cause failure. Thus, a well-defined project which we intend to pursue during this coming year is the design of joints for cast basalt structural elements.

Finite element mesh refinement criteria for stress analysis

NASA Technical Reports Server (NTRS)

Kittur, Madan G.; Huston, Ronald L.

1990-01-01

This paper discusses procedures for finite-element mesh selection and refinement. The objective is to improve accuracy. The procedures are based on (1) the minimization of the stiffness matrix race (optimizing node location); (2) the use of h-version refinement (rezoning, element size reduction, and increasing the number of elements); and (3) the use of p-version refinement (increasing the order of polynomial approximation of the elements). A step-by-step procedure of mesh selection, improvement, and refinement is presented. The criteria for 'goodness' of a mesh are based on strain energy, displacement, and stress values at selected critical points of a structure. An analysis of an aircraft lug problem is presented as an example.

Analysis and improvements of Adaptive Particle Refinement (APR) through CPU time, accuracy and robustness considerations

NASA Astrophysics Data System (ADS)

Chiron, L.; Oger, G.; de Leffe, M.; Le Touzé, D.

2018-02-01

While smoothed-particle hydrodynamics (SPH) simulations are usually performed using uniform particle distributions, local particle refinement techniques have been developed to concentrate fine spatial resolutions in identified areas of interest. Although the formalism of this method is relatively easy to implement, its robustness at coarse/fine interfaces can be problematic. Analysis performed in [16] shows that the radius of refined particles should be greater than half the radius of unrefined particles to ensure robustness. In this article, the basics of an Adaptive Particle Refinement (APR) technique, inspired by AMR in mesh-based methods, are presented. This approach ensures robustness with alleviated constraints. Simulations applying the new formalism proposed achieve accuracy comparable to fully refined spatial resolutions, together with robustness, low CPU times and maintained parallel efficiency.

Relative Packing Groups in Template-Based Structure Prediction: Cooperative Effects of True Positive Constraints

PubMed Central

Day, Ryan; Qu, Xiaotao; Swanson, Rosemarie; Bohannan, Zach; Bliss, Robert

2011-01-01

Abstract Most current template-based structure prediction methods concentrate on finding the correct backbone conformation and then packing sidechains within that backbone. Our packing-based method derives distance constraints from conserved relative packing groups (RPGs). In our refinement approach, the RPGs provide a level of resolution that restrains global topology while allowing conformational sampling. In this study, we test our template-based structure prediction method using 51 prediction units from CASP7 experiments. RPG-based constraints are able to substantially improve approximately two-thirds of starting templates. Upon deeper investigation, we find that true positive spatial constraints, especially those non-local in sequence, derived from the RPGs were important to building nearer native models. Surprisingly, the fraction of incorrect or false positive constraints does not strongly influence the quality of the final candidate. This result indicates that our RPG-based true positive constraints sample the self-consistent, cooperative interactions of the native structure. The lack of such reinforcing cooperativity explains the weaker effect of false positive constraints. Generally, these findings are encouraging indications that RPGs will improve template-based structure prediction. PMID:21210729

NMR crystallography of α-poly(L-lactide).

PubMed

Pawlak, Tomasz; Jaworska, Magdalena; Potrzebowski, Marek J

2013-03-07

A complementary approach that combines NMR measurements, analysis of X-ray and neutron powder diffraction data and advanced quantum mechanical calculations was employed to study the α-polymorph of L-polylactide. Such a strategy, which is known as NMR crystallography, to the best of our knowledge, is used here for the first time for the fine refinement of the crystal structure of a synthetic polymer. The GIPAW method was used to compute the NMR shielding parameters for the different models, which included the α-PLLA structure obtained by 2-dimensional wide-angle X-ray diffraction (WAXD) at -150 °C (model M1) and at 25 °C (model M2), neutron diffraction (WAND) measurements (model M3) and the fully optimized geometry of the PLLA chains in the unit cell with defined size (model M4). The influence of changes in the chain conformation on the (13)C σ(ii) NMR shielding parameters is shown. The correlation between the σ(ii) and δ(ii) values for the M1-M4 models revealed that the M4 model provided the best fit. Moreover, a comparison of the experimental (13)C NMR spectra with the spectra calculated using the M1-M4 models strongly supports the data for the M4 model. The GIPAW method, via verification using NMR measurements, was shown to be capable of the fine refinement of the crystal structures of polymers when coarse X-ray diffraction data for powdered samples are available.

A methodology for quadrilateral finite element mesh coarsening

DOE PAGES

Staten, Matthew L.; Benzley, Steven; Scott, Michael

2008-03-27

High fidelity finite element modeling of continuum mechanics problems often requires using all quadrilateral or all hexahedral meshes. The efficiency of such models is often dependent upon the ability to adapt a mesh to the physics of the phenomena. Adapting a mesh requires the ability to both refine and/or coarsen the mesh. The algorithms available to refine and coarsen triangular and tetrahedral meshes are very robust and efficient. However, the ability to locally and conformally refine or coarsen all quadrilateral and all hexahedral meshes presents many difficulties. Some research has been done on localized conformal refinement of quadrilateral and hexahedralmore » meshes. However, little work has been done on localized conformal coarsening of quadrilateral and hexahedral meshes. A general method which provides both localized conformal coarsening and refinement for quadrilateral meshes is presented in this paper. This method is based on restructuring the mesh with simplex manipulations to the dual of the mesh. Finally, this method appears to be extensible to hexahedral meshes in three dimensions.« less

Precipitation process in a Mg–Gd–Y alloy grain-refined by Al addition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dai, Jichun; CAST Cooperative Research Centre, Department of Materials Engineering, Monash University, Victoria 3800; Zhu, Suming, E-mail: suming.zhu@monash.edu

2014-02-15

The precipitation process in Mg–10Gd–3Y (wt.%) alloy grain-refined by 0.8 wt.% Al addition has been investigated by transmission electron microscopy. The alloy was given a solution treatment at 520 °C for 6 h plus 550 °C for 7 h before ageing at 250 °C. Plate-shaped intermetallic particles with the 18R-type long-period stacking ordered structure were observed in the solution-treated state. Upon isothermal ageing at 250 °C, the following precipitation sequence was identified for the α-Mg supersaturated solution: β″ (D0{sub 19}) → β′ (bco) → β{sub 1} (fcc) → β (fcc). The observed precipitation process and age hardening response in themore » Al grain-refined Mg–10Gd–3Y alloy are compared with those reported in the Zr grain-refined counterpart. - Highlights: • The precipitation process in Mg–10Gd–3Y–0.8Al (wt.%) alloy has been investigated. • Particles with the 18R-type LPSO structure were observed in the solution state. • Upon ageing at 250 °C, the precipitation sequence is: β″ → β′ → β1 (fcc) → β. • The Al grain-refined alloy has a lower hardness than the Zr refined counterpart.« less

PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structures.

PubMed

Andrejasic, Miha; Praaenikar, Jure; Turk, Dusan

2008-11-01

The number and variety of macromolecular structures in complex with ;hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh-Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/.

A Comparison of Spectral Element and Finite Difference Methods Using Statically Refined Nonconforming Grids for the MHD Island Coalescence Instability Problem

NASA Astrophysics Data System (ADS)

Ng, C. S.; Rosenberg, D.; Pouquet, A.; Germaschewski, K.; Bhattacharjee, A.

2009-04-01

A recently developed spectral-element adaptive refinement incompressible magnetohydrodynamic (MHD) code [Rosenberg, Fournier, Fischer, Pouquet, J. Comp. Phys. 215, 59-80 (2006)] is applied to simulate the problem of MHD island coalescence instability (\\ci) in two dimensions. \\ci is a fundamental MHD process that can produce sharp current layers and subsequent reconnection and heating in a high-Lundquist number plasma such as the solar corona [Ng and Bhattacharjee, Phys. Plasmas, 5, 4028 (1998)]. Due to the formation of thin current layers, it is highly desirable to use adaptively or statically refined grids to resolve them, and to maintain accuracy at the same time. The output of the spectral-element static adaptive refinement simulations are compared with simulations using a finite difference method on the same refinement grids, and both methods are compared to pseudo-spectral simulations with uniform grids as baselines. It is shown that with the statically refined grids roughly scaling linearly with effective resolution, spectral element runs can maintain accuracy significantly higher than that of the finite difference runs, in some cases achieving close to full spectral accuracy.

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

Refined structure of dimeric diphtheria toxin at 2.0 A resolution.

PubMed Central

Bennett, M. J.; Choe, S.; Eisenberg, D.

1994-01-01

The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution, based on 37,727 unique reflections (F > 1 sigma (F)), yields a final R factor of 19.5% with a model obeying standard geometry. The refined model consists of 523 amino acid residues, 1 molecule of the bound dinucleotide inhibitor adenylyl 3'-5' uridine 3' monophosphate (ApUp), and 405 well-ordered water molecules. The 2.0-A refined model reveals that the binding motif for ApUp includes residues in the catalytic and receptor-binding domains and is different from the Rossmann dinucleotide-binding fold. ApUp is bound in part by a long loop (residues 34-52) that crosses the active site. Several residues in the active site were previously identified as NAD-binding residues. Glu 148, previously identified as playing a catalytic role in ADP-ribosylation of elongation factor 2 by DT, is about 5 A from uracil in ApUp. The trigger for insertion of the transmembrane domain of DT into the endosomal membrane at low pH may involve 3 intradomain and 4 interdomain salt bridges that will be weakened at low pH by protonation of their acidic residues. The refined model also reveals that each molecule in dimeric DT has an "open" structure unlike most globular proteins, which we call an open monomer. Two open monomers interact by "domain swapping" to form a compact, globular dimeric DT structure. The possibility that the open monomer resembles a membrane insertion intermediate is discussed. PMID:7833807

An accurate global potential energy surface, dipole moment surface, and rovibrational frequencies for NH3

NASA Astrophysics Data System (ADS)

Huang, Xinchuan; Schwenke, David W.; Lee, Timothy J.

2008-12-01

A global potential energy surface (PES) that includes short and long range terms has been determined for the NH3 molecule. The singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations and the internally contracted averaged coupled-pair functional electronic structure methods have been used in conjunction with very large correlation-consistent basis sets, including diffuse functions. Extrapolation to the one-particle basis set limit was performed and core correlation and scalar relativistic contributions were included directly, while the diagonal Born-Oppenheimer correction was added. Our best purely ab initio PES, denoted "mixed," is constructed from two PESs which differ in whether the ic-ACPF higher-order correlation correction was added or not. Rovibrational transition energies computed from the mixed PES agree well with experiment and the best previous theoretical studies, but most importantly the quality does not deteriorate even up to 10300cm-1 above the zero-point energy (ZPE). The mixed PES was improved further by empirical refinement using the most reliable J =0-2 rovibrational transitions in the HITRAN 2004 database. Agreement between high-resolution experiment and rovibrational transition energies computed from our refined PES for J =0-6 is excellent. Indeed, the root mean square (rms) error for 13 HITRAN 2004 bands for J =0-2 is 0.023cm-1 and that for each band is always ⩽0.06cm-1. For J =3-5 the rms error is always ⩽0.15cm-1. This agreement means that transition energies computed with our refined PES should be useful in the assignment of new high-resolution NH3 spectra and in correcting mistakes in previous assignments. Ideas for further improvements to our refined PES and for extension to other isotopolog are discussed.

Hydrogen positions in single nanocrystals revealed by electron diffraction

NASA Astrophysics Data System (ADS)

Palatinus, L.; Brázda, P.; Boullay, P.; Perez, O.; Klementová, M.; Petit, S.; Eigner, V.; Zaarour, M.; Mintova, S.

2017-01-01

The localization of hydrogen atoms is an essential part of crystal structure analysis, but it is difficult because of their small scattering power. We report the direct localization of hydrogen atoms in nanocrystalline materials, achieved using the recently developed approach of dynamical refinement of precession electron diffraction tomography data. We used this method to locate hydrogen atoms in both an organic (paracetamol) and an inorganic (framework cobalt aluminophosphate) material. The results demonstrate that the technique can reliably reveal fine structural details, including the positions of hydrogen atoms in single crystals with micro- to nanosized dimensions.

FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web.

PubMed

Shapiro, Jessica; Brutlag, Douglas

2004-07-01

The FoldMiner web server (http://foldminer.stanford.edu/) provides remote access to methods for protein structure alignment and unsupervised motif discovery. FoldMiner is unique among such algorithms in that it improves both the motif definition and the sensitivity of a structural similarity search by combining the search and motif discovery methods and using information from each process to enhance the other. In a typical run, a query structure is aligned to all structures in one of several databases of single domain targets in order to identify its structural neighbors and to discover a motif that is the basis for the similarity among the query and statistically significant targets. This process is fully automated, but options for manual refinement of the results are available as well. The server uses the Chime plugin and customized controls to allow for visualization of the motif and of structural superpositions. In addition, we provide an interface to the LOCK 2 algorithm for rapid alignments of a query structure to smaller numbers of user-specified targets.

Validating neural-network refinements of nuclear mass models

NASA Astrophysics Data System (ADS)

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.

Supervised Machine-Learning-Based Determination of Three-Dimensional Structure of Metallic Nanoparticles

DOE PAGES

Timoshenko, Janis; Lu, Deyu; Lin, Yuewei; ...

2017-09-29

Tracking the structure of heterogeneous catalysts under operando conditions remains a challenge due to the paucity of experimental techniques that can provide atomic-level information for catalytic metal species. Here we report on the use of X-ray absorption near edge structure (XANES) spectroscopy and supervised machine learning (SML) for refining the three-dimensional geometry of metal catalysts. SML is used to unravel the hidden relationship between the XANES features and catalyst geometry. To train our SML method, we rely on ab-initio XANES simulations. Our approach allows one to solve the structure of a metal catalyst from its experimental XANES, as demonstrated heremore » by reconstructing the average size, shape and morphology of well-defined platinum nanoparticles. This method is applicable to the determination of the nanoparticle structure in operando studies and can be generalized to other nanoscale systems. In conclusion, it also allows on-the-fly XANES analysis, and is a promising approach for high-throughput and time-dependent studies.« less

Supervised Machine-Learning-Based Determination of Three-Dimensional Structure of Metallic Nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Timoshenko, Janis; Lu, Deyu; Lin, Yuewei

Tracking the structure of heterogeneous catalysts under operando conditions remains a challenge due to the paucity of experimental techniques that can provide atomic-level information for catalytic metal species. Here we report on the use of X-ray absorption near edge structure (XANES) spectroscopy and supervised machine learning (SML) for refining the three-dimensional geometry of metal catalysts. SML is used to unravel the hidden relationship between the XANES features and catalyst geometry. To train our SML method, we rely on ab-initio XANES simulations. Our approach allows one to solve the structure of a metal catalyst from its experimental XANES, as demonstrated heremore » by reconstructing the average size, shape and morphology of well-defined platinum nanoparticles. This method is applicable to the determination of the nanoparticle structure in operando studies and can be generalized to other nanoscale systems. In conclusion, it also allows on-the-fly XANES analysis, and is a promising approach for high-throughput and time-dependent studies.« less

Thermodynamics of Boron Removal from Silicon Using CaO-MgO-Al2O3-SiO2 Slags

NASA Astrophysics Data System (ADS)

Jakobsson, Lars Klemet; Tangstad, Merete

2018-04-01

Slag refining is one of few metallurgical methods for removal of boron from silicon. It is important to know the thermodynamic properties of boron in slags to understand the refining process. The relation of the distribution coefficient of boron to the activity of silica, partial pressure of oxygen, and capacity of slags for boron oxide was investigated. The link between these parameters explains why the distribution coefficient of boron does not change much with changing slag composition. In addition, the thermodynamic properties of dilute boron oxide in CaO-MgO-Al2O3-SiO2 slags was determined. The ratio of the activity coefficient of boron oxide and silica was found to be the most important parameter for understanding changes in the distribution coefficient of boron for different slags. Finally, the relation between the activity coefficient of boron oxide and slag structure was investigated. It was found that the structure can explain how the distribution coefficient of boron changes depending on slag composition.

Effect of Hypoeutectic Boron Additions on the Grain Size and Mechanical Properties of Ti-6Al-4V Manufactured with Powder Bed Electron Beam Additive Manufacturing

NASA Astrophysics Data System (ADS)

Mahbooba, Zaynab; West, Harvey; Harrysson, Ola; Wojcieszynski, Andrzej; Dehoff, Ryan; Nandwana, Peeyush; Horn, Timothy

2017-03-01

In additive manufacturing, microstructural control is feasible via processing parameter alteration. However, the window for parameter variation for certain materials, such as Ti-6Al-4V, is limited, and alternative methods must be employed to customize microstructures. Grain refinement and homogenization in cast titanium alloys has been demonstrated through the addition of hypoeutectic concentrations of boron. This work explores the influence of 0.00 wt.%, 0.25 wt.%, 0.50 wt.%, and 1.0 wt.% boron additions on the microstructure and bulk mechanical properties of Ti-6Al-4V samples fabricated in an Arcam A2 electron beam melting (EBM) system with commercial processing parameters for Ti-6Al-4V. Analyses of EBM fabricated Ti-6Al-4V + B indicate that the addition of 0.25-1.0 wt.% boron progressively refines the grain structure, and it improves hardness and elastic modulus. Despite a reduction in size, the β grain structure remained columnar as a result of directional heat transfer during EBM fabrication.

HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions

PubMed Central

Wang, Xiao-Tao; Cui, Wang

2017-01-01

Abstract A current question in the high-order organization of chromatin is whether topologically associating domains (TADs) are distinct from other hierarchical chromatin domains. However, due to the unclear TAD definition in tradition, the structural and functional uniqueness of TAD is not well studied. In this work, we refined TAD definition by further constraining TADs to the optimal separation on global intra-chromosomal interactions. Inspired by this constraint, we developed a novel method, called HiTAD, to detect hierarchical TADs from Hi-C chromatin interactions. HiTAD performs well in domain sensitivity, replicate reproducibility and inter cell-type conservation. With a novel domain-based alignment proposed by us, we defined several types of hierarchical TAD changes which were not systematically studied previously, and subsequently used them to reveal that TADs and sub-TADs differed statistically in correlating chromosomal compartment, replication timing and gene transcription. Finally, our work also has the implication that the refinement of TAD definition could be achieved by only utilizing chromatin interactions, at least in part. HiTAD is freely available online. PMID:28977529

Adaptive Mesh Refinement in Curvilinear Body-Fitted Grid Systems

NASA Technical Reports Server (NTRS)

Steinthorsson, Erlendur; Modiano, David; Colella, Phillip

1995-01-01

To be truly compatible with structured grids, an AMR algorithm should employ a block structure for the refined grids to allow flow solvers to take advantage of the strengths of unstructured grid systems, such as efficient solution algorithms for implicit discretizations and multigrid schemes. One such algorithm, the AMR algorithm of Berger and Colella, has been applied to and adapted for use with body-fitted structured grid systems. Results are presented for a transonic flow over a NACA0012 airfoil (AGARD-03 test case) and a reflection of a shock over a double wedge.

Crystal chemistry and structure refinement of five hydrated calcium borates

USGS Publications Warehouse

Clark, J.R.; Appleman, D.E.; Christ, C.L.

1964-01-01

The crystal structures of the five known members of the series Ca2B6O11??xH2O (x = 1, 5, 5, 7, 9, and 13) have been refined by full-matrix least-squares techniques, yielding bond distances and angles with standard errors of less than 0??01 A?? and 0??5??, respectively. The results illustrate the crystal chemical principles that govern the structures of hydrated borate compounds. The importance of hydrogen bonding in the ferroelectric transition of colemanite is confirmed by more accurate proton assignments. ?? 1964.

The finite cell method for polygonal meshes: poly-FCM

NASA Astrophysics Data System (ADS)

Duczek, Sascha; Gabbert, Ulrich

2016-10-01

In the current article, we extend the two-dimensional version of the finite cell method (FCM), which has so far only been used for structured quadrilateral meshes, to unstructured polygonal discretizations. Therefore, the adaptive quadtree-based numerical integration technique is reformulated and the notion of generalized barycentric coordinates is introduced. We show that the resulting polygonal (poly-)FCM approach retains the optimal rates of convergence if and only if the geometry of the structure is adequately resolved. The main advantage of the proposed method is that it inherits the ability of polygonal finite elements for local mesh refinement and for the construction of transition elements (e.g. conforming quadtree meshes without hanging nodes). These properties along with the performance of the poly-FCM are illustrated by means of several benchmark problems for both static and dynamic cases.

Structural studies of TiC{sub 1−x}O{sub x} solid solution by Rietveld refinement and first-principles calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Bo, E-mail: youqin5912@yahoo.com.cn; Hou, Na; Huang, Shanyan

2013-08-15

The lattice parameters, structural stability and electronic structure of titanium oxycarbides (TiC{sub 1−x}O{sub x}, 0≤x≤1) solid solution were investigated by Rietveld refinement and first-principles calculations. Series of TiC{sub 1−x}O{sub 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{sub 1−x}O{sub 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{submore » 1−Va}(C{sub 1−x}O{sub x}){sub 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{sub 1−x}O{sub 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{sub 1−x}O{sub 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.« less

Rapid reconstruction of 3D neuronal morphology from light microscopy images with augmented rayburst sampling.

PubMed

Ming, Xing; Li, Anan; Wu, Jingpeng; Yan, Cheng; Ding, Wenxiang; Gong, Hui; Zeng, Shaoqun; Liu, Qian

2013-01-01

Digital reconstruction of three-dimensional (3D) neuronal morphology from light microscopy images provides a powerful technique for analysis of neural circuits. It is time-consuming to manually perform this process. Thus, efficient computer-assisted approaches are preferable. In this paper, we present an innovative method for the tracing and reconstruction of 3D neuronal morphology from light microscopy images. The method uses a prediction and refinement strategy that is based on exploration of local neuron structural features. We extended the rayburst sampling algorithm to a marching fashion, which starts from a single or a few seed points and marches recursively forward along neurite branches to trace and reconstruct the whole tree-like structure. A local radius-related but size-independent hemispherical sampling was used to predict the neurite centerline and detect branches. Iterative rayburst sampling was performed in the orthogonal plane, to refine the centerline location and to estimate the local radius. We implemented the method in a cooperative 3D interactive visualization-assisted system named flNeuronTool. The source code in C++ and the binaries are freely available at http://sourceforge.net/projects/flneurontool/. We validated and evaluated the proposed method using synthetic data and real datasets from the Digital Reconstruction of Axonal and Dendritic Morphology (DIADEM) challenge. Then, flNeuronTool was applied to mouse brain images acquired with the Micro-Optical Sectioning Tomography (MOST) system, to reconstruct single neurons and local neural circuits. The results showed that the system achieves a reasonable balance between fast speed and acceptable accuracy, which is promising for interactive applications in neuronal image analysis.

Structure of the ThDP-dependent enzyme benzaldehyde lyase refined to 1.65 Å resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maraite, Andy; Schmidt, Thomas; Ansörge-Schumacher, Marion B.

2007-07-01

The X-ray crystal structure of the ThDP-dependent enzyme benzaldehyde lyase has been refined to 1.65 Å. Benzaldehyde lyase (BAL; EC 4.1.2.38) is a thiamine diphosphate (ThDP) dependent enzyme that catalyses the enantioselective carboligation of two molecules of benzaldehyde to form (R)-benzoin. BAL has hence aroused interest for its potential in the industrial synthesis of optically active benzoins and derivatives. The structure of BAL was previously solved to a resolution of 2.6 Å using MAD experiments on a selenomethionine derivative [Mosbacher et al. (2005 ▶), FEBS J.272, 6067–6076]. In this communication of parallel studies, BAL was crystallized in an alternative spacemore » group (P2{sub 1}2{sub 1}2{sub 1}) and its structure refined to a resolution of 1.65 Å, allowing detailed observation of the water structure, active-site interactions with ThDP and also the electron density for the co-solvent 2-methyl-2,4-pentanediol (MPD) at hydrophobic patches of the enzyme surface.« less

The value of continuity: Refined isogeometric analysis and fast direct solvers

DOE PAGES

Garcia, Daniel; Pardo, David; Dalcin, Lisandro; ...

2016-08-24

Here, we propose the use of highly continuous finite element spaces interconnected with low continuity hyperplanes to maximize the performance of direct solvers. Starting from a highly continuous Isogeometric Analysis (IGA) discretization, we introduce C0-separators to reduce the interconnection between degrees of freedom in the mesh. By doing so, both the solution time and best approximation errors are simultaneously improved. We call the resulting method “refined Isogeometric Analysis (rIGA)”. To illustrate the impact of the continuity reduction, we analyze the number of Floating Point Operations (FLOPs), computational times, and memory required to solve the linear system obtained by discretizing themore » Laplace problem with structured meshes and uniform polynomial orders. Theoretical estimates demonstrate that an optimal continuity reduction may decrease the total computational time by a factor between p 2 and p 3, with pp being the polynomial order of the discretization. Numerical results indicate that our proposed refined isogeometric analysis delivers a speed-up factor proportional to p 2. In a 2D mesh with four million elements and p=5, the linear system resulting from rIGA is solved 22 times faster than the one from highly continuous IGA. In a 3D mesh with one million elements and p=3, the linear system is solved 15 times faster for the refined than the maximum continuity isogeometric analysis.« less

Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data

PubMed Central

Lexa, Katrina W.; Carlson, Heather A.

2013-01-01

Computational approaches to fragment-based drug design (FBDD) can complement experiments and facilitate the identification of potential hot spots along the protein surface. However, the evaluation of computational methods for mapping binding sites frequently focuses upon the ability to reproduce crystallographic coordinates to within a low RMSD threshold. This dependency on the deposited coordinate data overlooks the original electron density from the experiment, thus techniques may be developed based upon subjective - or even erroneous - atomic coordinates. This can become a significant drawback in applications to systems where the location of hot spots is unknown. Based on comparison to crystallographic density, we previously showed that mixed-solvent molecular dynamics (MixMD) accurately identifies the active site for HEWL, with acetonitrile as an organic solvent. Here, we concentrated on the influence of protic solvent on simulation and refined the optimal MixMD approach for extrapolation of the method to systems without established sites. Our results establish an accurate approach for comparing simulations to experiment. We have outlined the most efficient strategy for MixMD, based on simulation length and number of runs. The development outlined here makes MixMD a robust method which should prove useful across a broad range of target structures. Lastly, our results with MixMD match experimental data so well that consistency between simulations and density may be a useful way to aid the identification of probes vs waters during the refinement of future MSCS crystallographic structures. PMID:23327200

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

PubMed

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.

Characterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase.

PubMed

Osipiuk, Jerzy; Mulligan, Rory; Bargassa, Monireh; Hamilton, John E; Cunningham, Mark A; Joachimiak, Andrzej

2012-06-01

The crystal structure of SO1698 protein from Shewanella oneidensis was determined by a SAD method and refined to 1.57 Å. The structure is a β sandwich that unexpectedly consists of two polypeptides; the N-terminal fragment includes residues 1-116, and the C-terminal one includes residues 117-125. Electron density also displayed the Lys-98 side chain covalently linked to Asp-116. The putative active site residues involved in self-cleavage were identified; point mutants were produced and characterized structurally and in a biochemical assay. Numerical simulations utilizing molecular dynamics and hybrid quantum/classical calculations suggest a mechanism involving activation of a water molecule coordinated by a catalytic aspartic acid.

Structured programming: Principles, notation, procedure

NASA Technical Reports Server (NTRS)

JOST

1978-01-01

Structured programs are best represented using a notation which gives a clear representation of the block encapsulation. In this report, a set of symbols which can be used until binding directives are republished is suggested. Structured programming also allows a new method of procedure for design and testing. Programs can be designed top down, that is, they can start at the highest program plane and can penetrate to the lowest plane by step-wise refinements. The testing methodology also is adapted to this procedure. First, the highest program plane is tested, and the programs which are not yet finished in the next lower plane are represented by so-called dummies. They are gradually replaced by the real programs.

Process for producing advanced ceramics

DOEpatents

Kwong, Kyei-Sing

1996-01-01

A process for the synthesis of homogeneous advanced ceramics such as SiC+AlN, SiAlON, SiC+Al.sub.2 O.sub.3, and Si.sub.3 N.sub.4 +AlN from natural clays such as kaolin, halloysite and montmorillonite by an intercalation and heat treatment method. Included are the steps of refining clays, intercalating organic compounds into the layered structure of clays, drying the intercalated mixture, firing the treated atmospheres and grinding the loosely agglomerated structure. Advanced ceramics produced by this procedure have the advantages of homogeneity, cost effectiveness, simplicity of manufacture, ease of grind and a short process time. Advanced ceramics produced by this process can be used for refractory, wear part and structure ceramics.

Use of Molecular Dynamics for the Refinement of an Electrostatic Model for the In Silico Design of a Polymer Antidote for the Anticoagulant Fondaparinux

PubMed Central

Kwok, Ezra; Gopaluni, Bhushan; Kizhakkedathu, Jayachandran N.

2013-01-01

Molecular dynamics (MD) simulations results are herein incorporated into an electrostatic model used to determine the structure of an effective polymer-based antidote to the anticoagulant fondaparinux. In silico data for the polymer or its cationic binding groups has not, up to now, been available, and experimental data on the structure of the polymer-fondaparinux complex is extremely limited. Consequently, the task of optimizing the polymer structure is a daunting challenge. MD simulations provided a means to gain microscopic information on the interactions of the binding groups and fondaparinux that would have otherwise been inaccessible. This was used to refine the electrostatic model and improve the quantitative model predictions of binding affinity. Once refined, the model provided guidelines to improve electrostatic forces between candidate polymers and fondaparinux in order to increase association rate constants. PMID:27006916

Structure refinement for tantalum nitrides nanocrystals with various morphologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Lianyun; School of Science, Beijing Jiaotong University, 3 Shang Yuan Cun, Haidian District, Beijing 100044; Huang, Kai

2012-07-15

Graphical abstract: Tantalum nitrides nanocrystals with various phases and morphologies for the first time have been synthesized through homogenous sodium reduction under low temperature with the subsequent annealing process under high vacuum. Highlights: ► The spherical TaN, cuboidal TaN{sub 0.83} and TaN{sub 0.5} nanocrystals have been synthesized through homogenous sodium reduction under low temperature with the subsequent annealing process under high vacuum. ► The crystal structures of different tantalum nitrides were determined by Rietveld refinement on the X-ray diffraction data and the examinations of electron microcopies. ► The specific surface area of the tantalum nitrides powders was around 10 m{supmore » 2} g{sup −1}. ► Tantalum nitrides powders could be suitable for capacitor with high specific capacitance. -- Abstract: Tantalum nitrides (TaN{sub x}) nanocrystals with different phase and morphology have been synthesized through homogenous sodium reduction under low temperature with the subsequent annealing process under high vacuum. The crystal structures of tantalum nitrides were determined by Rietveld refinement based on the X-ray diffraction data. The morphologies of various tantalum nitrides nanocrystals in high quality were analyzed through the electron microcopies examinations. The spherical TaN nanoparticles, cuboidal TaN{sub 0.83} and TaN{sub 0.5} nanocrystals have been selectively prepared at different annealing temperatures. In addition, the specific surface areas of the tantalum nitrides nanocrystals measured by BET method were around 9.87–11.64 m{sup 2} g{sup −1}, indicating that such nano-sized tantalum nitrides could be suitable for capacitor with high specific capacitance.« less

Rapid and reliable protein structure determination via chemical shift threading.

PubMed

Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

2018-01-01

Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

Physics-based method to validate and repair flaws in protein structures

PubMed Central

Martin, Osvaldo A.; Arnautova, Yelena A.; Icazatti, Alejandro A.; Scheraga, Harold A.; Vila, Jorge A.

2013-01-01

A method that makes use of information provided by the combination of 13Cα and 13Cβ chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed 13Cα and 13Cβ chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 Ǻ, in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models. PMID:24082119

Physics-based method to validate and repair flaws in protein structures.

PubMed

Martin, Osvaldo A; Arnautova, Yelena A; Icazatti, Alejandro A; Scheraga, Harold A; Vila, Jorge A

2013-10-15

A method that makes use of information provided by the combination of (13)C(α) and (13)C(β) chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed (13)C(α) and (13)C(β) chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed (13)C(α) and (13)C(β) chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 , in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models.

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

PubMed

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.

RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation.

PubMed

Sheffler, Will; Baker, David

2009-01-01

We present a novel method called RosettaHoles for visual and quantitative assessment of underpacking in the protein core. RosettaHoles generates a set of spherical cavity balls that fill the empty volume between atoms in the protein interior. For visualization, the cavity balls are aggregated into contiguous overlapping clusters and small cavities are discarded, leaving an uncluttered representation of the unfilled regions of space in a structure. For quantitative analysis, the cavity ball data are used to estimate the probability of observing a given cavity in a high-resolution crystal structure. RosettaHoles provides excellent discrimination between real and computationally generated structures, is predictive of incorrect regions in models, identifies problematic structures in the Protein Data Bank, and promises to be a useful validation tool for newly solved experimental structures.

RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation

PubMed Central

Sheffler, Will; Baker, David

2009-01-01

We present a novel method called RosettaHoles for visual and quantitative assessment of underpacking in the protein core. RosettaHoles generates a set of spherical cavity balls that fill the empty volume between atoms in the protein interior. For visualization, the cavity balls are aggregated into contiguous overlapping clusters and small cavities are discarded, leaving an uncluttered representation of the unfilled regions of space in a structure. For quantitative analysis, the cavity ball data are used to estimate the probability of observing a given cavity in a high-resolution crystal structure. RosettaHoles provides excellent discrimination between real and computationally generated structures, is predictive of incorrect regions in models, identifies problematic structures in the Protein Data Bank, and promises to be a useful validation tool for newly solved experimental structures. PMID:19177366

A short note on the use of the red-black tree in Cartesian adaptive mesh refinement algorithms

NASA Astrophysics Data System (ADS)

Hasbestan, Jaber J.; Senocak, Inanc

2017-12-01

Mesh adaptivity is an indispensable capability to tackle multiphysics problems with large disparity in time and length scales. With the availability of powerful supercomputers, there is a pressing need to extend time-proven computational techniques to extreme-scale problems. Cartesian adaptive mesh refinement (AMR) is one such method that enables simulation of multiscale, multiphysics problems. AMR is based on construction of octrees. Originally, an explicit tree data structure was used to generate and manipulate an adaptive Cartesian mesh. At least eight pointers are required in an explicit approach to construct an octree. Parent-child relationships are then used to traverse the tree. An explicit octree, however, is expensive in terms of memory usage and the time it takes to traverse the tree to access a specific node. For these reasons, implicit pointerless methods have been pioneered within the computer graphics community, motivated by applications requiring interactivity and realistic three dimensional visualization. Lewiner et al. [1] provides a concise review of pointerless approaches to generate an octree. Use of a hash table and Z-order curve are two key concepts in pointerless methods that we briefly discuss next.

FDD Massive MIMO Channel Estimation With Arbitrary 2D-Array Geometry

NASA Astrophysics Data System (ADS)

Dai, Jisheng; Liu, An; Lau, Vincent K. N.

2018-05-01

This paper addresses the problem of downlink channel estimation in frequency-division duplexing (FDD) massive multiple-input multiple-output (MIMO) systems. The existing methods usually exploit hidden sparsity under a discrete Fourier transform (DFT) basis to estimate the cdownlink channel. However, there are at least two shortcomings of these DFT-based methods: 1) they are applicable to uniform linear arrays (ULAs) only, since the DFT basis requires a special structure of ULAs, and 2) they always suffer from a performance loss due to the leakage of energy over some DFT bins. To deal with the above shortcomings, we introduce an off-grid model for downlink channel sparse representation with arbitrary 2D-array antenna geometry, and propose an efficient sparse Bayesian learning (SBL) approach for the sparse channel recovery and off-grid refinement. The main idea of the proposed off-grid method is to consider the sampled grid points as adjustable parameters. Utilizing an in-exact block majorization-minimization (MM) algorithm, the grid points are refined iteratively to minimize the off-grid gap. Finally, we further extend the solution to uplink-aided channel estimation by exploiting the angular reciprocity between downlink and uplink channels, which brings enhanced recovery performance.

Quadtree of TIN: a new algorithm of dynamic LOD

NASA Astrophysics Data System (ADS)

Zhang, Junfeng; Fei, Lifan; Chen, Zhen

2009-10-01

Currently, Real-time visualization of large-scale digital elevation model mainly employs the regular structure of GRID based on quadtree and triangle simplification methods based on irregular triangulated network (TIN). TIN is a refined means to express the terrain surface in the computer science, compared with GRID. However, the data structure of TIN model is complex, and is difficult to realize view-dependence representation of level of detail (LOD) quickly. GRID is a simple method to realize the LOD of terrain, but contains more triangle count. A new algorithm, which takes full advantage of the two methods' merit, is presented in this paper. This algorithm combines TIN with quadtree structure to realize the view-dependence LOD controlling over the irregular sampling point sets, and holds the details through the distance of viewpoint and the geometric error of terrain. Experiments indicate that this approach can generate an efficient quadtree triangulation hierarchy over any irregular sampling point sets and achieve dynamic and visual multi-resolution performance of large-scale terrain at real-time.

TLS from fundamentals to practice

PubMed Central

Urzhumtsev, Alexandre; Afonine, Pavel V.; Adams, Paul D.

2014-01-01

The Translation-Libration-Screw-rotation (TLS) model of rigid-body harmonic displacements introduced in crystallography by Schomaker & Trueblood (1968) is now a routine tool in macromolecular studies and is a feature of most modern crystallographic structure refinement packages. In this review we consider a number of simple examples that illustrate important features of the TLS model. Based on these examples simplified formulae are given for several special cases that may occur in structure modeling and refinement. The derivation of general TLS formulae from basic principles is also provided. This manuscript describes the principles of TLS modeling, as well as some select algorithmic details for practical application. An extensive list of applications references as examples of TLS in macromolecular crystallography refinement is provided. PMID:25249713

Robust membrane detection based on tensor voting for electron tomography.

PubMed

Martinez-Sanchez, Antonio; Garcia, Inmaculada; Asano, Shoh; Lucic, Vladan; Fernandez, Jose-Jesus

2014-04-01

Electron tomography enables three-dimensional (3D) visualization and analysis of the subcellular architecture at a resolution of a few nanometers. Segmentation of structural components present in 3D images (tomograms) is often necessary for their interpretation. However, it is severely hampered by a number of factors that are inherent to electron tomography (e.g. noise, low contrast, distortion). Thus, there is a need for new and improved computational methods to facilitate this challenging task. In this work, we present a new method for membrane segmentation that is based on anisotropic propagation of the local structural information using the tensor voting algorithm. The local structure at each voxel is then refined according to the information received from other voxels. Because voxels belonging to the same membrane have coherent structural information, the underlying global structure is strengthened. In this way, local information is easily integrated at a global scale to yield segmented structures. This method performs well under low signal-to-noise ratio typically found in tomograms of vitrified samples under cryo-tomography conditions and can bridge gaps present on membranes. The performance of the method is demonstrated by applications to tomograms of different biological samples and by quantitative comparison with standard template matching procedure. Copyright © 2014 Elsevier Inc. All rights reserved.

High-resolution Measurement of Contact Ion-pair Structures in Aqueous RbCl Solutions from the Simultaneous Corefinement of their Rb and Cl K-edge XAFS and XRD Spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, Van-Thai; Fulton, John L.

2016-06-21

In concentrated solutions of aqueous RbCl, all of the Rb+ and Cl- ions exist as contact ion pairs. This full structural assessment is derived from the refinement of three independent experimental measurements: the Rb and Cl K-edge x-ray absorption fine structure (XAFS) and the x-ray diffraction spectra (XRD). This simultaneous refinement of the XAFS and XRD data provides high accuracy since each method probes the structure of different local regions about the ions with high sensitivity. At high RbCl concentration (6 m (mol/kg )) the solution is dominated by Rb+ - Cl- contact ion pairs yielding an average of 1.5more » pairs at an Rb-Cl distance of 3.24 Å. Upon formation of these ion pairs, approximately 1.1 waters molecules are displaced from the Rb+ and 1.4 water molecules from Cl-. The hydration shells about both the cation and anion are also determined. These results greatly improve the understanding of monovalent ions and provide a basis for testing the Rb+-Cl- interaction potentials used in molecular dynamics (MD) simulation. This research was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.« less

Computer simulation of refining process of a high consistency disc refiner based on CFD

NASA Astrophysics Data System (ADS)

Wang, Ping; Yang, Jianwei; Wang, Jiahui

2017-08-01

In order to reduce refining energy consumption, the ANSYS CFX was used to simulate the refining process of a high consistency disc refiner. In the first it was assumed to be uniform Newton fluid of turbulent state in disc refiner with the k-ɛ flow model; then meshed grids and set the boundary conditions in 3-D model of the disc refiner; and then was simulated and analyzed; finally, the viscosity of the pulp were measured. The results show that the CFD method can be used to analyze the pressure and torque on the disc plate, so as to calculate the refining power, and streamlines and velocity vectors can also be observed. CFD simulation can optimize parameters of the bar and groove, which is of great significance to reduce the experimental cost and cycle.

Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods.

PubMed

McGuffin, Liam J; Shuid, Ahmad N; Kempster, Robert; Maghrabi, Ali H A; Nealon, John O; Salehe, Bajuna R; Atkins, Jennifer D; Roche, Daniel B

2018-03-01

Our aim in CASP12 was to improve our Template-Based Modeling (TBM) methods through better model selection, accuracy self-estimate (ASE) scores and refinement. To meet this aim, we developed two new automated methods, which we used to score, rank, and improve upon the provided server models. Firstly, the ModFOLD6_rank method, for improved global Quality Assessment (QA), model ranking and the detection of local errors. Secondly, the ReFOLD method for fixing errors through iterative QA guided refinement. For our automated predictions we developed the IntFOLD4-TS protocol, which integrates the ModFOLD6_rank method for scoring the multiple-template models that were generated using a number of alternative sequence-structure alignments. Overall, our selection of top models and ASE scores using ModFOLD6_rank was an improvement on our previous approaches. In addition, it was worthwhile attempting to repair the detected errors in the top selected models using ReFOLD, which gave us an overall gain in performance. According to the assessors' formula, the IntFOLD4 server ranked 3rd/5th (average Z-score > 0.0/-2.0) on the server only targets, and our manual predictions (McGuffin group) ranked 1st/2nd (average Z-score > -2.0/0.0) compared to all other groups. © 2017 Wiley Periodicals, Inc.

Improvements in mode-based waveform modeling and application to Eurasian velocity structure

NASA Astrophysics Data System (ADS)

Panning, M. P.; Marone, F.; Kim, A.; Capdeville, Y.; Cupillard, P.; Gung, Y.; Romanowicz, B.

2006-12-01

We introduce several recent improvements to mode-based 3D and asymptotic waveform modeling and examine how to integrate them with numerical approaches for an improved model of upper-mantle structure under eastern Eurasia. The first step in our approach is to create a large-scale starting model including shear anisotropy using Nonlinear Asymptotic Coupling Theory (NACT; Li and Romanowicz, 1995), which models the 2D sensitivity of the waveform to the great-circle path between source and receiver. We have recently improved this approach by implementing new crustal corrections which include a non-linear correction for the difference between the average structure of several large regions from the global model with further linear corrections to account for the local structure along the path between source and receiver (Marone and Romanowicz, 2006; Panning and Romanowicz, 2006). This model is further refined using a 3D implementation of Born scattering (Capdeville, 2005). We have made several recent improvements to this method, in particular introducing the ability to represent perturbations to discontinuities. While the approach treats all sensitivity as linear perturbations to the waveform, we have also experimented with a non-linear modification analogous to that used in the development of NACT. This allows us to treat large accumulated phase delays determined from a path-average approximation non-linearly, while still using the full 3D sensitivity of the Born approximation. Further refinement of shallow regions of the model is obtained using broadband forward finite-difference waveform modeling. We are also integrating a regional Spectral Element Method code into our tomographic modeling, allowing us to move beyond many assumptions inherent in the analytic mode-based approaches, while still taking advantage of their computational efficiency. Illustrations of the effects of these increasingly sophisticated steps will be presented.

Evaluation of MODFLOW-LGR in connection with a synthetic regional-scale model

USGS Publications Warehouse

Vilhelmsen, T.N.; Christensen, S.; Mehl, S.W.

2012-01-01

This work studies costs and benefits of utilizing local-grid refinement (LGR) as implemented in MODFLOW-LGR to simulate groundwater flow in a buried tunnel valley interacting with a regional aquifer. Two alternative LGR methods were used: the shared-node (SN) method and the ghost-node (GN) method. To conserve flows the SN method requires correction of sources and sinks in cells at the refined/coarse-grid interface. We found that the optimal correction method is case dependent and difficult to identify in practice. However, the results showed little difference and suggest that identifying the optimal method was of minor importance in our case. The GN method does not require corrections at the models' interface, and it uses a simpler head interpolation scheme than the SN method. The simpler scheme is faster but less accurate so that more iterations may be necessary. However, the GN method solved our flow problem more efficiently than the SN method. The MODFLOW-LGR results were compared with the results obtained using a globally coarse (GC) grid. The LGR simulations required one to two orders of magnitude longer run times than the GC model. However, the improvements of the numerical resolution around the buried valley substantially increased the accuracy of simulated heads and flows compared with the GC simulation. Accuracy further increased locally around the valley flanks when improving the geological resolution using the refined grid. Finally, comparing MODFLOW-LGR simulation with a globally refined (GR) grid showed that the refinement proportion of the model should not exceed 10% to 15% in order to secure method efficiency. ?? 2011, The Author(s). Ground Water ?? 2011, National Ground Water Association.

Use of noncrystallographic symmetry for automated model building at medium to low resolution.

PubMed

Wiegels, Tim; Lamzin, Victor S

2012-04-01

A novel method is presented for the automatic detection of noncrystallographic symmetry (NCS) in macromolecular crystal structure determination which does not require the derivation of molecular masks or the segmentation of density. It was found that throughout structure determination the NCS-related parts may be differently pronounced in the electron density. This often results in the modelling of molecular fragments of variable length and accuracy, especially during automated model-building procedures. These fragments were used to identify NCS relations in order to aid automated model building and refinement. In a number of test cases higher completeness and greater accuracy of the obtained structures were achieved, specifically at a crystallographic resolution of 2.3 Å or poorer. In the best case, the method allowed the building of up to 15% more residues automatically and a tripling of the average length of the built fragments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramadhar, Timothy R.; Zheng, Shao-Liang; Chen, Yu-Sheng

This report describes complete practical guidelines and insights for the crystalline sponge method, which have been derived through the first use of synchrotron radiation on these systems, and includes a procedure for faster synthesis of the sponges. These guidelines will be applicable to crystal sponge data collected at synchrotrons or in-house facilities, and will allow researchers to obtain reliable high-quality data and construct chemically and physically sensible models for guest structural determination. A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported.more » The procedure for the synthesis of the zinc-based metal–organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collection times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination.« less

Grid refinement in Cartesian coordinates for groundwater flow models using the divergence theorem and Taylor's series.

PubMed

Mansour, M M; Spink, A E F

2013-01-01

Grid refinement is introduced in a numerical groundwater model to increase the accuracy of the solution over local areas without compromising the run time of the model. Numerical methods developed for grid refinement suffered certain drawbacks, for example, deficiencies in the implemented interpolation technique; the non-reciprocity in head calculations or flow calculations; lack of accuracy resulting from high truncation errors, and numerical problems resulting from the construction of elongated meshes. A refinement scheme based on the divergence theorem and Taylor's expansions is presented in this article. This scheme is based on the work of De Marsily (1986) but includes more terms of the Taylor's series to improve the numerical solution. In this scheme, flow reciprocity is maintained and high order of refinement was achievable. The new numerical method is applied to simulate groundwater flows in homogeneous and heterogeneous confined aquifers. It produced results with acceptable degrees of accuracy. This method shows the potential for its application to solving groundwater heads over nested meshes with irregular shapes. © 2012, British Geological Survey © NERC 2012. Ground Water © 2012, National GroundWater Association.

Structural and Crystal Chemical Properties of Alkali Rare-earth Double Phosphates

DOE PAGES

Farmer, James Matthew; Boatner, Lynn A.; Chakoumakos, Bryan C.; ...

2016-01-01

When appropriately activated, alkali rare-earth double phosphates of the form: M 3RE(PO 4) 2 (where M denotes an alkali metal and RE represents either a rare-earth element or Y or Sc) are of interest for use as inorganic scintillators for radiation detection at relatively long optical emission wavelengths. These compounds exhibit layered crystal structures whose symmetry properties depend on the relative sizes of the rare-earth and alkali-metal cations. Single-crystal X-ray and powder neutron diffraction methods were used here to refine the structures of the series of rare-earth double phosphate compounds: K 3RE(PO 4) 2 with RE = Lu, Er, Ho,more » Dy, Gd, Nd, Ce, plus Y and Sc - as well as the compounds: A 3Lu(PO 4) 2, with A = Rb, and Cs. The double phosphate K 3Lu(PO 4) 2 was reported and structurally refined previously. This material had a hexagonal unit cell at room temperature with the Lu ion six-fold coordinated with oxygen atoms of the surrounding phosphate groups. Additionally two lower-temperature phases were observed for K 3Lu(PO 4) 2. The first phase transition to a monoclinic P21/m phase occurred at ~230 K, and the Lu ion retained its six-fold coordination. The second K 3Lu(PO 4) 2 phase transition occurred at ~130 K. The P21/m space group symmetry was retained, however, one of the phosphate groups rotated to increase the oxygen coordination number of Lu from six to seven. This structure then became isostructural with the room-temperature form of the compound K 3Yb(PO 4) 2 reported here that also exhibits an additional high-temperature phase which occurs at T = 120 °C with a transformation to hexagonal P-3 space group symmetry and a Yb-ion coordination number reduction from seven to six. This latter result was confirmed using EXAFS. The single-crystal growth methods structural systematics, and thermal expansion properties of the present series of alkali rare-earth double phosphates, as determined by X-ray and neutron diffraction methods, are treated here.« less

Structural and Crystal Chemical Properties of Alkali Rare-earth Double Phosphates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farmer, James Matthew; Boatner, Lynn A.; Chakoumakos, Bryan C.

When appropriately activated, alkali rare-earth double phosphates of the form: M 3RE(PO 4) 2 (where M denotes an alkali metal and RE represents either a rare-earth element or Y or Sc) are of interest for use as inorganic scintillators for radiation detection at relatively long optical emission wavelengths. These compounds exhibit layered crystal structures whose symmetry properties depend on the relative sizes of the rare-earth and alkali-metal cations. Single-crystal X-ray and powder neutron diffraction methods were used here to refine the structures of the series of rare-earth double phosphate compounds: K 3RE(PO 4) 2 with RE = Lu, Er, Ho,more » Dy, Gd, Nd, Ce, plus Y and Sc - as well as the compounds: A 3Lu(PO 4) 2, with A = Rb, and Cs. The double phosphate K 3Lu(PO 4) 2 was reported and structurally refined previously. This material had a hexagonal unit cell at room temperature with the Lu ion six-fold coordinated with oxygen atoms of the surrounding phosphate groups. Additionally two lower-temperature phases were observed for K 3Lu(PO 4) 2. The first phase transition to a monoclinic P21/m phase occurred at ~230 K, and the Lu ion retained its six-fold coordination. The second K 3Lu(PO 4) 2 phase transition occurred at ~130 K. The P21/m space group symmetry was retained, however, one of the phosphate groups rotated to increase the oxygen coordination number of Lu from six to seven. This structure then became isostructural with the room-temperature form of the compound K 3Yb(PO 4) 2 reported here that also exhibits an additional high-temperature phase which occurs at T = 120 °C with a transformation to hexagonal P-3 space group symmetry and a Yb-ion coordination number reduction from seven to six. This latter result was confirmed using EXAFS. The single-crystal growth methods structural systematics, and thermal expansion properties of the present series of alkali rare-earth double phosphates, as determined by X-ray and neutron diffraction methods, are treated here.« less

Multiscale Methods for Nuclear Reactor Analysis

NASA Astrophysics Data System (ADS)

Collins, Benjamin S.

The ability to accurately predict local pin powers in nuclear reactors is necessary to understand the mechanisms that cause fuel pin failure during steady state and transient operation. In the research presented here, methods are developed to improve the local solution using high order methods with boundary conditions from a low order global solution. Several different core configurations were tested to determine the improvement in the local pin powers compared to the standard techniques, that use diffusion theory and pin power reconstruction (PPR). Two different multiscale methods were developed and analyzed; the post-refinement multiscale method and the embedded multiscale method. The post-refinement multiscale methods use the global solution to determine boundary conditions for the local solution. The local solution is solved using either a fixed boundary source or an albedo boundary condition; this solution is "post-refinement" and thus has no impact on the global solution. The embedded multiscale method allows the local solver to change the global solution to provide an improved global and local solution. The post-refinement multiscale method is assessed using three core designs. When the local solution has more energy groups, the fixed source method has some difficulties near the interface: however the albedo method works well for all cases. In order to remedy the issue with boundary condition errors for the fixed source method, a buffer region is used to act as a filter, which decreases the sensitivity of the solution to the boundary condition. Both the albedo and fixed source methods benefit from the use of a buffer region. Unlike the post-refinement method, the embedded multiscale method alters the global solution. The ability to change the global solution allows for refinement in areas where the errors in the few group nodal diffusion are typically large. The embedded method is shown to improve the global solution when it is applied to a MOX/LEU assembly interface, the fuel/reflector interface, and assemblies where control rods are inserted. The embedded method also allows for multiple solution levels to be applied in a single calculation. The addition of intermediate levels to the solution improves the accuracy of the method. Both multiscale methods considered here have benefits and drawbacks, but both can provide improvements over the current PPR methodology.

Method of refining 2,2-isopropylidenebis-3,5- dibromophenylene-4-oxydiethanol

NASA Technical Reports Server (NTRS)

Kobayashi, T.; Nawata, K.; Hiratsuka, K.

1982-01-01

A method of refining 2,2-isopropylidenebis-3,5-dibromophenylene-4-oxydiethanol is described which is characterized by recrystallization of 2,2-isopropylidenebis-3,5-dibromophenylene-4-oxydiethanol using one or more aromatic hydrocarbons such as benzene, xylene, toluene, ethylbenzene or pseudocumene.

On the complexity of Engh and Huber refinement restraints: the angle τ as example

DOE Office of Scientific and Technical Information (OSTI.GOV)

Touw, Wouter G.; Vriend, Gert, E-mail: vriend@cmbi.ru.nl

2010-12-01

The angle τ (backbone N—C{sup α}—C) is the most contested Engh and Huber refinement target parameter. It is shown that this parameter is ‘correct’ as a PDB-wide average, but can be improved by taking into account residue types, secondary structures and many other aspects of our knowledge of the biophysical relations between residue type and protein structure. The Engh and Huber parameters for bond lengths and bond angles have been used uncontested in macromolecular structure refinement from 1991 until very recently, despite critical discussion of their ubiquitous validity by many authors. An extensive analysis of the backbone angle τ (N—C{supmore » α}—C) illustrates that the Engh and Huber parameters can indeed be improved and a recent study [Tronrud et al. (2010 ▶), Acta Cryst. D66, 834–842] confirms these ideas. However, the present study of τ shows that improving the Engh and Huber parameters will be considerably more complex than simply making the parameters a function of the backbone ϕ, ψ angles. Many other aspects, such as the cooperativity of hydrogen bonds, the bending of secondary-structure elements and a series of biophysical aspects of the 20 amino-acid types, will also need to be taken into account. Different sets of Engh and Huber parameters will be needed for conceptually different refinement programs.« less

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

DOE PAGES

Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; ...

2017-03-08

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 structuremore » 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.« less

Ba0.06(Na,Bi)0.94Ti1-x(Ni1/3Nb2/3)xO3 ceramics: X-ray diffraction and infrared spectroscopy studies

NASA Astrophysics Data System (ADS)

Mishra, R. K.; Prasad, Ashutosh; Chandra, K. P.; Prasad, K.

2018-05-01

Non-lead ceramic samples of Ba0.06(Na0.5Bi0.5)0.94Ti1-x(Ni1/3Nb2/3)xO3; 0 ≤ x ≤ 1.0 were prepared by standard high temperature ceramic synthesis method. Rietveld refinements of X-ray diffraction data of these ceramics were carried out using FullProf software and determined their crystal symmetry, space group and unit cell dimensions. Rietveld refinement revealed that Ba0.06(Na0.5Bi0.5)0.94TiO3 has a monoclinic structure with space group P4/m while B0.06(Na0.5Bi0.5)0.94(Ni1/3Nb2/3)O3 has tetragonal (pseudo-cubic) structure with space group P4/mmm. Partial replacement of Ti4+ ion by pseudo-cation (Ni1/33 +Nb2/3 5 +) 4 + resulted in the change of unit cell structure from monoclinic to tetragonal. SEM studies were carried out in order to access the quality of the prepared ceramics which showed a change in grain sizes with the increase of (Ni1/33 +Nb2/3 5 +) 4 + content. FTIR spectra confirmed the formation of perovskite type solid solutions.

Dimensional Representation and Gradient Boosting for Seismic Event Classification

NASA Astrophysics Data System (ADS)

Semmelmayer, F. C.; Kappedal, R. D.; Magana-Zook, S. A.

2017-12-01

In this research, we conducted experiments of representational structures on 5009 seismic signals with the intent of finding a method to classify signals as either an explosion or an earthquake in an automated fashion. We also applied a gradient boosted classifier. While perfect classification was not attained (approximately 88% was our best model), some cases demonstrate that many events can be filtered out as very high probability being explosions or earthquakes, diminishing subject-matter experts'(SME) workload for first stage analysis. It is our hope that these methods can be refined, further increasing the classification probability.

Incremental triangulation by way of edge swapping and local optimization

NASA Technical Reports Server (NTRS)

Wiltberger, N. Lyn

1994-01-01

This document is intended to serve as an installation, usage, and basic theory guide for the two dimensional triangulation software 'HARLEY' written for the Silicon Graphics IRIS workstation. This code consists of an incremental triangulation algorithm based on point insertion and local edge swapping. Using this basic strategy, several types of triangulations can be produced depending on user selected options. For example, local edge swapping criteria can be chosen which minimizes the maximum interior angle (a MinMax triangulation) or which maximizes the minimum interior angle (a MaxMin or Delaunay triangulation). It should be noted that the MinMax triangulation is generally only locally optical (not globally optimal) in this measure. The MaxMin triangulation, however, is both locally and globally optical. In addition, Steiner triangulations can be constructed by inserting new sites at triangle circumcenters followed by edge swapping based on the MaxMin criteria. Incremental insertion of sites also provides flexibility in choosing cell refinement criteria. A dynamic heap structure has been implemented in the code so that once a refinement measure is specified (i.e., maximum aspect ratio or some measure of a solution gradient for the solution adaptive grid generation) the cell with the largest value of this measure is continually removed from the top of the heap and refined. The heap refinement strategy allows the user to specify either the number of cells desired or refine the mesh until all cell refinement measures satisfy a user specified tolerance level. Since the dynamic heap structure is constantly updated, the algorithm always refines the particular cell in the mesh with the largest refinement criteria value. The code allows the user to: triangulate a cloud of prespecified points (sites), triangulate a set of prespecified interior points constrained by prespecified boundary curve(s), Steiner triangulate the interior/exterior of prespecified boundary curve(s), refine existing triangulations based on solution error measures, and partition meshes based on the Cuthill-McKee, spectral, and coordinate bisection strategies.

Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes.

PubMed

Uchikoga, Nobuyuki; Hirokawa, Takatsugu

2010-05-11

Protein-protein docking for proteins with large conformational changes was analyzed by using interaction fingerprints, one of the scales for measuring similarities among complex structures, utilized especially for searching near-native protein-ligand or protein-protein complex structures. Here, we have proposed a combined method for analyzing protein-protein docking by taking large conformational changes into consideration. This combined method consists of ensemble soft docking with multiple protein structures, refinement of complexes, and cluster analysis using interaction fingerprints and energy profiles. To test for the applicability of this combined method, various CaM-ligand complexes were reconstructed from the NMR structures of unbound CaM. For the purpose of reconstruction, we used three known CaM-ligands, namely, the CaM-binding peptides of cyclic nucleotide gateway (CNG), CaM kinase kinase (CaMKK) and the plasma membrane Ca2+ ATPase pump (PMCA), and thirty-one structurally diverse CaM conformations. For each ligand, 62000 CaM-ligand complexes were generated in the docking step and the relationship between their energy profiles and structural similarities to the native complex were analyzed using interaction fingerprint and RMSD. Near-native clusters were obtained in the case of CNG and CaMKK. The interaction fingerprint method discriminated near-native structures better than the RMSD method in cluster analysis. We showed that a combined method that includes the interaction fingerprint is very useful for protein-protein docking analysis of certain cases.

Large-scale model quality assessment for improving protein tertiary structure prediction.

PubMed

Cao, Renzhi; Bhattacharya, Debswapna; Adhikari, Badri; Li, Jilong; Cheng, Jianlin

2015-06-15

Sampling structural models and ranking them are the two major challenges of protein structure prediction. Traditional protein structure prediction methods generally use one or a few quality assessment (QA) methods to select the best-predicted models, which cannot consistently select relatively better models and rank a large number of models well. Here, we develop a novel large-scale model QA method in conjunction with model clustering to rank and select protein structural models. It unprecedentedly applied 14 model QA methods to generate consensus model rankings, followed by model refinement based on model combination (i.e. averaging). Our experiment demonstrates that the large-scale model QA approach is more consistent and robust in selecting models of better quality than any individual QA method. Our method was blindly tested during the 11th Critical Assessment of Techniques for Protein Structure Prediction (CASP11) as MULTICOM group. It was officially ranked third out of all 143 human and server predictors according to the total scores of the first models predicted for 78 CASP11 protein domains and second according to the total scores of the best of the five models predicted for these domains. MULTICOM's outstanding performance in the extremely competitive 2014 CASP11 experiment proves that our large-scale QA approach together with model clustering is a promising solution to one of the two major problems in protein structure modeling. The web server is available at: http://sysbio.rnet.missouri.edu/multicom_cluster/human/. © The Author 2015. Published by Oxford University Press.

Refining Linear Fuzzy Rules by Reinforcement Learning

NASA Technical Reports Server (NTRS)

Berenji, Hamid R.; Khedkar, Pratap S.; Malkani, Anil

1996-01-01

Linear fuzzy rules are increasingly being used in the development of fuzzy logic systems. Radial basis functions have also been used in the antecedents of the rules for clustering in product space which can automatically generate a set of linear fuzzy rules from an input/output data set. Manual methods are usually used in refining these rules. This paper presents a method for refining the parameters of these rules using reinforcement learning which can be applied in domains where supervised input-output data is not available and reinforcements are received only after a long sequence of actions. This is shown for a generalization of radial basis functions. The formation of fuzzy rules from data and their automatic refinement is an important step in closing the gap between the application of reinforcement learning methods in the domains where only some limited input-output data is available.

Quantitative Structure Retention Relationships of Polychlorinated Dibenzodioxins and Dibenzofurans

DTIC Science & Technology

1991-08-01

be a projection onto the X-Y plane. The algorithm for this calculation can be found in Stouch and Jurs (22), but was further refined by Rohrbaugh and...throughspace distances. WPSA2 (c) Weighted positive charged surface area. MOMH2 (c) Second major moment of inertia with hydrogens attached. CSTR 3 (d) Sum...of the models. The robust regression analysis method calculates a regression model using a least median squares algorithm which is not as susceptible

Fabrication of the Ti5Si3/Ti composite inoculants and its refining mechanism on pure titanium

NASA Astrophysics Data System (ADS)

Li, Nuo; Cui, Chunxiang; Liu, Shaungjin; Zhao, Long; Liu, Shuiqing

2017-03-01

The in situ Ti5Si3/Ti inoculants were successfully prepared by vacuum arc-melting and melt-spinning method. An efficient route by adding a small quantity of Ti5Si3/Ti inoculants to Ti melt has been first proposed to modify the coarse grains of as cast microstructure of pure titanium in this paper. It was found that the microstructure of ribbon inoculants was cellular structure that composed of Ti5Si3 and α-Ti phases. The grain refining effect of the inoculants was significantly improved with the adding ratio range from 0.2% to 0.5% in weight. With the increase of addition amount of inoculants on Ti melt, the tensile strength, yield strength and microhardness of pure titanium are significantly improved except elongation. The excellent grain refining effect can be attributed to the heterogeneous nucleation of the titanium grain on the precipitated Ti5Si3 phases in the Si-rich regions and the constitutional supercooling of Si in the Si-poverty regions. It is suggested that the in situ Ti5Si3/Ti inoculants is a promising inoculants for titanium alloys.

Refining Parameters of the XO-5 Planetary System with High-Precision Transit Photometry

NASA Astrophysics Data System (ADS)

Maciejewski, G.; Seeliger, M.; Adam, Ch.; Raetz, St.; Neuhäuser, R.

2011-03-01

Studies of transiting extrasolar planets provide unique opportunity to get to know the internal structure of those worlds. The transiting exoplanet XO-5 b was found to have an anomalously high Safronov number and surface gravity. Our aim was to refine parameters of this intriguing system and search for signs of transit timing variations. We gathered high-precision light curves for two transits of XO-5 b. Assuming three different limb darkening laws, we found the best-fitting model and redetermined parameters of the system, including planet-to-star radius ratio, impact parameter and central time of transits. Error estimates were derived by the prayer bead method and Monte Carlo simulations. Although system's parameters obtained by us were found to agree with previous studies within one sigma, the planet was found to be notable smaller with the radius of 1.03+0.06-0.05 Jupiter radii. Our results confirm the high Safronov number and surface gravity of the planet. With two new mid-transit times, the ephemeris was refined to BJDTDB=(2454485.66842±0.00028)+(4.1877537±0.000017)E. No significant transit timing variation was detected.

Controlling the energy of defects and interfaces in the amplitude expansion of the phase-field crystal model

NASA Astrophysics Data System (ADS)

Salvalaglio, Marco; Backofen, Rainer; Voigt, Axel; Elder, Ken R.

2017-08-01

One of the major difficulties in employing phase-field crystal (PFC) modeling and the associated amplitude (APFC) formulation is the ability to tune model parameters to match experimental quantities. In this work, we address the problem of tuning the defect core and interface energies in the APFC formulation. We show that the addition of a single term to the free-energy functional can be used to increase the solid-liquid interface and defect energies in a well-controlled fashion, without any major change to other features. The influence of the newly added term is explored in two-dimensional triangular and honeycomb structures as well as bcc and fcc lattices in three dimensions. In addition, a finite-element method (FEM) is developed for the model that incorporates a mesh refinement scheme. The combination of the FEM and mesh refinement to simulate amplitude expansion with a new energy term provides a method of controlling microscopic features such as defect and interface energies while simultaneously delivering a coarse-grained examination of the system.

A modern optical character recognition system in a real world clinical setting: some accuracy and feasibility observations.

PubMed

Biondich, Paul G; Overhage, J Marc; Dexter, Paul R; Downs, Stephen M; Lemmon, Larry; McDonald, Clement J

2002-01-01

Advances in optical character recognition (OCR) software and computer hardware have stimulated a reevaluation of the technology and its ability to capture structured clinical data from preexisting paper forms. In our pilot evaluation, we measured the accuracy and feasibility of capturing vitals data from a pediatric encounter form that has been in use for over twenty years. We found that the software had a digit recognition rate of 92.4% (95% confidence interval: 91.6 to 93.2) overall. More importantly, this system was approximately three times as fast as our existing method of data entry. These preliminary results suggest that with further refinements in the approach and additional development, we may be able to incorporate OCR as another method for capturing structured clinical data.

Applying transfer matrix method to the estimation of the modal characteristics of the NASA Mini-Mass Truss

NASA Technical Reports Server (NTRS)

Shen, Ji-Yao; Taylor, Lawrence W., Jr.

1994-01-01

It is beneficial to use a distributed parameter model for large space structures because the approach minimizes the number of model parameters. Holzer's transfer matrix method provides a useful means to simplify and standardize the procedure for solving the system of partial differential equations. Any large space structures can be broken down into sub-structures with simple elastic and dynamical properties. For each single element, such as beam, tether, or rigid body, we can derive the corresponding transfer matrix. Combining these elements' matrices enables the solution of the global system equations. The characteristics equation can then be formed by satisfying the appropriate boundary conditions. Then natural frequencies and mode shapes can be determined by searching the roots of the characteristic equation at frequencies within the range of interest. This paper applies this methodology, and the maximum likelihood estimation method, to refine the modal characteristics of the NASA Mini-Mast Truss by successively matching the theoretical response to the test data of the truss. The method is being applied to more complex configurations.

Ensemble modeling of very small ZnO nanoparticles.

PubMed

Niederdraenk, Franziska; Seufert, Knud; Stahl, Andreas; Bhalerao-Panajkar, Rohini S; Marathe, Sonali; Kulkarni, Sulabha K; Neder, Reinhard B; Kumpf, Christian

2011-01-14

The detailed structural characterization of nanoparticles is a very important issue since it enables a precise understanding of their electronic, optical and magnetic properties. Here we introduce a new method for modeling the structure of very small particles by means of powder X-ray diffraction. Using thioglycerol-capped ZnO nanoparticles with a diameter of less than 3 nm as an example we demonstrate that our ensemble modeling method is superior to standard XRD methods like, e.g., Rietveld refinement. Besides fundamental properties (size, anisotropic shape and atomic structure) more sophisticated properties like imperfections in the lattice, a size distribution as well as strain and relaxation effects in the particles and-in particular-at their surface (surface relaxation effects) can be obtained. Ensemble properties, i.e., distributions of the particle size and other properties, can also be investigated which makes this method superior to imaging techniques like (high resolution) transmission electron microscopy or atomic force microscopy, in particular for very small nanoparticles. For the particles under study an excellent agreement of calculated and experimental X-ray diffraction patterns could be obtained with an ensemble of anisotropic polyhedral particles of three dominant sizes, wurtzite structure and a significant relaxation of Zn atoms close to the surface.

Efficient parallel seismic simulations including topography and 3-D material heterogeneities on locally refined composite grids

NASA Astrophysics Data System (ADS)

Petersson, Anders; Rodgers, Arthur

2010-05-01

The finite difference method on a uniform Cartesian grid is a highly efficient and easy to implement technique for solving the elastic wave equation in seismic applications. However, the spacing in a uniform Cartesian grid is fixed throughout the computational domain, whereas the resolution requirements in realistic seismic simulations usually are higher near the surface than at depth. This can be seen from the well-known formula h ≤ L-P which relates the grid spacing h to the wave length L, and the required number of grid points per wavelength P for obtaining an accurate solution. The compressional and shear wave lengths in the earth generally increase with depth and are often a factor of ten larger below the Moho discontinuity (at about 30 km depth), than in sedimentary basins near the surface. A uniform grid must have a grid spacing based on the small wave lengths near the surface, which results in over-resolving the solution at depth. As a result, the number of points in a uniform grid is unnecessarily large. In the wave propagation project (WPP) code, we address the over-resolution-at-depth issue by generalizing our previously developed single grid finite difference scheme to work on a composite grid consisting of a set of structured rectangular grids of different spacings, with hanging nodes on the grid refinement interfaces. The computational domain in a regional seismic simulation often extends to depth 40-50 km. Hence, using a refinement ratio of two, we need about three grid refinements from the bottom of the computational domain to the surface, to keep the local grid size in approximate parity with the local wave lengths. The challenge of the composite grid approach is to find a stable and accurate method for coupling the solution across the grid refinement interface. Of particular importance is the treatment of the solution at the hanging nodes, i.e., the fine grid points which are located in between coarse grid points. WPP implements a new, energy conserving, coupling procedure for the elastic wave equation at grid refinement interfaces. When used together with our single grid finite difference scheme, it results in a method which is provably stable, without artificial dissipation, for arbitrary heterogeneous isotropic elastic materials. The new coupling procedure is based on satisfying the summation-by-parts principle across refinement interfaces. From a practical standpoint, an important advantage of the proposed method is the absence of tunable numerical parameters, which seldom are appreciated by application experts. In WPP, the composite grid discretization is combined with a curvilinear grid approach that enables accurate modeling of free surfaces on realistic (non-planar) topography. The overall method satisfies the summation-by-parts principle and is stable under a CFL time step restriction. A feature of great practical importance is that WPP automatically generates the composite grid based on the user provided topography and the depths of the grid refinement interfaces. The WPP code has been verified extensively, for example using the method of manufactured solutions, by solving Lamb's problem, by solving various layer over half- space problems and comparing to semi-analytic (FK) results, and by simulating scenario earthquakes where results from other seismic simulation codes are available. WPP has also been validated against seismographic recordings of moderate earthquakes. WPP performs well on large parallel computers and has been run on up to 32,768 processors using about 26 Billion grid points (78 Billion DOF) and 41,000 time steps. WPP is an open source code that is available under the Gnu general public license.

Weak data do not make a free lunch, only a cheap meal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Zhipu; Rajashankar, Kanagalaghatta; Dauter, Zbigniew, E-mail: dauter@anl.gov

2014-02-01

Refinement and analysis of four structures with various data resolution cutoffs suggests that at present there are no reliable criteria for judging the diffraction data resolution limit and the condition I/σ(I) = 2.0 is reasonable. However, extending the limit by about 0.2 Å beyond the resolution defined by this threshold does not deteriorate the quality of refined structures and in some cases may be beneficial. Four data sets were processed at resolutions significantly exceeding the criteria traditionally used for estimating the diffraction data resolution limit. The analysis of these data and the corresponding model-quality indicators suggests that the criteria ofmore » resolution limits widely adopted in the past may be somewhat conservative. Various parameters, such as R{sub merge} and I/σ(I), optical resolution and the correlation coefficients CC{sub 1/2} and CC*, can be used for judging the internal data quality, whereas the reliability factors R and R{sub free} as well as the maximum-likelihood target values and real-space map correlation coefficients can be used to estimate the agreement between the data and the refined model. However, none of these criteria provide a reliable estimate of the data resolution cutoff limit. The analysis suggests that extension of the maximum resolution by about 0.2 Å beyond the currently adopted limit where the I/σ(I) value drops to 2.0 does not degrade the quality of the refined structural models, but may sometimes be advantageous. Such an extension may be particularly beneficial for significantly anisotropic diffraction. Extension of the maximum resolution at the stage of data collection and structure refinement is cheap in terms of the required effort and is definitely more advisable than accepting a too conservative resolution cutoff, which is unfortunately quite frequent among the crystal structures deposited in the Protein Data Bank.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deus, R.C.; Cortés, J.A., E-mail: leandrosrr89@gmail.com; Ramirez, M.A.

Highlights: • CeO{sub 2} nanoparticles were obtained by microwave-hydrothermal method. • Rietveld refinement reveals a cubic structure. • KOH mineralizer agent exhibit weak agglomeration at low temperature and shorter time. - Abstract: The structural and photoluminescent properties at room temperature of CeO{sub 2} and La-doped CeO{sub 2} particles were undertaken. The obtained particles were synthesized by a microwave-assisted hydrothermal method (MAH) under different lanthanum contents. X-ray diffraction (XRD), Fourier transform infrared (FT-IR), Fourier transform Raman (FT-Raman), Ultra-violet spectroscopy (UV–vis) and photoluminescence (PL) measurements were carried out. XRD revealed that the powders are free of secondary phases and crystallize in themore » cubic structure. Raman data show that increasing La doping content increase oxygen vacancies due to lattice expansion. The UV/vis absorption spectroscopy suggested the presence of intermediate energy levels in the band gap of structurally ordered powders. Lanthanum addition creates oxygen vacancies and shifts the photoluminescence in the low energy range leading to intense PL emission.« less

NASA Handbook for Spacecraft Structural Dynamics Testing

NASA Technical Reports Server (NTRS)

Kern, Dennis L.; Scharton, Terry D.

2005-01-01

Recent advances in the area of structural dynamics and vibrations, in both methodology and capability, have the potential to make spacecraft system testing more effective from technical, cost, schedule, and hardware safety points of view. However, application of these advanced test methods varies widely among the NASA Centers and their contractors. Identification and refinement of the best of these test methodologies and implementation approaches has been an objective of efforts by the Jet Propulsion Laboratory on behalf of the NASA Office of the Chief Engineer. But to develop the most appropriate overall test program for a flight project from the selection of advanced methodologies, as well as conventional test methods, spacecraft project managers and their technical staffs will need overall guidance and technical rationale. Thus, the Chief Engineer's Office has recently tasked JPL to prepare a NASA Handbook for Spacecraft Structural Dynamics Testing. An outline of the proposed handbook, with a synopsis of each section, has been developed and is presented herein. Comments on the proposed handbook are solicited from the spacecraft structural dynamics testing community.

NASA Handbook for Spacecraft Structural Dynamics Testing

NASA Technical Reports Server (NTRS)

Kern, Dennis L.; Scharton, Terry D.

2004-01-01

Recent advances in the area of structural dynamics and vibrations, in both methodology and capability, have the potential to make spacecraft system testing more effective from technical, cost, schedule, and hardware safety points of view. However, application of these advanced test methods varies widely among the NASA Centers and their contractors. Identification and refinement of the best of these test methodologies and implementation approaches has been an objective of efforts by the Jet Propulsion Laboratory on behalf of the NASA Office of the Chief Engineer. But to develop the most appropriate overall test program for a flight project from the selection of advanced methodologies, as well as conventional test methods, spacecraft project managers and their technical staffs will need overall guidance and technical rationale. Thus, the Chief Engineer's Office has recently tasked JPL to prepare a NASA Handbook for Spacecraft Structural Dynamics Testing. An outline of the proposed handbook, with a synopsis of each section, has been developed and is presented herein. Comments on the proposed handbook is solicited from the spacecraft structural dynamics testing community.

Synthesis and structural study of 4-(2-chlorophenyl)-2-ethoxy-5,6,7,8,9,10-hexahydrocycloocta[B] pyridine-3-carbonitrile

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fathima, K. Saiadali; Vasumathi, M.; Anitha, K., E-mail: singlecrystalxrd@gmail.com

2016-05-23

The novel organic material C{sub 20}H{sub 21}ClN{sub 2}O was synthesized by One-Pot synthesis method and the single crystals were grown by slow evaporation solution growth technique. The crystal structure was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R=0.039 for 2746 reflections. Crystal system of the grown crystal was found to be monoclinic with the space group P2{sub 1}/a and a=9.196(4) Å, b=13.449(4) Å, c=14.818(4) Å, β= 101.542(3)°, V=1795.6(11) Å{sup 3} and Z=4. In this crystal structure, cyclooctanone prefers to reside in a chair-boat conformation. Themore » structure is stabilized by attractive molecular force such as CH/π interaction called hydrophobic interaction.« less

Blade loss transient dynamics analysis, volume 2. Task 2: Theoretical and analytical development. Task 3: Experimental verification

NASA Technical Reports Server (NTRS)

Gallardo, V. C.; Storace, A. S.; Gaffney, E. F.; Bach, L. J.; Stallone, M. J.

1981-01-01

The component element method was used to develop a transient dynamic analysis computer program which is essentially based on modal synthesis combined with a central, finite difference, numerical integration scheme. The methodology leads to a modular or building-block technique that is amenable to computer programming. To verify the analytical method, turbine engine transient response analysis (TETRA), was applied to two blade-out test vehicles that had been previously instrumented and tested. Comparison of the time dependent test data with those predicted by TETRA led to recommendations for refinement or extension of the analytical method to improve its accuracy and overcome its shortcomings. The development of working equations, their discretization, numerical solution scheme, the modular concept of engine modelling, the program logical structure and some illustrated results are discussed. The blade-loss test vehicles (rig full engine), the type of measured data, and the engine structural model are described.

Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta

PubMed Central

Zhang, Zhe; Schindler, Christina E. M.; Lange, Oliver F.; Zacharias, Martin

2015-01-01

The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC) based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamiltonian replica exchange and well-tempered ensemble approaches, have been combined with the MC method and were evaluated on 20 protein complexes using unbound partner structures. The well-tempered ensemble method combined with a 2-dimensional temperature and Hamiltonian replica exchange scheme (WTE-H-REMC) was identified as the most efficient search strategy. Comparison with prolonged MC searches indicates that the WTE-H-REMC approach requires approximately 5 times fewer MC steps to identify near native docking geometries compared to conventional MC searches. PMID:26053419

Experimental conformational energy maps of proteins and peptides.

PubMed

Balaji, Govardhan A; Nagendra, H G; Balaji, Vitukudi N; Rao, Shashidhar N

2017-06-01

We have presented an extensive analysis of the peptide backbone dihedral angles in the PDB structures and computed experimental Ramachandran plots for their distributions seen under a various constraints on X-ray resolution, representativeness at different sequence identity percentages, and hydrogen bonding distances. These experimental distributions have been converted into isoenergy contour plots using the approach employed previously by F. M. Pohl. This has led to the identification of energetically favored minima in the Ramachandran (ϕ, ψ) plots in which global minima are predominantly observed either in the right-handed α-helical or the polyproline II regions. Further, we have identified low energy pathways for transitions between various minima in the (ϕ,ψ) plots. We have compared and presented the experimental plots with published theoretical plots obtained from both molecular mechanics and quantum mechanical approaches. In addition, we have developed and employed a root mean square deviation (RMSD) metric for isoenergy contours in various ranges, as a measure (in kcal.mol -1 ) to compare any two plots and determine the extent of correlation and similarity between their isoenergy contours. In general, we observe a greater degree of compatibility with experimental plots for energy maps obtained from molecular mechanics methods compared to most quantum mechanical methods. The experimental energy plots we have investigated could be helpful in refining protein structures obtained from X-ray, NMR, and electron microscopy and in refining force field parameters to enable simulations of peptide and protein structures that have higher degree of consistency with experiments. Proteins 2017; 85:979-1001. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A Flexile and High Precision Calibration Method for Binocular Structured Light Scanning System

PubMed Central

Yuan, Jianying; Wang, Qiong; Li, Bailin

2014-01-01

3D (three-dimensional) structured light scanning system is widely used in the field of reverse engineering, quality inspection, and so forth. Camera calibration is the key for scanning precision. Currently, 2D (two-dimensional) or 3D fine processed calibration reference object is usually applied for high calibration precision, which is difficult to operate and the cost is high. In this paper, a novel calibration method is proposed with a scale bar and some artificial coded targets placed randomly in the measuring volume. The principle of the proposed method is based on hierarchical self-calibration and bundle adjustment. We get initial intrinsic parameters from images. Initial extrinsic parameters in projective space are estimated with the method of factorization and then upgraded to Euclidean space with orthogonality of rotation matrix and rank 3 of the absolute quadric as constraint. Last, all camera parameters are refined through bundle adjustment. Real experiments show that the proposed method is robust, and has the same precision level as the result using delicate artificial reference object, but the hardware cost is very low compared with the current calibration method used in 3D structured light scanning system. PMID:25202736