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Sample records for dynamics simulations reveal

  1. Peptide crystal simulations reveal hidden dynamics

    PubMed Central

    Janowski, Pawel A.; Cerutti, David S.; Holton, James; Case, David A.

    2013-01-01

    Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in the X-ray diffraction data. We present here 9.6 microseconds of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to within 0.28 Å backbone and 0.42 Å all-atom rmsd; a model refined against the average simulation density agrees with the experimental structure to within 0.20 Å backbone and 0.33 Å all-atom rmsd. The R-factor between the experimental structure factors and those derived from this unrestrained simulation is 23% to 1.0 Å resolution. The B-factors for most heavy atoms agree well with experiment (Pearson correlation of 0.90), but B-factors obtained by refinement against the average simulation density underestimate the coordinate fluctuations in the underlying simulation where the simulation samples alternate conformations. A dynamic flow of water molecules through channels within the crystal lattice is observed, yet the average water density is in remarkable agreement with experiment. A minor population of unit cells is characterized by reduced water content, 310 helical propensity and a gauche(−) side-chain rotamer for one of the valine residues. Careful examination of the experimental data suggests that transitions of the helices are a simulation artifact, although there is indeed evidence for alternate valine conformers and variable water content. This study highlights the potential for crystal simulations to detect dynamics and heterogeneity in experimental diffraction data, as well as to validate computational chemistry methods. PMID:23631449

  2. Chain networking revealed by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing

    Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)

  3. Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation

    SciTech Connect

    Petridis, Loukas; Pingali, Sai Venkatesh; Urban, Volker; Heller, William T; O'Neill, Hugh Michael; Foston, Marcus B; Ragauskas, Arthur J; Smith, Jeremy C

    2011-01-01

    Lignin, a major polymeric component of plant cell walls, forms aggregates in vivo and poses a barrier to cellulosic ethanol production. Here, neutron scattering experiments and molecular dynamics simulations reveal that lignin aggregates are characterized by a surface fractal dimension that is invariant under change of scale from 1 1000 A. The simulations also reveal extensive water penetration of the aggregates and heterogeneous chain dynamics corresponding to a rigid core with a fluid surface.

  4. Structure-Based Simulations Reveal Concerted Dynamics of GPCR Activation

    PubMed Central

    Leioatts, Nicholas; Suresh, Pooja; Romo, Tod D.; Grossfield, Alan

    2014-01-01

    G protein-coupled receptors (GPCRs) are a vital class of proteins that transduce biological signals across the cell membrane. However, their allosteric activation mechanism is not fully understood; crystal structures of active and inactive receptors have been reported, but the functional pathway between these two states remains elusive. Here, we employ structure-based (Gō-like) models to simulate activation of two GPCRs, rhodopsin and the β2 adrenergic receptor (β2AR). We used data-derived reaction coordinates that capture the activation mechanism for both proteins, showing that activation proceeds through quantitatively different paths in the two systems. Both reaction coordinates are determined from the dominant concerted motions in the simulations so the technique is broadly applicable. There were two surprising results. First, the main structural changes in the simulations were distributed throughout the transmembrane bundle, and not localized to the obvious areas of interest, such as the intracellular portion of helix 6. Second, the activation (and deactivation) paths were distinctly non-monotonic, populating states that were not simply interpolations between the inactive and active structures. These transitions also suggest a functional explanation for β2AR’s basal activity: it can proceed through a more broadly defined path during the observed transitions. PMID:24889093

  5. Molecular Dynamics Simulation Reveals Correlated Inter-Lobe Motion in Protein Lysine Methyltransferase SMYD2

    PubMed Central

    Spellmon, Nicholas; Sun, Xiaonan; Sirinupong, Nualpun; Edwards, Brian; Li, Chunying; Yang, Zhe

    2015-01-01

    SMYD proteins are an exciting field of study as they are linked to many types of cancer-related pathways. Cardiac and skeletal muscle development and function also depend on SMYD proteins opening a possible avenue for cardiac-related treatment. Previous crystal structure studies have revealed that this special class of protein lysine methyltransferases have a bilobal structure, and an open–closed motion may regulate substrate specificity. Here we use the molecular dynamics simulation to investigate the still-poorly-understood SMYD2 dynamics. Cross-correlation analysis reveals that SMYD2 exhibits a negative correlated inter-lobe motion. Principle component analysis suggests that this correlated dynamic is contributed to by a twisting motion of the C-lobe with respect to the N-lobe and a clamshell-like motion between the lobes. Dynamical network analysis defines possible allosteric paths for the correlated dynamics. There are nine communities in the dynamical network with six in the N-lobe and three in the C-lobe, and the communication between the lobes is mediated by a lobe-bridging β hairpin. This study provides insight into the dynamical nature of SMYD2 and could facilitate better understanding of SMYD2 substrate specificity. PMID:26717235

  6. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

    PubMed

    Koldsø, Heidi; Autzen, Henriette Elisabeth; Grouleff, Julie; Schiøtt, Birgit

    2013-01-01

    The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design. PMID:23776432

  7. Ligand Induced Conformational Changes of the Human Serotonin Transporter Revealed by Molecular Dynamics Simulations

    PubMed Central

    Grouleff, Julie; Schiøtt, Birgit

    2013-01-01

    The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design. PMID:23776432

  8. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations

    PubMed Central

    Hertig, Samuel

    2016-01-01

    Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein’s constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery—the fact that the two sites involved influence one another in a symmetrical manner—can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest. PMID:27285999

  9. Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles.

    PubMed

    Fornili, Arianna; Pandini, Alessandro; Lu, Hui-Chun; Fraternali, Franca

    2013-11-12

    The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein

  10. Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles

    PubMed Central

    2013-01-01

    The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein

  11. Nanomechanical Behavior of Single Crystalline SiC Nanotubes Revealed by Molecular Dynamics Simulations

    SciTech Connect

    Wang, Zhiguo; Zu, Xiaotao T.; Gao, Fei; Weber, William J.

    2008-11-01

    Molecular dynamics simulations with Tersoff potentials were used to study the response of single crystalline SiC nanotubes under tensile, compressive, torsional, combined tension-torsional and combined compression-torsional strains. The simulation results reveal that the nanotubes deform through bond-stretching and breaking and exhibit brittle properties under uniaxial tensile strain, except for the thinnest nanotube at high temperatures, which fails in a ductile manner. Under uniaxial compressive strain, the SiC nanotubes buckle with two modes, i.e. shell buckling and column buckling, depending on the length of the nanotubes. Under torsional strain, the nanotubes buckle either collapse in the middle region into a dumbbell-like structure for thinner wall thicknesses or fail by bond breakage for the largest wall thickness. Both the tensile failure stress and buckling stress decrease under combined tension-torsional and combined compression-torsional strain, and they decrease with increasing torsional rate under combined loading.

  12. Mechanically Untying a Protein Slipknot: Multiple Pathways Revealed by Force Spectroscopy and Steered Molecular Dynamics Simulations

    PubMed Central

    He, Chengzhi; Genchev, Georgi Z.; Lu, Hui; Li, Hongbin

    2013-01-01

    Protein structure is highly diverse when considering a wide range of protein types, helping to give rise to the multitude of functions that proteins perform. In particular, certain proteins are known to adopt a knotted or slipknotted fold. How such proteins undergo mechanical unfolding was investigated utilizing a combination of single molecule atomic force microscopy (AFM), protein engineering and steered molecular dynamics (SMD) simulations to show the mechanical unfolding mechanism of the slipknotted protein AFV3-109. Our results reveal that the mechancial unfolding of AFV3-109 can proceed via multiple parallel unfolding pathways that all cause the protein slipknot to untie, and the polypeptide chain to completely extend. These distinct unfolding pathways proceed either via a two-state or three-state unfolding process involving the formation of a well-defined, stable intermediate state. SMD simulations predict the same contour length increments for different unfolding pathways as single molecule AFM results, thus provding a plausible molecular mechanism for the mechanical unfolding of AFV3-109. These SMD simulations also reveal that two-state unfolding is initiated from both the N- and C-termini, while three-state unfolding is initiated only from the C-terminus. In both pathways, the protein slipknot was untied during unfolding, and no tightened slipknot conformation observed. Detailed analysis revealed that interactions between key structural elements lock the knotting loop in place, preventing it from shrinking and the formation of a tightened slipknot conformation. Our results demonstrate the bifurcation of the mechancial unfolding pathway of AFV3-109, and point to the generality of a kinetic partitioning mechanism for protein folding/unfolding. PMID:22626004

  13. Molecular dynamics simulations reveal specific interactions of post-translational palmitoyl modifications with rhodopsin in membranes

    PubMed Central

    Olausson, Bjoern E.S.; Grossfield, Alan; Pitman, Michael C.; Brown, Michael F.; Feller, Scott E.; Vogel, Alexander

    2012-01-01

    We present a detailed analysis of the behavior of the highly flexible post-translational lipid modifications of rhodopsin from multiple-microsecond all-atom molecular dynamics simulations. Rhodopsin was studied in a realistic membrane environment that includes cholesterol, as well as saturated and polyunsaturated lipids with phosphocholine and phosphoethanolamine headgroups. The simulation reveals striking differences between the palmitoylations at Cys322 and Cys323 as well as between the palmitoyl chains and the neighboring lipids. Notably the palmitoyl group at Cys322 shows considerably greater contact with helix H1 of rhodopsin, yielding frequent chain upturns with longer reorientational correlation times, and relatively low order parameters. While the palmitoylation at Cys323 makes fewer protein contacts and has increased order compared to Cys322, it nevertheless exhibits greater flexibility with smaller order parameters than the stearoyl chains of the surrounding lipids. The dynamical structure of the palmitoylations—as well as their extensive fluctuations—suggests a complex function for the post-translational modifications in rhodopsin and potentially other G protein-coupled receptors, going beyond their role as membrane anchoring elements. Rather, we propose that the palmitoylation at Cys323 has a potential role as a lipid anchor, whereas the palmitoyl-protein interaction observed for Cys322 suggests a more specific interaction that affects the stability of the dark state of rhodopsin. PMID:22280374

  14. Function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations

    SciTech Connect

    Nutt, David; Smith, Jeremy C

    2008-10-01

    Atomistic molecular dynamics simulations are used to investigate the mechanism by which the antifreeze protein from the spruce budworm, Choristoneura fumiferana, binds to ice. Comparison of structural and dynamic properties of the water around the three faces of the triangular prism-shaped protein in aqueous solution reveals that at low temperature the water structure is ordered and the dynamics slowed down around the ice-binding face of the protein, with a disordering effect observed around the other two faces. These results suggest a dual role for the solvation water around the protein. The preconfigured solvation shell around the ice-binding face is involved in the initial recognition and binding of the antifreeze protein to ice by lowering the barrier for binding and consolidation of the protein:ice interaction surface. Thus, the antifreeze protein can bind to the molecularly rough ice surface by becoming actively involved in the formation of its own binding site. Also, the disruption of water structure around the rest of the protein helps prevent the adsorbed protein becoming covered by further ice growth.

  15. Molecular Dynamic Simulations Reveal the Structural Determinants of Fatty Acid Binding to Oxy-Myoglobin

    PubMed Central

    Chintapalli, Sree V.; Bhardwaj, Gaurav; Patel, Reema; Shah, Natasha; Patterson, Randen L.; van Rossum, Damian B.; Anishkin, Andriy; Adams, Sean H.

    2015-01-01

    The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolites; however, the binding pocket and regulation of the interaction remains to be established. In this study, we employed a computational strategy to elucidate the structural determinants of fatty acids (palmitic & oleic acid) binding to Mb. Sequence analysis and docking simulations with a horse (Equus caballus) structural Mb reference reveals a fatty acid-binding site in the hydrophobic cleft near the heme region in Mb. Both palmitic acid and oleic acid attain a “U” shaped structure similar to their conformation in pockets of other fatty acid-binding proteins. Specifically, we found that the carboxyl head group of palmitic acid coordinates with the amino group of Lys45, whereas the carboxyl group of oleic acid coordinates with both the amino groups of Lys45 and Lys63. The alkyl tails of both fatty acids are supported by surrounding hydrophobic residues Leu29, Leu32, Phe33, Phe43, Phe46, Val67, Val68 and Ile107. In the saturated palmitic acid, the hydrophobic tail moves freely and occasionally penetrates deeper inside the hydrophobic cleft, making additional contacts with Val28, Leu69, Leu72 and Ile111. Our simulations reveal a dynamic and stable binding pocket in which the oxygen molecule and heme group in Mb are required for additional hydrophobic interactions. Taken together, these findings support a mechanism in which Mb acts as a muscle transporter for fatty acid when it is in the oxygenated state and releases fatty acid when Mb converts to deoxygenated state. PMID:26030763

  16. Molecular dynamic simulations reveal the structural determinants of Fatty Acid binding to oxy-myoglobin.

    PubMed

    Chintapalli, Sree V; Bhardwaj, Gaurav; Patel, Reema; Shah, Natasha; Patterson, Randen L; van Rossum, Damian B; Anishkin, Andriy; Adams, Sean H

    2015-01-01

    The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolites; however, the binding pocket and regulation of the interaction remains to be established. In this study, we employed a computational strategy to elucidate the structural determinants of fatty acids (palmitic & oleic acid) binding to Mb. Sequence analysis and docking simulations with a horse (Equus caballus) structural Mb reference reveals a fatty acid-binding site in the hydrophobic cleft near the heme region in Mb. Both palmitic acid and oleic acid attain a "U" shaped structure similar to their conformation in pockets of other fatty acid-binding proteins. Specifically, we found that the carboxyl head group of palmitic acid coordinates with the amino group of Lys45, whereas the carboxyl group of oleic acid coordinates with both the amino groups of Lys45 and Lys63. The alkyl tails of both fatty acids are supported by surrounding hydrophobic residues Leu29, Leu32, Phe33, Phe43, Phe46, Val67, Val68 and Ile107. In the saturated palmitic acid, the hydrophobic tail moves freely and occasionally penetrates deeper inside the hydrophobic cleft, making additional contacts with Val28, Leu69, Leu72 and Ile111. Our simulations reveal a dynamic and stable binding pocket in which the oxygen molecule and heme group in Mb are required for additional hydrophobic interactions. Taken together, these findings support a mechanism in which Mb acts as a muscle transporter for fatty acid when it is in the oxygenated state and releases fatty acid when Mb converts to deoxygenated state. PMID:26030763

  17. Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model

    PubMed Central

    Zeng, Xiaojun; Zhang, Liyun; Xiao, Xiuchan; Jiang, Yuanyuan; Guo, Yanzhi; Yu, Xinyan; Pu, Xuemei; Li, Menglong

    2016-01-01

    Thrombin-binding aptamer (TBA) with the sequence 5′GGTTGGTGTGGTTGG3′ could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation. PMID:27045335

  18. Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model

    NASA Astrophysics Data System (ADS)

    Zeng, Xiaojun; Zhang, Liyun; Xiao, Xiuchan; Jiang, Yuanyuan; Guo, Yanzhi; Yu, Xinyan; Pu, Xuemei; Li, Menglong

    2016-04-01

    Thrombin-binding aptamer (TBA) with the sequence 5‧GGTTGGTGTGGTTGG3‧ could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation.

  19. The Gating Mechanism of the Human Aquaporin 5 Revealed by Molecular Dynamics Simulations

    PubMed Central

    Janosi, Lorant; Ceccarelli, Matteo

    2013-01-01

    Aquaporins are protein channels located across the cell membrane with the role of conducting water or other small sugar alcohol molecules (aquaglyceroporins). The high-resolution X-ray structure of the human aquaporin 5 (HsAQP5) shows that HsAQP5, as all the other known aquaporins, exhibits tetrameric structure. By means of molecular dynamics simulations we analyzed the role of spontaneous fluctuations on the structural behavior of the human AQP5. We found that different conformations within the tetramer lead to a distribution of monomeric channel structures, which can be characterized as open or closed. The switch between the two states of a channel is a tap-like mechanism at the cytoplasmic end which regulates the water passage through the pore. The channel is closed by a translation of the His67 residue inside the pore. Moreover, water permeation rate calculations revealed that the selectivity filter, located at the other end of the channel, regulates the flow rate of water molecules when the channel is open, by locally modifying the orientation of His173. Furthermore, the calculated permeation rates of a fully open channel are in good agreement with the reported experimental value. PMID:23565173

  20. Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands

    NASA Astrophysics Data System (ADS)

    Vettoretti, Gerolamo; Moroni, Elisabetta; Sattin, Sara; Tao, Jiahui; Agard, David A.; Bernardi, Anna; Colombo, Giorgio

    2016-04-01

    Controlling biochemical pathways through chemically designed modulators may provide novel opportunities to develop therapeutic drugs and chemical tools. The underlying challenge is to design new molecular entities able to act as allosteric chemical switches that selectively turn on/off functions by modulating the conformational dynamics of their target protein. We examine the origins of the stimulation of ATPase and closure kinetics in the molecular chaperone Hsp90 by allosteric modulators through atomistic molecular dynamics (MD) simulations and analysis of protein-ligand interactions. In particular, we focus on the cross-talk between allosteric ligands and protein conformations and its effect on the dynamic properties of the chaperone’s active state. We examine the impact of different allosteric modulators on the stability, structural and internal dynamics properties of Hsp90 closed state. A critical aspect of this study is the development of a quantitative model that correlates Hsp90 activation to the presence of a certain compound, making use of information on the dynamic adaptation of protein conformations to the presence of the ligand, which allows to capture conformational states relevant in the activation process. We discuss the implications of considering the conformational dialogue between allosteric ligands and protein conformations for the design of new functional modulators.

  1. Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands

    PubMed Central

    Vettoretti, Gerolamo; Moroni, Elisabetta; Sattin, Sara; Tao, Jiahui; Agard, David A.; Bernardi, Anna; Colombo, Giorgio

    2016-01-01

    Controlling biochemical pathways through chemically designed modulators may provide novel opportunities to develop therapeutic drugs and chemical tools. The underlying challenge is to design new molecular entities able to act as allosteric chemical switches that selectively turn on/off functions by modulating the conformational dynamics of their target protein. We examine the origins of the stimulation of ATPase and closure kinetics in the molecular chaperone Hsp90 by allosteric modulators through atomistic molecular dynamics (MD) simulations and analysis of protein-ligand interactions. In particular, we focus on the cross-talk between allosteric ligands and protein conformations and its effect on the dynamic properties of the chaperone’s active state. We examine the impact of different allosteric modulators on the stability, structural and internal dynamics properties of Hsp90 closed state. A critical aspect of this study is the development of a quantitative model that correlates Hsp90 activation to the presence of a certain compound, making use of information on the dynamic adaptation of protein conformations to the presence of the ligand, which allows to capture conformational states relevant in the activation process. We discuss the implications of considering the conformational dialogue between allosteric ligands and protein conformations for the design of new functional modulators. PMID:27032695

  2. Unique aspects of the structure and dynamics of elementary Iβ cellulose microfibrils revealed by computational simulations.

    PubMed

    Oehme, Daniel P; Downton, Matthew T; Doblin, Monika S; Wagner, John; Gidley, Michael J; Bacic, Antony

    2015-05-01

    The question of how many chains an elementary cellulose microfibril contains is critical to understanding the molecular mechanism(s) of cellulose biosynthesis and regulation. Given the hexagonal nature of the cellulose synthase rosette, it is assumed that the number of chains must be a multiple of six. We present molecular dynamics simulations on three different models of Iβ cellulose microfibrils, 18, 24, and 36 chains, to investigate their structure and dynamics in a hydrated environment. The 36-chain model stays in a conformational space that is very similar to the initial crystalline phase, while the 18- and 24-chain models sample a conformational space different from the crystalline structure yet similar to conformations observed in recent high-temperature molecular dynamics simulations. Major differences in the conformations sampled between the different models result from changes to the tilt of chains in different layers, specifically a second stage of tilt, increased rotation about the O2-C2 dihedral, and a greater sampling of non-TG exocyclic conformations, particularly the GG conformation in center layers and GT conformation in solvent-exposed exocyclic groups. With a reinterpretation of nuclear magnetic resonance data, specifically for contributions made to the C6 peak, data from the simulations suggest that the 18- and 24-chain structures are more viable models for an elementary cellulose microfibril, which also correlates with recent scattering and diffraction experimental data. These data inform biochemical and molecular studies that must explain how a six-particle cellulose synthase complex rosette synthesizes microfibrils likely comprised of either 18 or 24 chains. PMID:25786828

  3. Mechanism of Mcl-1 Conformational Regulation Upon Small Molecule Binding Revealed by Molecular Dynamic Simulation.

    PubMed

    Wang, Anhui; Song, Ting; Wang, Ziqian; Liu, Yubo; Fan, Yudan; Zhang, Yahui; Zhang, Zhichao

    2016-04-01

    Inhibition of interactions between Mcl-1 and proapoptotic proteins is considered to be a therapeutic strategy to induce apoptosis in cancer cells. Here, we adopted molecular dynamics simulation with molecular mechanics-Poisson Boltzmann/surface area method (MM-PB/SA) to study the inhibition mechanism of three Mcl-1 inhibitors, compounds 1, 2 and 3. Analysis of energy components shows that the better binding free energy of compound 3 than compounds 1 and 2 is attributable to the van der Waals energy (ΔEvdw ) and non-polar solvation energy (ΔGnp ) upon binding. In addition to the excellent agreement with previous experimentally determined affinities, our simulation results further show a bend of helix 4 on Mcl-1 upon compound 3 binding, which is driven by hydrophobic interaction with residue Val(253) , leading to a narrowed BH3-binding groove to impede Puma(BH) (3) binding. The computational result is consistent with our competitive isothermal titration calorimetry (ITC) assays, which shows that the competitive ability of compound 3 toward Mcl-1/Puma(BH) (3) complex is improved beyond its direct binding affinity toward Mcl-1 itself, and compound 3 exhibits much more efficiency to compete with Puma(BH) (3) than compound 2. Our study provides a new strategy to improve inhibitory activity on Mcl-1 based on the conformational dynamic change. PMID:26518611

  4. A model of lipid-free Apolipoprotein A-I revealed by iterative molecular dynamics simulation

    DOE PAGESBeta

    Zhang, Xing; Lei, Dongsheng; Zhang, Lei; Rames, Matthew; Zhang, Shengli

    2015-03-20

    Apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS). Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore,more » by integrating various experimental results, we proposed a new structural model for lipidfree apo A-I, which contains a bundled four-helix N-terminal domain (1–192) that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193–243). This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation.« less

  5. A model of lipid-free Apolipoprotein A-I revealed by iterative molecular dynamics simulation

    SciTech Connect

    Zhang, Xing; Lei, Dongsheng; Zhang, Lei; Rames, Matthew; Zhang, Shengli

    2015-03-20

    Apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS). Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore, by integrating various experimental results, we proposed a new structural model for lipidfree apo A-I, which contains a bundled four-helix N-terminal domain (1–192) that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193–243). This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation.

  6. A Model of Lipid-Free Apolipoprotein A-I Revealed by Iterative Molecular Dynamics Simulation

    PubMed Central

    Zhang, Xing; Lei, Dongsheng; Zhang, Lei; Rames, Matthew; Zhang, Shengli

    2015-01-01

    Apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS). Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore, by integrating various experimental results, we proposed a new structural model for lipid-free apo A-I, which contains a bundled four-helix N-terminal domain (1–192) that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193–243). This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation. PMID:25793886

  7. Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

    SciTech Connect

    Naritomi, Yusuke; Fuchigami, Sotaro

    2013-12-07

    We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of C{sub α} atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

  8. Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

    NASA Astrophysics Data System (ADS)

    Naritomi, Yusuke; Fuchigami, Sotaro

    2013-12-01

    We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of Cα atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

  9. Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations.

    PubMed

    Li, Yan; Li, Xiang; Dong, Zigang

    2014-10-14

    In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4-ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level. PMID:25231537

  10. Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design.

    PubMed

    Tan, Yaw Sing; Reeks, Judith; Brown, Christopher J; Thean, Dawn; Ferrer Gago, Fernando Jose; Yuen, Tsz Ying; Goh, Eunice Tze Leng; Lee, Xue Er Cheryl; Jennings, Claire E; Joseph, Thomas L; Lakshminarayanan, Rajamani; Lane, David P; Noble, Martin E M; Verma, Chandra S

    2016-09-01

    Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although they have proven hugely successful at reproducing experimental structural data, their ability to predict new binding sites that are yet to be identified and characterized has not been demonstrated. Here, we report the use of benzenes as probe molecules in ligand-mapping MD (LMMD) simulations to predict the existence of two novel binding sites on the surface of the oncoprotein MDM2. One of them was serendipitously confirmed by biophysical assays and X-ray crystallography to be important for the binding of a new family of hydrocarbon stapled peptides that were specifically designed to target the other putative site. These results highlight the predictive power of LMMD and suggest that predictions derived from LMMD simulations can serve as a reliable basis for the identification of novel ligand binding sites in structure-based drug design. PMID:27532490

  11. Molecular energetics in the capsomere of virus-like particle revealed by molecular dynamics simulations.

    PubMed

    Zhang, Lin; Tang, Ronghong; Bai, Shu; Connors, Natalie K; Lua, Linda H L; Chuan, Yap P; Middelberg, Anton P J; Sun, Yan

    2013-05-01

    Virus-like particles (VLPs) are highly organized nanoparticles that have great potential in vaccinology, gene therapy, drug delivery, and materials science. However, the application of VLPs is hindered by obstacles in their design and production due to low efficiency of self-assembly. In the present study, all-atom (AA) molecular dynamics (MD) simulations coupled with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method are utilized to examine the molecular interactions in the capsomere of a murine polyomavirus (MPV) VLP. It is found that both low ionic strength and the intracapsomere disulfide bonds are favorable for maintaining a stable capsomere. Simulation results examining the effects of solution conditions on the stabilization of a capsomere were verified by calorimetry experiments. Simulation results of free energy decomposition indicate that hydrophobic interaction is favorable for the formation of a capsomere, whereas electrostatic interaction is unfavorable. With increasing ionic strength, the dominant interaction for the stabilization of a capsomere changes from hydrophobic to electrostatic. By comprehensive analyses, the key amino acid residues (hot spots) in VP1 protein aiding formation of a capsomere in different solution conditions have been identified. These results provide molecular insights into the stabilization of building blocks for VLP and are expected to have implications in their partitioning between the correct and off-pathway reactions in VLP assembly. PMID:23586433

  12. Looking inside the tube: what molecular dynamics simulations are revealing about polymer entanglements

    NASA Astrophysics Data System (ADS)

    Larson, Ron

    2007-03-01

    Using concepts developed over the years by de Gennes, Doi, Edwards, Marrucci, Rubinstein, McLeish, Milner, and others, a kind of ``standard model'' for entangled polymer relaxation and rheology has been developed, which, like the ``standard model'' of high-energy physics, has a number of ad hoc assumptions and fitting parameters. The ``standard model'' of polymer relaxation is based on a phenomenological ``tube'' surrounding each polymer chain that represents the effect on that chain of non-crossability constraints imposed by surrounding chains. As a result of its confinement to the tube, the chain relaxes by reptation -- or sliding along the tube, accordion-like fluctuations of the chain within the tube, and movement of, or dilation of, the tube due to motion of the surrounding chains creating the tube-like region. Increasing computer speed and advanced simulation methods are now making possible the direct molecular dynamics simulations of entangled polymers resolved at the monomer scale, over time scales sufficient to test the underlying assumptions of the tube model and allow direct calculation of some of the phenomenological parameters. Here we illustrate how these simulations allow us to estimate the distribution of tube lengths, the average diameter of the tube, and the mobility of the branch point in a simple ``star'' branched polymer. These findings confirm the validity of the tube ansatz, but suggest that some corrections to the ``standard model'' may be needed.

  13. ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin

    PubMed Central

    Lawrimore, Josh; Aicher, Joseph K.; Hahn, Patrick; Fulp, Alyona; Kompa, Ben; Vicci, Leandra; Falvo, Michael; Taylor, Russell M.; Bloom, Kerry

    2016-01-01

    ChromoShake is a three-dimensional simulator designed to find the thermodynamically favored states for given chromosome geometries. The simulator has been applied to a geometric model based on experimentally determined positions and fluctuations of DNA and the distribution of cohesin and condensin in the budding yeast centromere. Simulations of chromatin in differing initial configurations reveal novel principles for understanding the structure and function of a eukaryotic centromere. The entropic position of DNA loops mirrors their experimental position, consistent with their radial displacement from the spindle axis. The barrel-like distribution of cohesin complexes surrounding the central spindle in metaphase is a consequence of the size of the DNA loops within the pericentromere to which cohesin is bound. Linkage between DNA loops of different centromeres is requisite to recapitulate experimentally determined correlations in DNA motion. The consequences of radial loops and cohesin and condensin binding are to stiffen the DNA along the spindle axis, imparting an active function to the centromere in mitosis. PMID:26538024

  14. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    PubMed Central

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang

    2015-01-01

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL. PMID:25737239

  15. Molecular Dynamics Simulation and Statistics Analysis Reveals the Defense Response Mechanism in Plants

    NASA Astrophysics Data System (ADS)

    Liu, Zhichao; Zhao, Yunjie; Zeng, Chen; Computational Biophysics Lab Team

    As the main protein of the bacterial flagella, flagellin plays an important role in perception and defense response. The newly discovered locus, FLS2, is ubiquitously expressed. FLS2 encodes a putative receptor kinase and shares many homologies with some plant resistance genes and even with some components of immune system of mammals and insects. In Arabidopsis, FLS2 perception is achieved by the recognition of epitope flg22, which induces FLS2 heteromerization with BAK1 and finally the plant immunity. Here we use both analytical methods such as Direct Coupling Analysis (DCA) and Molecular Dynamics (MD) Simulations to get a better understanding of the defense mechanism of FLS2. This may facilitate a redesign of flg22 or de-novo design for desired specificity and potency to extend the immune properties of FLS2 to other important crops and vegetables.

  16. Docking Studies and Molecular Dynamic Simulations Reveal Different Features of IDO1 Structure.

    PubMed

    Greco, Francesco Antonio; Bournique, Answald; Coletti, Alice; Custodi, Chiara; Dolciami, Daniela; Carotti, Andrea; Macchiarulo, Antonio

    2016-09-01

    In the last decade, indoleamine 2,3-dioxygenase 1 (IDO1) has attracted a great deal of attention being recognized as key regulator of immunosuppressive pathways in the tumor immuno-editing process. Several classes of inhibitors have been developed as potential anticancer agents, but only few of them have advanced in clinical trials. Hence, the quest of novel potent and selective inhibitors of the enzyme is still active and mostly pursued by structure-based drug design strategies based on early and more recent crystal structures of IDO1. Combining docking studies and molecular dynamic simulations, in this work we have comparatively investigated the structural features of each crystal structure of IDO1. The results pinpoint different features in specific crystal structures of the enzyme that may benefit the medicinal chemistry arena aiding the design of novel potent and selective inhibitors of IDO1. PMID:27546049

  17. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    DOE PAGESBeta

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; et al

    2015-03-04

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobicmore » environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.« less

  18. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    SciTech Connect

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang

    2015-03-04

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.

  19. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang

    2015-03-01

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.

  20. Molecular Dynamics Simulations Reveal that Water Diffusion between Graphene Oxide Layers is Slow

    NASA Astrophysics Data System (ADS)

    Devanathan, Ram; Chase-Woods, Dylan; Shin, Yongsoon; Gotthold, David W.

    2016-07-01

    Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of an integrated study that combines experiment and molecular dynamics simulation of water intercalated between GO layers. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in layer spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 15% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. Slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step.

  1. Molecular Dynamics Simulations Reveal that Water Diffusion between Graphene Oxide Layers is Slow.

    PubMed

    Devanathan, Ram; Chase-Woods, Dylan; Shin, Yongsoon; Gotthold, David W

    2016-01-01

    Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of an integrated study that combines experiment and molecular dynamics simulation of water intercalated between GO layers. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in layer spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 15% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. Slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step. PMID:27388562

  2. Molecular Dynamics Simulations Reveal that Water Diffusion between Graphene Oxide Layers is Slow

    PubMed Central

    Devanathan, Ram; Chase-Woods, Dylan; Shin, Yongsoon; Gotthold, David W.

    2016-01-01

    Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of an integrated study that combines experiment and molecular dynamics simulation of water intercalated between GO layers. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in layer spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 15% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. Slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step. PMID:27388562

  3. The Dynamic Conformational Cycle of the Group I Chaperonin C-Termini Revealed via Molecular Dynamics Simulation

    PubMed Central

    Dalton, Kevin M.; Frydman, Judith; Pande, Vijay S.

    2015-01-01

    Chaperonins are large ring shaped oligomers that facilitate protein folding by encapsulation within a central cavity. All chaperonins possess flexible C-termini which protrude from the equatorial domain of each subunit into the central cavity. Biochemical evidence suggests that the termini play an important role in the allosteric regulation of the ATPase cycle, in substrate folding and in complex assembly and stability. Despite the tremendous wealth of structural data available for numerous orthologous chaperonins, little structural information is available regarding the residues within the C-terminus. Herein, molecular dynamics simulations are presented which localize the termini throughout the nucleotide cycle of the group I chaperonin, GroE, from Escherichia coli. The simulation results predict that the termini undergo a heretofore unappreciated conformational cycle which is coupled to the nucleotide state of the enzyme. As such, these results have profound implications for the mechanism by which GroE utilizes nucleotide and folds client proteins. PMID:25822285

  4. The dynamic conformational cycle of the group I chaperonin C-termini revealed via molecular dynamics simulation.

    PubMed

    Dalton, Kevin M; Frydman, Judith; Pande, Vijay S

    2015-01-01

    Chaperonins are large ring shaped oligomers that facilitate protein folding by encapsulation within a central cavity. All chaperonins possess flexible C-termini which protrude from the equatorial domain of each subunit into the central cavity. Biochemical evidence suggests that the termini play an important role in the allosteric regulation of the ATPase cycle, in substrate folding and in complex assembly and stability. Despite the tremendous wealth of structural data available for numerous orthologous chaperonins, little structural information is available regarding the residues within the C-terminus. Herein, molecular dynamics simulations are presented which localize the termini throughout the nucleotide cycle of the group I chaperonin, GroE, from Escherichia coli. The simulation results predict that the termini undergo a heretofore unappreciated conformational cycle which is coupled to the nucleotide state of the enzyme. As such, these results have profound implications for the mechanism by which GroE utilizes nucleotide and folds client proteins. PMID:25822285

  5. Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations.

    PubMed

    Sun, Tianjun; Gauthier, Sherry Y; Campbell, Robert L; Davies, Peter L

    2015-10-01

    Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein-protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein-protein crystal contacts with few surface waters. Here we have changed the protein-protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. The waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters. PMID:26371748

  6. The biophysical properties of ethanolamine plasmalogens revealed by atomistic molecular dynamics simulations.

    PubMed

    Rog, Tomasz; Koivuniemi, Artturi

    2016-01-01

    Given the importance of plasmalogens in cellular membranes and neurodegenerative diseases, a better understanding of how plasmalogens affect the lipid membrane properties is needed. Here we carried out molecular dynamics simulations to study a lipid membrane comprised of ethanolamine plasmalogens (PE-plasmalogens). We compared the results to the PE-diacyl counterpart and palmitoyl-oleyl-phosphatidylcholine (POPC) bilayers. Results show that PE-plasmalogens form more compressed, thicker, and rigid lipid bilayers in comparison with the PE-diacyl and POPC membranes. The results also point out that the vinyl-ether linkage increases the ordering of sn-1 chain substantially and the ordering of the sn-2 chain to a minor extent. Further, the vinyl-ether linkage changes the orientation of the lipid head group, but it does not cause changes in the head group and glycerol backbone tilt angles with respect to the bilayer normal. The vinyl-ether linkage also packs the proximal regions of the sn-1 and sn-2 chains more closely together which also decreases the distance between the rest of the sn-1 and sn-2 chains. PMID:26522077

  7. Mechanisms of triggering H1 helix in prion proteins unfolding revealed by molecular dynamic simulation

    NASA Astrophysics Data System (ADS)

    Tseng, Chih-Yuan; Lee, H. C.

    2006-03-01

    In template-assistance model, normal Prion protein (PrP^C), the pathogen to cause several prion diseases such as Creutzfeldt-Jakob (CJD) in human, Bovine Spongiform Encephalopathy (BSE) in cow, and scrapie in sheep, converts to infectious prion (PrP^Sc) through a transient interaction with PrP^Sc. Furthermore, conventional studies showed S1-H1-S2 region in PrP^C to be the template of S1-S2 β-sheet in PrP^Sc, and Prion protein's conformational conversion may involve an unfolding of H1 and refolding into β-sheet. Here we prepare several mouse prion peptides that contain S1-H1-S2 region with specific different structures, which are corresponding to specific interactions, to investigate possible mechanisms to trigger H1 α-helix unfolding process via molecular dynamic simulation. Three properties, conformational transition, salt-bridge in H1, and hydrophobic solvent accessible surface (SAS) are analyzed. From these studies, we found the interaction that triggers H1 unfolding to be the one that causes dihedral angle at residue Asn^143 changes. Whereas interactions that cause S1 segment's conformational changes play a minor in this process. These studies offers an additional evidence for template-assistance model.

  8. The biophysical properties of ethanolamine plasmalogens revealed by atomistic molecular dynamics simulations

    PubMed Central

    Rog, Tomasz; Koivuniemi, Artturi

    2016-01-01

    Given the importance of plasmalogens in cellular membranes and neurodegenerative diseases, a better understanding of how plasmalogens affect the lipid membrane properties is needed. Here we carried out molecular dynamics simulations to study a lipid membrane comprised of ethanolamine plasmalogens (PE–plasmalogens). We compared the results to the PE–diacyl counterpart and palmitoyl-oleyl-phosphatidylcholine (POPC) bilayers. Results show that PE–plasmalogens form more compressed, thicker, and rigid lipid bilayers in comparison with the PE–diacyl and POPC membranes. The results also point out that the vinyl–ether linkage increases the ordering of sn-1 chain substantially and the ordering of the sn-2 chain to a minor extent. Further, the vinyl–ether linkage changes the orientation of the lipid head group, but it does not cause changes in the head group and glycerol backbone tilt angles with respect to the bilayer normal. The vinyl–ether linkage also packs the proximal regions of the sn-1 and sn-2 chains more closely together which also decreases the distance between the rest of the sn-1 and sn-2 chains. PMID:26522077

  9. Mechanisms of crazing in glassy polymers revealed by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mahajan, Dhiraj K.; Hartmaier, Alexander

    2012-08-01

    Mechanisms leading to initiation of crazing type failure in a glassy polymer are not clearly understood. This is mainly due to the difficulty in characterizing the stress state and polymer configuration sufficiently locally at the craze initiation site. Using molecular dynamics simulations, we have now been able to access this information and have shown that the local heterogeneous deformation leads to craze initiation in glassy polymers. We found that zones of high plastic activity are constrained by their neighborhood and become unstable, initiating crazing from these sites. Furthermore, based on the constant flow stresses observed in the unstable zones, we conclude that microcavitation is the essential local deformation mode to trigger crazing in glassy polymers. Our results demonstrate the basic difference in the local deformation mode as well as the conditions that lead to either shear-yielding or crazing type failures in glassy polymers. We anticipate our paper to help in devising a new criterion for craze initiation that not only considers the stress state, but also considers local deformation heterogeneities that form the necessary condition for crazing in glassy polymers.

  10. Mechanisms of crazing in glassy polymers revealed by molecular dynamics simulations.

    PubMed

    Mahajan, Dhiraj K; Hartmaier, Alexander

    2012-08-01

    Mechanisms leading to initiation of crazing type failure in a glassy polymer are not clearly understood. This is mainly due to the difficulty in characterizing the stress state and polymer configuration sufficiently locally at the craze initiation site. Using molecular dynamics simulations, we have now been able to access this information and have shown that the local heterogeneous deformation leads to craze initiation in glassy polymers. We found that zones of high plastic activity are constrained by their neighborhood and become unstable, initiating crazing from these sites. Furthermore, based on the constant flow stresses observed in the unstable zones, we conclude that microcavitation is the essential local deformation mode to trigger crazing in glassy polymers. Our results demonstrate the basic difference in the local deformation mode as well as the conditions that lead to either shear-yielding or crazing type failures in glassy polymers. We anticipate our paper to help in devising a new criterion for craze initiation that not only considers the stress state, but also considers local deformation heterogeneities that form the necessary condition for crazing in glassy polymers. PMID:23005778

  11. Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Liu, Fu-Feng; Ji, Luo; Zhang, Lin; Dong, Xiao-Yan; Sun, Yan

    2010-06-01

    Molecular dynamics simulations of chymotrypsin inhibitor 2 in different polyols (glycerol, xylitol, sorbitol, trehalose, and sucrose) at 363 K were performed to probe the molecular basis of the stabilizing effect, and the data in water, ethanol, and glycol were compared. It is found that protein protection by polyols is positively correlated with both the molecular volume and the fractional polar surface area, and the former contributes more significantly to the protein's stability. Polyol molecules have only a few direct hydrogen bonds with the protein, and the number of hydrogen bonds between a polyol and the protein is similar for different polyols. Thus, it is concluded that the direct interactions contribute little to the stabilizing effect. It is clarified that the preferential exclusion of the polyols is the origin of their protective effects, and it increases with increasing polyol size. Namely, there is preferential hydration on the protein surface (2 Å), and polyol molecules cluster around the protein at a distance of about 4 Å. The preferential exclusion of polyols leads to indirect interactions that prevent the protein from thermal unfolding. The water structure becomes more ordered with increasing the polyol size. So, the entropy of water in the first hydration shell decreases, and a larger extent of decrease is observed with increasing polyol size, leading to larger transfer free energy. The findings suggest that polyols protect the protein from thermal unfolding via indirect interactions. The work has thus elucidated the molecular mechanism of structural stability of the protein in polyol solutions.

  12. Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations.

    PubMed

    Liu, Fu-Feng; Ji, Luo; Zhang, Lin; Dong, Xiao-Yan; Sun, Yan

    2010-06-14

    Molecular dynamics simulations of chymotrypsin inhibitor 2 in different polyols (glycerol, xylitol, sorbitol, trehalose, and sucrose) at 363 K were performed to probe the molecular basis of the stabilizing effect, and the data in water, ethanol, and glycol were compared. It is found that protein protection by polyols is positively correlated with both the molecular volume and the fractional polar surface area, and the former contributes more significantly to the protein's stability. Polyol molecules have only a few direct hydrogen bonds with the protein, and the number of hydrogen bonds between a polyol and the protein is similar for different polyols. Thus, it is concluded that the direct interactions contribute little to the stabilizing effect. It is clarified that the preferential exclusion of the polyols is the origin of their protective effects, and it increases with increasing polyol size. Namely, there is preferential hydration on the protein surface (2 A), and polyol molecules cluster around the protein at a distance of about 4 A. The preferential exclusion of polyols leads to indirect interactions that prevent the protein from thermal unfolding. The water structure becomes more ordered with increasing the polyol size. So, the entropy of water in the first hydration shell decreases, and a larger extent of decrease is observed with increasing polyol size, leading to larger transfer free energy. The findings suggest that polyols protect the protein from thermal unfolding via indirect interactions. The work has thus elucidated the molecular mechanism of structural stability of the protein in polyol solutions. PMID:20550422

  13. Three steps to gold: mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations.

    PubMed

    Ozboyaci, M; Kokh, D B; Wade, R C

    2016-04-21

    The addition of three N-terminal histidines to β-lactamase inhibitor protein was shown experimentally to increase its binding potency to an Au(111) surface substantially but the binding mechanism was not resolved. Here, we propose a complete adsorption mechanism for this fusion protein by means of a multi-scale simulation approach and free energy calculations. We find that adsorption is a three-step process: (i) recognition of the surface predominantly by the histidine fusion peptide and formation of an encounter complex facilitated by a reduced dielectric screening of water in the interfacial region, (ii) adsorption of the protein on the surface and adoption of a specific binding orientation, and (iii) adaptation of the protein structure on the metal surface accompanied by induced fit. We anticipate that the mechanistic features of protein adsorption to an Au(111) surface revealed here can be extended to other inorganic surfaces and proteins and will therefore aid the design of specific protein-surface interactions. PMID:27021898

  14. Revealing the toughening mechanism of graphene-polymer nanocomposite through molecular dynamics simulation.

    PubMed

    Liu, Jun; Shen, Jianxiang; Zheng, Zijian; Wu, Youping; Zhang, Liqun

    2015-07-24

    By employing united atom molecular dynamics simulation, we have investigated the effects of polymer-graphene interaction ε(np) volume fraction of grapheme φ thermodynamics of polymer matrix (rubbery versus glassy), interfacial interaction in the case of the same dispersion state, shape of nanoparticles (NPs) such as C60 CNT and graphene at the same loading on the toughening efficiency of polymer nanocomposites. By beginning with the pure polymer, we observe that a plateau stress occurs at long chain length because entangled polymer chains in fibrils cannot become broken. We find that the work needed to dissipate during the failure increases with the increase of ε(np) and φ and the yield point in the stress-strain behavior occurs at a smaller strain for an attractive NPs filled system compared to the pure case, attributed to the more mechanically heterogeneous environment. The thermodynamics of the polymer matrix (below and above Tg) seems to have a significant effect on the toughening efficiency of graphene sheets. In the case of the same dispersion state, stronger interfacial interaction always induces long and highly orientated polymer fibrils along the deformation direction, with graphene sheets being encapsulated in these fiber-like bundles. By characterizing the interaction energy between polymer-polymer and polymer-graphene as a function of the strain, we find that the separation of polymer chains from the graphene sheets cease immediately after the yield point, followed by the continuous propagation of the cavities by excluding surrounded polymer chains and graphene sheets together. We also find that at the same attractive interfacial interaction and same loading, the toughening efficiency exhibits the following order: graphene > CNT > C60 Generally, the toughening mechanism of graphene sheets results from the formation of long and highly orientated polymer fibrils to prevent the occurrence of the rupture, which can be greatly improved by the strong

  15. Revealing the toughening mechanism of graphene-polymer nanocomposite through molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Liu, Jun; Shen, Jianxiang; Zheng, Zijian; Wu, Youping; Zhang, Liqun

    2015-07-01

    By employing united atom molecular dynamics simulation, we have investigated the effects of polymer-graphene interaction {\\varepsilon }np, volume fraction of graphene φ , thermodynamics of polymer matrix (rubbery versus glassy), interfacial interaction in the case of the same dispersion state, shape of nanoparticles (NPs) such as {{{C}}}60, CNT and graphene at the same loading on the toughening efficiency of polymer nanocomposites. By beginning with the pure polymer, we observe that a plateau stress occurs at long chain length because entangled polymer chains in fibrils cannot become broken. We find that the work needed to dissipate during the failure increases with the increase of {\\varepsilon }np and φ , and the yield point in the stress-strain behavior occurs at a smaller strain for an attractive NPs filled system compared to the pure case, attributed to the more mechanically heterogeneous environment. The thermodynamics of the polymer matrix (below and above Tg) seems to have a significant effect on the toughening efficiency of graphene sheets. In the case of the same dispersion state, stronger interfacial interaction always induces long and highly orientated polymer fibrils along the deformation direction, with graphene sheets being encapsulated in these fiber-like bundles. By characterizing the interaction energy between polymer-polymer and polymer-graphene as a function of the strain, we find that the separation of polymer chains from the graphene sheets cease immediately after the yield point, followed by the continuous propagation of the cavities by excluding surrounded polymer chains and graphene sheets together. We also find that at the same attractive interfacial interaction and same loading, the toughening efficiency exhibits the following order: graphene > CNT > {{{C}}}60. Generally, the toughening mechanism of graphene sheets results from the formation of long and highly orientated polymer fibrils to prevent the occurrence of the rupture, which

  16. Structural Diversity of Ligand-Binding Androgen Receptors Revealed by Microsecond Long Molecular Dynamics Simulations and Enhanced Sampling.

    PubMed

    Duan, Mojie; Liu, Na; Zhou, Wenfang; Li, Dan; Yang, Minghui; Hou, Tingjun

    2016-09-13

    Androgen receptor (AR) plays important roles in the development of prostate cancer (PCa). The antagonistic drugs, which suppress the activity of AR, are widely used in the treatment of PCa. However, the molecular mechanism of antagonism about how ligands affect the structures of AR remains elusive. To better understand the conformational variability of ARs bound with agonists or antagonists, we performed long time unbiased molecular dynamics (MD) simulations and enhanced sampling simulations for the ligand binding domain of AR (AR-LBD) in complex with various ligands. Based on the simulation results, we proposed an allosteric pathway linking ligands and helix 12 (H12) of AR-LBD, which involves the interactions among the ligands and the residues W741, H874, and I899. The interaction pathway provides an atomistic explanation of how ligands affect the structure of AR-LBD. A repositioning of H12 was observed, but it is facilitated by the C-terminal of H12, instead of by the loop between helix 11 (H11) and H12. The bias-exchange metadynamics simulations further demonstrated the above observations. More importantly, the free energy profiles constructed by the enhanced sampling simulations revealed the transition process between the antagonistic form and agonistic form of AR-LBD. Our results would be helpful for the design of more efficient antagonists of AR to combat PCa. PMID:27560203

  17. Crystal Structures and Molecular Dynamics Simulations of Thermophilic Malate Dehydrogenase Reveal Critical Loop Motion for Co-Substrate Binding

    PubMed Central

    Luo, Huei-Ru; Wu, Szu-Pei; Hsu, Chun-Hua

    2013-01-01

    Malate dehydrogenase (MDH) catalyzes the conversion of oxaloacetate and malate by using the NAD/NADH coenzyme system. The system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in therapeutic applications and hormones. We elucidated the biochemical and structural features of MDH from Thermus thermophilus (TtMDH) for use in various biotechnological applications. The biochemical characterization of recombinant TtMDH revealed greatly increased activity above 60°C and specific activity of about 2,600 U/mg with optimal temperature of 90°C. Analysis of crystal structures of apo and NAD-bound forms of TtMDH revealed a slight movement of the binding loop and few structural elements around the co-substrate binding packet in the presence of NAD. The overall structures did not change much and retained all related positions, which agrees with the CD analyses. Further molecular dynamics (MD) simulation at higher temperatures were used to reconstruct structures from the crystal structure of TtMDH. Interestingly, at the simulated structure of 353 K, a large change occurred around the active site such that with increasing temperature, a mobile loop was closed to co-substrate binding region. From biochemical characterization, structural comparison and MD simulations, the thermal-induced conformational change of the co-substrate binding loop of TtMDH may contribute to the essential movement of the enzyme for admitting NAD and may benefit the enzyme's activity. PMID:24386145

  18. Dynamics simulation of soybean agglutinin (SBA) dimer reveals the impact of glycosylation on its enhanced structural stability.

    PubMed

    Halder, Swagata; Surolia, Avadhesha; Mukhopadhyay, Chaitali

    2016-06-16

    The legume lectins are widely used as a model system for studying protein-carbohydrate and protein-protein interactions. They exhibit a fascinating quaternary structure variation. Recently, it has become clear that lectins exist as oligomers. Soybean agglutinin is a tetrameric legume lectin, each of whose subunits are glycosylated. In the present study we explore the main origin for the stability of soybean agglutinin dimer. In order to understand the role of glycosylation on the dimeric interface, we have carried out normal (298K), high temperatures (380K, 500K) long explicit solvent molecular dynamics (MD) simulations and compared the structural and conformational changes between the glycosylated and non-glycosylated dimers. The study reveals that the high degree of stability at normal temperature is mostly contributed by interfacial ionic interactions (~200 kcal/mol) between polar residues like Lys, Arg, Asp, Thr, Ser, Asn and Gln (62%). It maintains its overall folded conformation due to high subunit interactions at the non-canonical interface. Mainly five important hydrogen bonds between CO of one β sheet of one subunit with the N-H of other β strand of the other subunit help to maintain the structural integrity. Ten inter subunit salt-bridge interactions between Arg 185-Asṕ192, Lys 163-Asṕ169, Asp 169-Lyś 163 and Asp 192-Arǵ 185 at non-canonical interface appear to be important to maintain the three dimensional structure of SBA dimer. Moreover, our simulation results revealed that increase in vibrational entropy could decrease the free energy and contribute to the glycan-induced stabilization by ~45 kcal/mol at normal temperature. PMID:27108103

  19. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Yu, Hang; Han, Wei; Ma, Wen; Schulten, Klaus

    2015-12-01

    Parkinson's disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and 3J(HNHCα)-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.

  20. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation

    SciTech Connect

    Yu, Hang; Ma, Wen; Han, Wei; Schulten, Klaus

    2015-12-28

    Parkinson’s disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and {sup 3}J(H{sub N}H{sub C{sub α}})-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.

  1. Energetic changes caused by antigenic module insertion in a virus-like particle revealed by experiment and molecular dynamics simulations.

    PubMed

    Zhang, Lin; Tang, Ronghong; Bai, Shu; Connors, Natalie K; Lua, Linda H L; Chuan, Yap P; Middelberg, Anton P J; Sun, Yan

    2014-01-01

    The success of recombinant virus-like particles (VLPs) for human papillomavirus and hepatitis B demonstrates the potential of VLPs as safe and efficacious vaccines. With new modular designs emerging, the effects of antigen module insertion on the self-assembly and structural integrity of VLPs should be clarified so as to better enabling improved design. Previous work has revealed insights into the molecular energetics of a VLP subunit, capsomere, comparing energetics within various solution conditions known to drive or inhibit self-assembly. In the present study, molecular dynamics (MD) simulations coupled with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method were performed to examine the molecular interactions and energetics in a modular capsomere of a murine polyomavirus (MPV) VLP designed to protect against influenza. Insertion of an influenza antigenic module is found to lower the binding energy within the capsomere, and a more active state is observed in Assembly Buffer as compared with that in Stabilization Buffer, which has been experimentally validated through measurements using differential scanning calorimetry. Further in-depth analysis based on free-energy decomposition indicates that destabilized binding can be attributed to electrostatic interaction induced by the chosen antigen module. These results provide molecular insights into the conformational stability of capsomeres and their abilities to be exploited for antigen presentation, and are expected to be beneficial for the biomolecular engineering of VLP vaccines. PMID:25215874

  2. Molecular dynamics simulations reveal highly permeable oxygen exit channels shared with water uptake channels in photosystem II.

    PubMed

    Vassiliev, Serguei; Zaraiskaya, Tatiana; Bruce, Doug

    2013-10-01

    Photosystem II (PSII) catalyzes the oxidation of water in the conversion of light energy into chemical energy in photosynthesis. Water delivery and oxygen removal from the oxygen evolving complex (OEC), buried deep within PSII, are critical requirements to facilitate the reaction and minimize reactive oxygen damage. It has often been assumed that water and oxygen travel through separate channels within PSII, as demonstrated in cytochrome c oxidase. This study describes all-atom molecular dynamics simulations of PSII designed to investigate channels by fully characterizing the distribution and permeation of both water and oxygen. Interestingly, most channels found in PSII were permeable to both oxygen and water, however individual channels exhibited different energetic barriers for the two solutes. Several routes for oxygen diffusion within PSII with low energy permeation barriers were found, ensuring its fast removal from the OEC. In contrast, all routes for water showed significant energy barriers, corresponding to a much slower permeation rate for water through PSII. Two major factors were responsible for this selectivity: (1) hydrogen bonds between water and channel amino acids, and (2) steric restraints. Our results reveal the presence of a shared network of channels in PSII optimized to both facilitate the quick removal of oxygen and effectively restrict the water supply to the OEC to help stabilize and protect it from small water soluble inhibitors. PMID:23816955

  3. Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mo, Yuxiang; Lu, Yan; Wei, Guanghong; Derreumaux, Philippe

    2009-03-01

    The human islet amyloid polypeptide (hIAPP) or amylin is a 37-residue hormone found as amyloid deposits in pancreatic extracts of nearly all type 2 diabetes patients. The fragment 20-29 of sequence SNNFGAILSS (hIAPP20-29) has been shown to be responsible for the amyloidogenic propensities of the full length protein. Various polymorphic forms of hIAPP20-29 fibrils were described by using Fourier transform infrared (FTIR) and solid-state NMR experiments: unseeded hIAPP20-29 fibril with out-of-register antiparallel β-strands, and two forms of seeded hIAPP20-29 fibril, with in-register antiparallel or in-register parallel β-strands. As a first step toward understanding this polymorphism, we explore the equilibrium structures of the soluble hIAPP20-29 trimer, using multiple molecular dynamics (MD) simulations with the Optimized Potential for Efficient structure Prediction (OPEP) coarse-grained implicit solvent force field for a total length of 3.2 μs. Although, the trimer is found mainly random coil, consistent with the signal measured experimentally during the lag phase of hIAPP20-29 fibril formation, the central FGAIL residues have a relative high propensity to form interpeptide β-sheets and antiparallel β-strands are more probable than parallel β-strands. One MD-predicted out-of-register antiparallel three-stranded β-sheet matches exactly the FTIR-derived unseeded hIAPP20-29 fibril model. Our simulations, however, do not reveal any evidence of in-register parallel or in-register antiparallel β-sheets as reported for seeded hIAPP20-29 fibrils. All these results indicate that fibril polymorphism is partially encoded in a trimer.

  4. A new insight into the conformation and melt dynamics of hydrogenated polybutadiene as revealed by computer simulations.

    PubMed

    Ramos, Javier; Vega, Juan F; Martínez-Salazar, Javier

    2016-05-01

    Extensive molecular dynamics simulations of the macromolecular conformation and the melt dynamics for model polymers of different molecular weights have been carried out. The selected models are hydrogenated polybutadienes with a 2% content of ethyl branches and linear polyethylene. It will be shown that the density and chain stiffness are clearly affected by both the molecular weight and the presence of ethyl branches. Furthermore, the results obtained from the simulations on the molecular size and, more remarkably, chain dynamics, perfectly match the neutron scattering experiments performed by Zamponi et al. in hydrogenated polybutadienes. We observe a clear chain contraction and a slow dynamics for the hydrogenated polybutadiene with respect to the linear chain of the same molecular length. Using the Likhtman-McLeish definitions, the obtained values of the entanglement relaxation time (τe) and the tube diameter (a) are found to be in agreement with the available experimental data (by rheology and neutron spin echo) as well as with those obtained by the simulations. Finally, a very good agreement of diffusion coefficients as a function of the molecular weight between simulations and experiments is observed. Therefore, there exists a clear difference between the results obtained for branched and linear polyethylene, accounting for a definitive effect of the short chain branching on the conformational properties and the melt dynamics of polyolefins. PMID:27003544

  5. Using force-matching to reveal essential differences between density functionals in ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Izvekov, Sergei; Swanson, Jessica M. J.

    2011-05-01

    The exchange-correlation (XC) functional and value of the electronic fictitious mass μ can be two major sources of systematic errors in ab initio Car-Parrinello Molecular Dynamics (CPMD) simulations, and have a significant impact on the structural and dynamic properties of condensed-phase systems. In this work, an attempt is made to identify the origin of differences in liquid water properties generated from CPMD simulations run with the BLYP and HCTH/120 XC functionals and two different values of μ (representative of "small" and "large" limits) by analyzing the effective pairwise atom-atom interactions. The force-matching (FM) algorithm is used to map CPMD interactions into non-polarizable, empirical potentials defined by bonded interactions, pairwise short-ranged interactions in numerical form, and Coulombic interactions via atomic partial charges. The effective interaction models are derived for the BLYP XC functional with μ = 340 a.u. and μ = 1100 a.u. (BLYP-340 and BLYP-1100 simulations) and the HCTH/120 XC functional with μ = 340 a.u. (HCTH-340 simulation). The BLYP-340 simulation results in overstructured water with slow dynamics. In contrast, the BLYP-1100 and HCTH-340 simulations both produce radial distribution functions (indicative of structure) that are in reasonably good agreement with experiment. It is shown that the main difference between the BLYP-340 and HCTH-340 effective potentials arises in the short-ranged nonbonded interactions (in hydrogen bonding regions), while the difference between the BLYP-340 and BLYP-1100 interactions is mainly in the long-ranged electrostatic components. Collectively, these results demonstrate how the FM method can be used to further characterize various simulation ensembles (e.g., density-functional theory via CPMD). An analytical representation of each effective interaction water model, which is easy to implement, is presented.

  6. Molecular dynamics simulations of the Escherichia coli HPPK apo-enzyme reveal a network of conformational transitions.

    PubMed

    Gao, Kaifu; He, Hongqing; Yang, Minghui; Yan, Honggao

    2015-11-10

    6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the first reaction in the folate biosynthetic pathway. Comparison of its X-ray and nuclear magnetic resonance structures suggests that the enzyme undergoes significant conformational change upon binding to its substrates, especially in three catalytic loops. Experimental research has shown that even when confined by crystal contacts, loops 2 and 3 remain rather flexible when the enzyme is in its apo form, raising questions about the putative large-scale induced-fit conformational change of HPPK. To investigate the loop dynamics in a crystal-free environment, we performed conventional molecular dynamics simulations of the apo-enzyme at two different temperatures (300 and 350 K). Our simulations show that the crystallographic B-factors considerably underestimate the loop dynamics; multiple conformations of loops 2 and 3, including the open, semi-open, and closed conformations that an enzyme must adopt throughout its catalytic cycle, are all accessible to the apo-enzyme. These results revise our previous view of the functional mechanism of conformational change upon MgATP binding and offer valuable structural insights into the workings of HPPK. In this paper, conformational network analysis and principal component analysis related to the loops are discussed to support the presented conclusions. PMID:26492157

  7. Relevant interactions of antimicrobial iron chelators and membrane models revealed by nuclear magnetic resonance and molecular dynamics simulations.

    PubMed

    Coimbra, João T S; Moniz, Tânia; Brás, Natércia F; Ivanova, Galya; Fernandes, Pedro A; Ramos, Maria J; Rangel, Maria

    2014-12-18

    The dynamics and interaction of 3-hydroxy-4-pyridinone fluorescent iron chelators, exhibiting antimicrobial properties, with biological membranes were evaluated through NMR and molecular dynamics simulations. Both NMR and MD simulation results support a strong interaction of the chelators with the lipid bilayers that seems to be strengthened for the rhodamine containing compounds, in particular for compounds that include ethyl groups and a thiourea link. For the latter type of compounds the interaction reaches the hydrophobic core of the lipid bilayer. The molecular docking and MD simulations performed for the potential interaction of the chelators with DC-SIGN receptors provide valuable information regarding the cellular uptake of these compounds since the results show that the fluorophore fragment of the molecular framework is essential for an efficient binding. Putting together our previous and present results, we put forward the hypothesis that all the studied fluorescent chelators have access to the cell, their uptake occurs through different pathways and their permeation properties correlate with a better access to the cell and its compartments and, consequently, with the chelators antimicrobial properties. PMID:25482538

  8. Factors Influencing Local Membrane Curvature Induction by N-BAR Domains as Revealed by Molecular Dynamics Simulations

    PubMed Central

    Blood, Philip D.; Swenson, Richard D.; Voth, Gregory A.

    2008-01-01

    N-BAR domains are protein modules that bind to and induce curvature in membranes via a charged concave surface and N-terminal amphipathic helices. Recently, molecular dynamics simulations have demonstrated that the N-BAR domain can induce a strong local curvature that matches the curvature of the BAR domain surface facing the bilayer. Here we present further molecular dynamics simulations that examine in greater detail the roles of the concave surface and amphipathic helices in driving local membrane curvature. We find that the strong curvature induction observed in our previous simulations requires the stable presentation of the charged concave surface to the membrane and is not driven by the membrane-embedded amphipathic helices. Nevertheless, without these amphipathic helices embedded in the membrane, the N-BAR domain does not maintain a close association with the bilayer, and fails to drive membrane curvature. Increasing the membrane negative charge through the addition of PIP2 facilitates closer association with the membrane in the absence of embedded helices. At sufficiently high concentrations, amphipathic helices embedded in the membrane drive membrane curvature independently of the BAR domain. PMID:18469070

  9. Ab initio molecular dynamics simulations reveal localization and time evolution dynamics of an excess electron in heterogeneous CO{sub 2}–H{sub 2}O systems

    SciTech Connect

    Liu, Ping; Zhao, Jing; Liu, Jinxiang; Zhang, Meng; Bu, Yuxiang

    2014-01-28

    In view of the important implications of excess electrons (EEs) interacting with CO{sub 2}–H{sub 2}O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO{sub 2}–H{sub 2}O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO{sub 2} molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO{sub 2}, an EE can stably reside in the empty, low-lying π{sup *} orbital of a CO{sub 2} molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO{sub 2}{sup −} oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO{sub 2}-bound solvated EE in [CO{sub 2}(H{sub 2}O){sub n}]{sup −} systems. Interestingly, hydration occurs not only on the O atoms of the core CO{sub 2}{sup −} through formation of O⋯H–O H–bond(s), but also on the C atom, through formation of a C⋯H–O H–bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H–O H–bonds, and vice versa. The number of water molecules associated with the CO{sub 2}{sup −} anion in the first hydration shell is about 4∼7. No dimer-core (C{sub 2}O{sub 4}{sup −}) and core-switching were observed in the double CO{sub 2} aqueous media. This work provides molecular dynamics

  10. Influence of thermal barrier effect of grain boundaries on bulk cascades in alpha-zirconium revealed by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Jin, Yanan; Lai, Wensheng

    2016-03-01

    The effect of grain boundaries (GBs) on bulk cascades in nano-structured alpha-zirconium has been studied by molecular dynamics (MD) simulations. It turns out that the existence of GBs increases the defect productivity in grains, suggesting that the GBs may act as a thermal barrier and postpone the annihilation of defects within grains. Moreover, it is found that the thermal barrier effect of GBs facilitates the shift of symmetric tilt GBs to the grain with higher temperature, and the smaller the tilt angle is, the easier the boundary shift will be. Thus, the influence of GBs on radiation damage in the nano-structured materials comes from the competition between damage increase in grains and defect annihilation at GBs.

  11. Atomistic mechanisms of huntingtin N-terminal fragment insertion on a phospholipid bilayer revealed by molecular dynamics simulations.

    PubMed

    Côté, Sébastien; Wei, Guanghong; Mousseau, Normand

    2014-07-01

    The huntingtin protein is characterized by a segment of consecutive glutamines (Q(N)) that is responsible for its fibrillation. As with other amyloid proteins, misfolding of huntingtin is related to Huntington's disease through pathways that can involve interactions with phospholipid membranes. Experimental results suggest that the N-terminal 17-amino-acid sequence (htt(NT)) positioned just before the Q(N) region is important for the binding of huntingtin to membranes. Through all-atom explicit solvent molecular dynamics simulations, we unveil the structure and dynamics of the htt(NT)Q(N) fragment on a phospholipid membrane at the atomic level. We observe that the insertion dynamics of this peptide can be described by four main steps-approach, reorganization, anchoring, and insertion-that are very diverse at the atomic level. On the membrane, the htt(NT) peptide forms a stable α-helix essentially parallel to the membrane with its nonpolar side-chains-mainly Leu-4, Leu-7, Phe-11 and Leu-14-positioned in the hydrophobic core of the membrane. Salt-bridges involving Glu-5, Glu-12, Lys-6, and Lys-15, as well as hydrogen bonds involving Thr-3 and Ser-13 with the phospholipids also stabilize the structure and orientation of the htt(NT) peptide. These observations do not significantly change upon adding the Q(N) region whose role is rather to provide, through its hydrogen bonds with the phospholipids' head group, a stable scaffold facilitating the partitioning of the htt(NT) region in the membrane. Moreover, by staying accessible to the solvent, the amyloidogenic Q(N) region could also play a key role for the oligomerization of htt(NT)Q(N) on phospholipid membranes. PMID:24415136

  12. The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations.

    PubMed

    Caldarini, M; Sonar, P; Valpapuram, I; Tavella, D; Volonté, C; Pandini, V; Vanoni, M A; Aliverti, A; Broglia, R A; Tiana, G; Cecconi, C

    2014-12-01

    We have used optical tweezers and molecular dynamics simulations to investigate the unfolding and refolding process of a stable monomeric form of HIV-1-protease (PR). We have characterized the behavior under tension of the native state (N), and that of the ensemble of partially folded (PF) conformations the protein visits en route to N, which collectively act as a long-lived state controlling the slow kinetic phase of the folding process. Our results reveal a rich network of unfolding events, where the native state unfolds either in a two-state manner or by populating an intermediate state I, while the PF state unravels through a multitude of pathways, underscoring its structural heterogeneity. Refolding of mechanically denatured HIV-1-PR monomers is also a multiple-pathway process. Molecular dynamics simulations allowed us to gain insight into possible conformations the protein adopts along the unfolding pathways, and provide information regarding possible structural features of the PF state. PMID:25194276

  13. A wrench in the works of human acetylcholinesterase: Soman induced conformational changes revealed by molecular dynamics simulations

    SciTech Connect

    Bennion, Brian J.; Essiz, Sebnem G.; Lau, Edmond Y.; Fattebert, Jean -Luc; Emigh, Aiyana; Lightstone, Felice C.; Salsbury , Jr, Freddie

    2015-04-13

    Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone and sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.

  14. A wrench in the works of human acetylcholinesterase: Soman induced conformational changes revealed by molecular dynamics simulations

    DOE PAGESBeta

    Bennion, Brian J.; Essiz, Sebnem G.; Lau, Edmond Y.; Fattebert, Jean -Luc; Emigh, Aiyana; Lightstone, Felice C.; Salsbury , Jr, Freddie

    2015-04-13

    Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone andmore » sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.« less

  15. A Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations

    PubMed Central

    Fattebert, Jean-Luc; Emigh, Aiyana

    2015-01-01

    Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone and sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures. PMID:25874456

  16. Molecular Basis for the Cu2+ Binding-Induced Destabilization of β2-Microglobulin Revealed by Molecular Dynamics Simulation

    PubMed Central

    Deng, Nan-Jie; Yan, Lisa; Singh, Deepak; Cieplak, Piotr

    2006-01-01

    According to experimental data, binding of the Cu2+ ions destabilizes the native state of β2-microglobulin (β2m). The partial unfolding of the protein was generally considered an early step toward fibril formation in dialysis-related amyloidosis. Recent NMR studies have suggested that the destabilization of the protein might be achieved through increased flexibility upon Cu2+ binding. However, the molecular mechanism of destabilization due to Cu2+, its role in amyloid formation, and the relative contributions of different potential copper-binding sites remain unclear. To elucidate the effect of ion ligation at atomic detail, a series of molecular dynamics simulations were carried out on apo- and Cu2+-β2m systems in explicit aqueous solutions, with varying numbers of bound ions. Simulations at elevated temperatures (360 K) provide detailed pictures for the process of Cu2+-binding-induced destabilization of the native structure at the nanosecond timescale, which are in agreement with experiments. Conformational transitions toward partially unfolded states were observed in protein solutions containing bound copper ions at His-31 and His-51, which is marked by an increase in the protein vibrational entropy, with TΔS(vibr) ranging from 30 to 69 kcal/mol. The binding of Cu2+ perturbs the secondary structure and the hydrogen bonding pattern disrupts the native hydrophobic contacts in the neighboring segments, which include the β-strand D2 and part of the β-strand E, B, and C and results in greater exposure of the D-E loop and the B-C loop to the water environment. Analysis of the MD trajectories suggests that the changes in the hydrophobic environment near the copper-binding sites lower the barrier of conformational transition and stabilize the more disordered conformation. The results also indicate that the binding of Cu2+ at His-13 has little effect on the conformational stability, whereas the copper-binding site His-31, and to a lesser extent His-51, are

  17. NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1†

    PubMed Central

    Parkesh, Raman; Fountain, Matthew; Disney, Matthew D.

    2011-01-01

    The NMR structure of an RNA with a copy of the 5′CUG/3′GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single hydrogen bonded structure; however, the UU protons undergo exchange indicating structural dynamics. Molecular dynamics simulations show that the single hydrogen bonded structure is the most populated one but the UU pair interconverts between 0, 1, and 2 hydrogen bonded pairs. These studies have implications for the recognition of the DM1 RNA by small molecules and proteins. PMID:21204525

  18. Molecular Dynamics Simulation Reveals the Selective Binding of Human Leukocyte Antigen Alleles Associated with Behçet's Disease

    PubMed Central

    Kongkaew, Sirilak; Yotmanee, Pathumwadee; Rungrotmongkol, Thanyada; Kaiyawet, Nopporn; Meeprasert, Arthitaya; Kaburaki, Toshikatsu; Noguchi, Hiroshi; Takeuchi, Fujio; Kungwan, Nawee; Hannongbua, Supot

    2015-01-01

    Behçet’s disease (BD), a multi-organ inflammatory disorder, is associated with the presence of the human leukocyte antigen (HLA) HLA-B*51 allele in many ethnic groups. The possible antigen involvement of the major histocompatibility complex class I chain related gene A transmembrane (MICA-TM) nonapeptide (AAAAAIFVI) has been reported in BD symptomatic patients. This peptide has also been detected in HLA-A*26:01 positive patients. To investigate the link of BD with these two specific HLA alleles, molecular dynamics (MD) simulations were applied on the MICA-TM nonapeptide binding to the two BD-associated HLA alleles in comparison with the two non-BD-associated HLA alleles (B*35:01 and A*11:01). The MD simulations were applied on the four HLA/MICA-TM peptide complexes in aqueous solution. As a result, stabilization for the incoming MICA-TM was found to be predominantly contributed from van der Waals interactions. The P2/P3 residue close to the N-terminal and the P9 residue at the C-terminal of the MICA-TM nonapeptide served as the anchor for the peptide accommodated at the binding groove of the BD associated HLAs. The MM/PBSA free energy calculation predicted a stronger binding of the HLA/peptide complexes for the BD-associated HLA alleles than for the non-BD-associated ones, with a ranked binding strength of B*51:01 > B*35:01 and A*26:01 > A*11:01. Thus, the HLAs associated with BD pathogenesis expose the binding efficiency with the MICA-TM nonapeptide tighter than the non-associated HLA alleles. In addition, the residues 70, 73, 99, 146, 147 and 159 of the two BD-associated HLAs provided the conserved interaction for the MICA-TM peptide binding. PMID:26331842

  19. Diffusion behavior of helium in titanium and the effect of grain boundaries revealed by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Gui-Jun, Cheng; Bao-Qin, Fu; Qing, Hou; Xiao-Song, Zhou; Jun, Wang

    2016-07-01

    The microstructures of titanium (Ti), an attractive tritium (T) storage material, will affect the evolution process of the retained helium (He). Understanding the diffusion behavior of He at the atomic scale is crucial for the mechanism of material degradation. The novel diffusion behavior of He has been reported by molecular dynamics (MD) simulation for the bulk hcp-Ti system and the system with grain boundary (GB). It is observed that the diffusion of He in the bulk hcp-Ti is significantly anisotropic (the diffusion coefficient of the [0001] direction is higher than that of the basal plane), as represented by the different migration energies. Different from convention, the GB accelerates the diffusion of He in one direction but not in the other. It is observed that a twin boundary (TB) can serve as an effective trapped region for He. The TB accelerates diffusion of He in the direction perpendicular to the twinning direction (TD), while it decelerates the diffusion in the TD. This finding is attributable to the change of diffusion path caused by the distortion of the local favorable site for He and the change of its number in the TB region. Project supported by the National Natural Science Foundation of China (Grant No. 51501119), the Scientific Research Starting Foundation for Younger Teachers of Sichuan University, China (Grant No. 2015SCU11058), the National Magnetic Confinement Fusion Science Program of China (Grant No. 2013GB109002), and the Cooperative Research Project “Research of Diffusion Behaviour of He in Grain Boundary of HCP-Titanium”, China.

  20. Bifurcate localization modes of excess electron in aqueous Ca(2+)amide solution revealed by ab initio molecular dynamics simulation: towards hydrated electron versus hydrated amide anion.

    PubMed

    Zhang, Ru; Bu, Yuxiang

    2016-07-28

    In this work, we conduct ab initio molecular dynamics simulations on the localization dynamics of an excess electron (EE) in acetamide/Ca(2+) aqueous solutions with three different interaction modes of Ca(2+) with acetamide: tight contact, solvent-shared state, and separated interaction. The simulated results reveal that an EE could exhibit two different localization behaviors in these acetamide/Ca(2+) aqueous solutions depending on different amideCa(2+) interactions featuring different contact distances. For the tight contact and solvent-shared state of amideCa(2+) solutions, vertically injected diffuse EEs follow different mechanisms with different dynamics, forming a cavity-shaped hydrated electron or a hydrated amide anion, respectively. Meanwhile, for the separated state, only one localization pattern of a vertically injected diffuse EE towards the formation of hydrated amide anion is observed. The hindrance of hydrated Ca(2+) and the attraction of the hydrated amide group originating from its polarity and low energy π* orbital are the main driving forces. Additionally, different EE localization modes have different effects on the interaction between the amide group and Ca(2+) in turn. This work provides an important basis for further understanding the mechanisms and dynamics of localizations/transfers of radiation-produced EEs and associated EE-induced lesions and damage to biological species in real biological environments or other aqueous solutions. PMID:27351489

  1. Molecular dynamics simulations of metalloproteinases types 2 and 3 reveal differences in the dynamic behavior of the S1' binding pocket.

    PubMed

    de Oliveira, Cesar Augusto F; Zissen, Maurice; Mongon, John; McCammon, J Andrew

    2007-01-01

    Matrix Metalloproteinases (MMPs) are zinc-containing proteinases that are responsible for the metabolism of extracellular matrix proteins. Overexpression of MMPs has been associated with a wide range of pathological diseases such as arthritis, cancer, multiple sclerosis and Alzheimer's disease. The excessive and unregulated activity of Matrix Metalloproteinases type 2 (MMP-2), also known as gelatinase A, has been identified in a numbers of cancer metastases. Several MMP inhibitors (MMPi) have been proposed in the literature aiming to interfere in the MMPs activity. In this work we performed long MD simulations in order to study the dynamical behavior of the binding pocket S1' in the apo forms of MMP type 2 and 3, and identify, at the molecular level, the structural properties relevant for the designing of specific inhibitor of MMP-2. PMID:18220784

  2. New Insights into Active Site Conformation Dynamics of E. coli PNP Revealed by Combined H/D Exchange Approach and Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Kazazić, Saša; Bertoša, Branimir; Luić, Marija; Mikleušević, Goran; Tarnowski, Krzysztof; Dadlez, Michal; Narczyk, Marta; Bzowska, Agnieszka

    2016-01-01

    The biologically active form of purine nucleoside phosphorylase (PNP) from Escherichia coli (EC 2.4.2.1) is a homohexamer unit, assembled as a trimer of dimers. Upon binding of phosphate, neighboring monomers adopt different active site conformations, described as open and closed. To get insight into the functions of the two distinctive active site conformations, virtually inactive Arg24Ala mutant is complexed with phosphate; all active sites are found to be in the open conformation. To understand how the sites of neighboring monomers communicate with each other, we have combined H/D exchange (H/DX) experiments with molecular dynamics (MD) simulations. Both methods point to the mobility of the enzyme, associated with a few flexible regions situated at the surface and within the dimer interface. Although H/DX provides an average extent of deuterium uptake for all six hexamer active sites, it was able to indicate the dynamic mechanism of cross-talk between monomers, allostery. Using this technique, it was found that phosphate binding to the wild type (WT) causes arrest of the molecular motion in backbone fragments that are flexible in a ligand-free state. This was not the case for the Arg24Ala mutant. Upon nucleoside substrate/inhibitor binding, some release of the phosphate-induced arrest is observed for the WT, whereas the opposite effects occur for the Arg24Ala mutant. MD simulations confirmed that phosphate is bound tightly in the closed active sites of the WT; conversely, in the open conformation of the active site of the WT phosphate is bound loosely moving towards the exit of the active site. In Arg24Ala mutant binary complex Pi is bound loosely, too.

  3. Structure and conformational dynamics of the domain 5 RNA hairpin of a bacterial group II intron revealed by solution nuclear magnetic resonance and molecular dynamics simulations.

    PubMed

    Pechlaner, Maria; Sigel, Roland K O; van Gunsteren, Wilfred F; Dolenc, Jožica

    2013-10-01

    Nuclear magnetic resonance (NMR) nuclear Overhauser enhancement (NOE) data obtained for a 35-nucleotide RNA segment of a bacterial group II intron indicate a helical hairpin structure in which three parts, a terminal pentaloop, a bulge, and a G-A mismatch, display no Watson-Crick base pairing. The 668 NOE upper distance bounds for atom pairs are insufficient to uniquely determine the conformation of these segments. Therefore, molecular dynamics simulations including time-averaged distance restraints have been used to obtain a conformational ensemble compatible with the observed NMR data. The ensemble shows alternating hydrogen bonding patterns for the mentioned segments. In particular, in the pentaloop and in the bulge, the hydrogen bonding networks correspond to distinct conformational clusters that could not be captured by using conventional single-structure refinement techniques. This implies that, to obtain a realistic picture of the conformational ensemble of such flexible biomolecules, it is necessary to properly account for the conformational variability in the structure refinement of RNA fragments. PMID:24001362

  4. Factors affecting the interactions between beta-lactoglobulin and fatty acids as revealed in molecular dynamics simulations.

    PubMed

    Yi, Changhong; Wambo, Thierry O

    2015-09-21

    Beta-lactoglobulin (BLG), a bovine dairy protein, is a promiscuously interacting protein that can bind multiple hydrophobic ligands. Fatty acids (FAs), common hydrophobic molecules bound to BLG, are important sources of fuel for life because they yield large quantities of ATP when metabolized. The binding affinity increases with the length of the ligands, indicating the importance of the van der Waals (vdW) interactions between the hydrocarbon tail and the hydrophobic calyx of BLG. An exception to this rule is caprylic acid (OCA) which is two-carbon shorter but has a stronger binding affinity than capric acid. Theoretical calculations in the current literature are not accurate enough to shed light on the underlying physics of this exception. The computed affinity values are greater for longer fatty acids without respect for the caprylic exception and those values are generally several orders of magnitude away from the experimental data. In this work, we used hybrid steered molecular dynamics to accurately compute the binding free energies between BLG and the five saturated FAs of 8 to 16 carbon atoms. The computed binding free energies agree well with experimental data not only in rank but also in absolute values. We gained insights into the exceptional behavior of caprylic acid in the computed values of entropy and electrostatic interactions. We found that the electrostatic interaction between the carboxyl group of caprylic acid and the two amino groups of K60/69 in BLG is much stronger than the vdW force between the OCA's hydrophobic tail and the BLG calyx. This pulls OCA to the top of the beta barrel where it is easier to fluctuate, giving rise to greater entropy of OCA at the binding site. PMID:26272099

  5. Excess electron reactivity in amino acid aqueous solution revealed by ab initio molecular dynamics simulation: anion-centered localization and anion-relayed electron transfer dissociation.

    PubMed

    Wu, Xiuxiu; Gao, Liang; Liu, Jinxiang; Yang, Hongfang; Wang, Shoushan; Bu, Yuxiang

    2015-10-28

    Studies on the structure, states, and reactivity of excess electrons (EEs) in biological media are of great significance. Although there is information about EE interaction with desolvated biological molecules, solution effects are hardly explored. In this work, we present an ab initio molecular dynamics simulation study on the interaction and reactivity of an EE with glycine in solution. Our simulations reveal two striking results. Firstly, a pre-solvated EE partially localizes on the negatively charged -COO(-) group of the zwitterionic glycine and the remaining part delocalizes over solvent water molecules, forming an anion-centered quasi-localized structure, due to relative alignment of the lowest unoccupied molecular orbital energy levels of potential sites for EE residence in the aqueous solution. Secondly, after a period of anion-centered localization of an EE, the zwitterionic glycine is induced to spontaneously fragment through the cleavage of the N-Cα bond, losing ammonia (deamination), and leaving a ˙CH2-COO(-) anion radical, in good agreement with experimental observations. Introduction of the same groups (-COO(-) or -NH3(+)) in the side chain (taking lysine and aspartic acid as examples) can affect EE localization, with the fragmentation of the backbone part of these amino acids dependent on the properties of the side chain groups. These findings provide insights into EE interaction mechanisms with the backbone parts of amino acids and low energy EE induced fragmentation of amino acids and even peptides and proteins. PMID:26399512

  6. Molecular dynamics simulations of apo, holo, and inactivator bound GABA-at reveal the role of active site residues in PLP dependent enzymes.

    PubMed

    Gökcan, Hatice; Monard, Gerald; Sungur Konuklar, F Aylin

    2016-07-01

    The pyridoxal 5-phosphate (PLP) cofactor is a significant organic molecule in medicinal chemistry. It is often found covalently bound to lysine residues in proteins to form PLP dependent enzymes. An example of this family of PLP dependent enzymes is γ-aminobutyric acid aminotransferase (GABA-AT) which is responsible for the degradation of the neurotransmitter GABA. Its inhibition or inactivation can be used to prevent the reduction of GABA concentration in brain which is the source of several neurological disorders. As a test case for PLP dependent enzymes, we have performed molecular dynamics simulations of GABA-AT to reveal the roles of the protein residues and its cofactor. Three different states have been considered: the apoenzyme, the holoenzyme, and the inactive state obtained after the suicide inhibition by vigabatrin. Different protonation states have also been considered for PLP and two key active site residues: Asp298 and His190. Together, 24 independent molecular dynamics trajectories have been simulated for a cumulative total of 2.88 µs. Our results indicate that, unlike in aqueous solution, the PLP pyridine moiety is protonated in GABA-AT. This is a consequence of a pKa shift triggered by a strong charge-charge interaction with an ionic "diad" formed by Asp298 and His190 that would help the activation of the first half-reaction of the catalytic mechanism in GABA-AT: the conversion of PLP to free pyridoxamine phosphate (PMP). In addition, our MD simulations exhibit additional strong hydrogen bond networks between the protein and PLP: the phosphate group is held in place by the donation of at least three hydrogen bonds while the carbonyl oxygen of the pyridine ring interacts with Gln301; Phe181 forms a π-π stacking interaction with the pyridine ring and works as a gate keeper with the assistance of Val300. All these interactions are hypothesized to help maintain free PMP in place inside the protein active site to facilitate the second half

  7. Tether Dynamics Simulation

    NASA Technical Reports Server (NTRS)

    1987-01-01

    The proceedings of the conference are presented. The objective was to provide a forum for the discussion of the structure and status of existing computer programs which are used to simulate the dynamics of a variety of tether applications in space. A major topic was different simulation models and the process of validating them. Guidance on future work in these areas was obtained from a panel discussion; the panel was composed of resource and technical managers and dynamic analysts in the tether field. The conclusions of this panel are also presented.

  8. Molecular dynamics simulation of human serum paraoxonase 1 in DPPC bilayer reveals a critical role of transmembrane helix H1 for HDL association.

    PubMed

    Patra, Mahesh Chandra; Rath, Surya Narayan; Pradhan, Sukanta Kumar; Maharana, Jitendra; De, Sachinandan

    2014-01-01

    Serum paraoxonase 1 (PON1) is a high-density lipoprotein (HDL)-bound mammalian enzyme exhibiting antiatherosclerotic activity. Despite years of research, an accurate model for the binding interaction between PON1 and HDL has not been established. However, it is reported that anchoring of PON1 to HDL is mainly governed by an N-terminal alpha helix H1 and another short helix H2. Here, we studied the molecular association of full-length human PON1 (huPON1) with a HDL-mimetic dipalmitoylphosphatidylcholine (DPPC) bilayer using homology modeling and molecular dynamics simulations. Our results indicate that H1 is the highly dynamic part of huPON1, showing clockwise rotation of up to 30° within the DPPC bilayer. However, without phospholipid molecules, H1 experiences helical distortions, illustrating an incompatible HDL-anchoring conformation. Snorkeling interactions of K3, R18, and R27 together with aromatic locks formed by Y187, Y190, W194, and W202 are highly essential for anchoring of huPON1 to HDL's surface. Molecular mechanics/Poisson-Boltzmann solvent-accessible surface area (MM/PBSA) binding free energy calculation revealed that H1 displays greater binding affinity towards lipid molecules compared with H2 and H3, suggesting that H1 is the most probable HDL-binding domain of PON1. Binding free energy decomposition showed that K3, R18, and R27 interact with polar headgroups of DPPC membrane through electrostatic interaction. Moreover, Y187, Y190, W194, and W202 interact with DPPC lipids mainly through van der Waals interaction. Taken together, these results show that the transmembrane helix H1 along with the interfacial positively charged and aromatic resides were crucial for PON1's association with HDL particle. The current study will be useful towards understanding the antiatherosclerotic and bioscavenging properties of this promiscuous enzyme. PMID:24297451

  9. Face-to-Face Packing of 2,3,9,10-Tetrasubstituted Pentacene Derivatives Revealed through a Solid State [4 + 4] Thermal Cycloaddition and Molecular Dynamic Simulation.

    PubMed

    Pal, Bikash; Lin, Bo-Chao; Dela Cerna, Mark Vincent Carreon; Hsu, Chao-Ping; Lin, Chih-Hsiu

    2016-08-01

    2,3,9,10-Substituted pentacene tetraesters and pentacene diester-dinitriles were synthesized. These pentacene derivatives underwent an unusual solid state [4 + 4] thermal dimerization with good efficiency and complete stereoselectivity. This observation indicates this series of pentacene derivatives adopt π-π stacking geometry with large mutual overlap in solid state. This notion was confirmed by molecualr dynamic simulation. PMID:27362625

  10. Dynamic load simulator

    NASA Technical Reports Server (NTRS)

    Joncas, K. P.

    1972-01-01

    Concepts and techniques for identifying and simulating both the steady state and dynamic characteristics of electrical loads for use during integrated system test and evaluation are discussed. The investigations showed that it is feasible to design and develop interrogation and simulation equipment to perform the desired functions. During the evaluation, actual spacecraft loads were interrogated by stimulating the loads with their normal input voltage and measuring the resultant voltage and current time histories. Elements of the circuits were optimized by an iterative process of selecting element values and comparing the time-domain response of the model with those obtained from the real equipment during interrogation.

  11. Steered molecular dynamics simulations of a bacterial type IV pilus reveal characteristics of an experimentally-observed, force-induced conformational transition

    NASA Astrophysics Data System (ADS)

    Baker, Joseph; Biais, Nicolas; Tama, Florence

    2011-10-01

    Type IV pili (T4P) are long, filamentous structures that emanate from the cellular surface of many infectious bacteria. They are built from a 158 amino acid long subunit called pilin. T4P can grow to many micrometers in length, and can withstand large tension forces. During the infection process, pili attach themselves to host cells, and therefore naturally find themselves under tension. We investigated the response of a T4 pilus to a pulling force using the method of steered molecular dynamics (SMD) simulation. Our simulations expose to the external environment an amino acid sequence initially hidden in the native filament, in agreement with experimental data. Therefore, our simulations might be probing the initial stage of the transition to a force-induced conformation of the T4 pilus. Additional exposed amino acid sequences that might be useful targets for drugs designed to mitigate bacterial infection were also predicted.

  12. Na/Ca Intermixing around Silicate and Phosphate Groups in Bioactive Phosphosilicate Glasses Revealed by Heteronuclear Solid-State NMR and Molecular Dynamics Simulations.

    PubMed

    Mathew, Renny; Stevensson, Baltzar; Edén, Mattias

    2015-04-30

    We characterize the intermixing of network-modifying Na(+)/Ca(2+) ions around the silicate (QSi(n)) and phosphate (QP(n)) tetrahedra in a series of 16 Na2O–CaO–SiO2–P2O5 glasses, whose P content and silicate network connectivity were varied independently. The set includes both bioactive and bioinactive compositions and also encompasses two soda-lime-silicate members devoid of P, as well as two CaO–SiO2 glasses and one Na2O–SiO2–P2O5 glass. The various Si/P↔Na/Ca contacts were probed by molecular dynamics (MD) simulations together with heteronuclear magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) experimentation utilizing (23)Na{(31)P} and (23)Na{(29)Si} REDOR, as well as (31)P{ (23)Na} and (29)Si{(23)Na} REAPDOR. We introduce an approach for quantifying the extent of Na(+)/Ca(2+) ordering around a given QP(n) or QSi(n) group, encoded by the preference factor 0⩽ PM ⩽ 1 conveying the relative weights of a random cation intermixing (PM = 0) and complete preference/ordering (PM = 1) for one of the species M, which represents either Na(+) or Ca(2+). The MD-derived preference factors reveal phosphate and silicate species surrounded by Na(+)/Ca(2+) ions intermixed nearly randomly (PM ≲ 0.15), except for the QSi(4) and QSi(1) groups, which manifest more significant cation ordering with preference for Na+ and Ca2+, respectively. The overall weak preferences are essentially independent of the Si and P contents of the glass, whereas PM primarily correlates with the total amount of network modifiers: as the latter is increased, the Na/Ca distribution around the {QP(0), QSi(1), QSi(2)} groups with preference for Ca2(+ )tend to randomize (i.e., PCa decreases), while the PNa-values grow slightly for the {QP(1), QSi(3), QSi(4)} species already preferring coordination of Na. The set of experimental preference factors {PCa} for the orthophosphate (QP(0)) groups extracted from (31)P{(23)Na} REAPDOR NMR-derived M2(P–Na) dipolar second moments agrees

  13. Cantera Aerosol Dynamics Simulator

    SciTech Connect

    Moffat, Harry

    2004-09-01

    The Cantera Aerosol Dynamics Simulator (CADS) package is a general library for aerosol modeling to address aerosol general dynamics, including formation from gas phase reactions, surface chemistry (growth and oxidation), bulk particle chemistry, transport by Brownian diffusion, thermophoresis, and diffusiophoresis with linkage to DSMC studies, and thermal radiative transport. The library is based upon Cantera, a C++ Cal Tech code that handles gas phase species transport, reaction, and thermodynamics. The method uses a discontinuous galerkin formulation for the condensation and coagulation operator that conserves particles, elements, and enthalpy up to round-off error. Both O-D and 1-D time dependent applications have been developed with the library. Multiple species in the solid phase are handled as well. The O-D application, called Tdcads (Time Dependent CADS) is distributed with the library. Tdcads can address both constant volume and constant pressure adiabatic homogeneous problems. An extensive set of sample problems for Tdcads is also provided.

  14. Data Systems Dynamic Simulator

    NASA Technical Reports Server (NTRS)

    Rouff, Christopher; Clark, Melana; Davenport, Bill; Message, Philip

    1993-01-01

    The Data System Dynamic Simulator (DSDS) is a discrete event simulation tool. It was developed for NASA for the specific purpose of evaluating candidate architectures for data systems of the Space Station era. DSDS provides three methods for meeting this requirement. First, the user has access to a library of standard pre-programmed elements. These elements represent tailorable components of NASA data systems and can be connected in any logical manner. Secondly, DSDS supports the development of additional elements. This allows the more sophisticated DSDS user the option of extending the standard element set. Thirdly, DSDS supports the use of data streams simulation. Data streams is the name given to a technique that ignores packet boundaries, but is sensitive to rate changes. Because rate changes are rare compared to packet arrivals in a typical NASA data system, data stream simulations require a fraction of the CPU run time. Additionally, the data stream technique is considerably more accurate than another commonly-used optimization technique.

  15. Eye Movements Reveal Dynamics of Task Control

    ERIC Educational Resources Information Center

    Mayr, Ulrich; Kuhns, David; Rieter, Miranda

    2013-01-01

    With the goal to determine the cognitive architecture that underlies flexible changes of control settings, we assessed within-trial and across-trial dynamics of attentional selection by tracking of eye movements in the context of a cued task-switching paradigm. Within-trial dynamics revealed a switch-induced, discrete delay in onset of…

  16. Dispersion of Response Times Reveals Cognitive Dynamics

    PubMed Central

    Holden, John G.; Van Orden, Guy C.; Turvey, Michael T.

    2013-01-01

    Trial to trial variation in word pronunciation times exhibits 1/f scaling. One explanation is that human performances are consequent on multiplicative interactions among interdependent processes – interaction dominant dynamics. This article describes simulated distributions of pronunciation times in a further test for multiplicative interactions and interdependence. Individual participant distributions of ≈1100 word pronunciation times are successfully mimicked for each participant in combinations of lognormal and power law behavior. Successful hazard function simulations generalize these results to establish interaction dominant dynamics, in contrast with component dominant dynamics, as a likely mechanism for cognitive activity. PMID:19348544

  17. Look-ahead Dynamic Simulation

    Energy Science and Technology Software Center (ESTSC)

    2015-10-20

    Look-ahead dynamic simulation software system incorporates the high performance parallel computing technologies, significantly reduces the solution time for each transient simulation case, and brings the dynamic simulation analysis into on-line applications to enable more transparency for better reliability and asset utilization. It takes the snapshot of the current power grid status, functions in parallel computing the system dynamic simulation, and outputs the transient response of the power system in real time.

  18. Molecular dynamics simulations

    SciTech Connect

    Alder, B.J.

    1985-07-01

    The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs.

  19. Cantera Aerosol Dynamics Simulator

    Energy Science and Technology Software Center (ESTSC)

    2004-09-01

    The Cantera Aerosol Dynamics Simulator (CADS) package is a general library for aerosol modeling to address aerosol general dynamics, including formation from gas phase reactions, surface chemistry (growth and oxidation), bulk particle chemistry, transport by Brownian diffusion, thermophoresis, and diffusiophoresis with linkage to DSMC studies, and thermal radiative transport. The library is based upon Cantera, a C++ Cal Tech code that handles gas phase species transport, reaction, and thermodynamics. The method uses a discontinuous galerkinmore » formulation for the condensation and coagulation operator that conserves particles, elements, and enthalpy up to round-off error. Both O-D and 1-D time dependent applications have been developed with the library. Multiple species in the solid phase are handled as well. The O-D application, called Tdcads (Time Dependent CADS) is distributed with the library. Tdcads can address both constant volume and constant pressure adiabatic homogeneous problems. An extensive set of sample problems for Tdcads is also provided.« less

  20. Functional conformations of the L11–ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations

    PubMed Central

    Li, Wen; Sengupta, Jayati; Rath, Bimal K.; Frank, Joachim

    2006-01-01

    The interaction between the GTPase-associated center (GAC) and the aminoacyl-tRNA·EF-Tu·GTP ternary complex is of crucial importance in the dynamic process of decoding and tRNA accommodation. The GAC includes protein L11 and helices 43–44 of 23S rRNA (referred to as L11–rRNA complex). In this study, a method of fitting based on a systematic comparison between cryo-electron microscopy (cryo-EM) density maps and structures obtained by molecular dynamics simulations has been developed. This method has led to the finding of atomic models of the GAC that fit the EM maps with much improved cross-correlation coefficients compared with the fitting of the X-ray structure. Two types of conformations of the L11–rRNA complex, produced by the simulations, match the cryo-EM maps representing the states either bound or unbound to the aa-tRNA·EF-Tu·GTP ternary complex. In the bound state, the N-terminal domain of L11 is extended from its position in the crystal structure, and the base of nucleotide A1067 in the 23S ribosomal RNA is flipped out. This position of the base allows the RNA to reach the elbow region of the aminoacyl-tRNA when the latter is bound in the A/T site. In the unbound state, the N-terminal domain of L11 is rotated only slightly, and A1067 of the RNA is flipped back into the less-solvent-exposed position, as in the crystal structure. By matching our experimental cryo-EM maps with much improved cross-correlation coefficients compared to the crystal structure, these two conformations prove to be strong candidates of the two functional states. PMID:16682558

  1. Revealing Origin of Decrease in Potency of Darunavir and Amprenavir against HIV-2 relative to HIV-1 Protease by Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Chen, Jianzhong; Liang, Zhiqiang; Wang, Wei; Yi, Changhong; Zhang, Shaolong; Zhang, Qinggang

    2014-11-01

    Clinical inhibitors Darunavir (DRV) and Amprenavir (APV) are less effective on HIV-2 protease (PR2) than on HIV-1 protease (PR1). To identify molecular basis associated with the lower inhibition, molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations were performed to investigate the effectiveness of the PR1 inhibitors DRV and APV against PR1/PR2. The rank of predicted binding free energies agrees with the experimental determined one. Moreover, our results show that two inhibitors bind less strongly to PR2 than to PR1, again in agreement with the experimental findings. The decrease in binding free energies for PR2 relative to PR1 is found to arise from the reduction of the van der Waals interactions induced by the structural adjustment of the triple mutant V32I, I47V and V82I. This result is further supported by the difference between the van der Waals interactions of inhibitors with each residue in PR2 and in PR1. The results from the principle component analysis suggest that inhibitor binding tends to make the flaps of PR2 close and the one of PR1 open. We expect that this study can theoretically provide significant guidance and dynamics information for the design of potent dual inhibitors targeting PR1/PR2.

  2. Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation

    PubMed Central

    Satoh, Mikiya; Saburi, Hajime; Tanaka, Tomoyuki; Matsuura, Yoshinori; Naitow, Hisashi; Shimozono, Rieko; Yamamoto, Naoyoshi; Inoue, Hideki; Nakamura, Noriko; Yoshizawa, Yoshitaka; Aoki, Takumi; Tanimura, Ryuji; Kunishima, Naoki

    2015-01-01

    Keap1 protein acts as a cellular sensor for oxidative stresses and regulates the transcription level of antioxidant genes through the ubiquitination of a corresponding transcription factor, Nrf2. A small molecule capable of binding to the Nrf2 interaction site of Keap1 could be a useful medicine. Here, we report two crystal structures, referred to as the soaking and the cocrystallization forms, of the Kelch domain of Keap1 with a small molecule, Ligand1. In these two forms, the Ligand1 molecule occupied the binding site of Keap1 so as to mimic the ETGE motif of Nrf2, although the mode of binding differed in the two forms. Because the Ligand1 molecule mediated the crystal packing in both the forms, the influence of crystal packing on the ligand binding was examined using a molecular dynamics (MD) simulation in aqueous conditions. In the MD structures from the soaking form, the ligand remained bound to Keap1 for over 20 ns, whereas the ligand tended to dissociate in the cocrystallization form. The MD structures could be classified into a few clusters that were related to but distinct from the crystal structures, indicating that the binding modes observed in crystals might be atypical of those in solution. However, the dominant ligand recognition residues in the crystal structures were commonly used in the MD structures to anchor the ligand. Therefore, the present structural information together with the MD simulation will be a useful basis for pharmaceutical drug development. PMID:26199865

  3. Molecular basis of the selectivity of the immunoproteasome catalytic subunit LMP2-specific inhibitor revealed by molecular modeling and dynamics simulations.

    PubMed

    Lei, Beilei; Abdul Hameed, Mohamed Diwan M; Hamza, Adel; Wehenkel, Marie; Muzyka, Jennifer L; Yao, Xiao-Jun; Kim, Kyung-Bo; Zhan, Chang-Guo

    2010-09-30

    Given that immunoproteasome inhibitors are currently being developed for a variety of potent therapeutic purposes, the unique specificity of an α',β'-epoxyketone peptide (UK101) toward the LMP2 subunit of the immunoproteasome (analogous to β5 subunit of the constitutive proteasome) has been investigated in this study for the first time by employing homology modeling, molecular docking, molecular dynamics simulation, and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations. On the basis of the simulated binding structures, the calculated binding free energies are in qualitative agreement with the corresponding experimental data, and the selectivity of UK101 is explained reasonably. The observed selectivity of UK101 for the LMP2 subunit is rationalized by the requirement for both a linear hydrocarbon chain at the N terminus and a bulky group at the C terminus of the inhibitor, because the LMP2 subunit has a much more favorable hydrophobic pocket interacting with the linear hydrocarbon chain, and the bulky group at the C terminus has a steric clash with the Tyr 169 in β5 subunit. Finally, our results help to clarify why UK101 is specific to the LMP2 subunit of immunoproteasome, and this investigation should be valuable for rational design of more potent LMP2-specific inhibitors. PMID:20812720

  4. Molecular Basis of the Selectivity of the Immunoproteasome Catalytic Subunit LMP2-Specific Inhibitor Revealed by Molecular Modeling and Dynamics Simulations

    PubMed Central

    Lei, Beilei; AbdulHameed, Mohamed Diwan M.; Hamza, Adel; Wehenkel, Marie; Muzyka, Jennifer L.; Yao, Xiao-Jun; Kim, Kyung-Bo; Zhan, Chang-Guo

    2010-01-01

    Given that immunoproteasome inhibitors are currently being developed for a variety of potent therapeutic purposes, the unique specificity of an α′,β′-epoxyketone peptide (UK101) towards the LMP2 subunit of the immunoproteasome (analogous to β5 subunit of the constitutive proteasome) has been investigated in this study for the first time by employing homology modeling, molecular docking, molecular dynamics simulation, and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations. Based on the simulated binding structures, the calculated binding free energies are in qualitative agreement with the corresponding experimental data and the selectivity of UK101 is explained reasonably. The observed selectivity of UK101 for the LMP2 subunit is rationalized by the requirement for both a linear hydrocarbon chain at the N-terminus and a bulky group at the C-terminus of the inhibitor, because that LMP2 subunit has a much more favorable hydrophobic pocket interacting with the linear hydrocarbon chain, and the bulky group at the C-terminus has a steric clash with the Tyr 169 in β5 subunit. Finally, our results help to clarify why UK101 is specific to the LMP2 subunit of immunoproteasome, and this investigation should be valuable for rational design of more potent LMP2-specific inhibitors. PMID:20812720

  5. Dispersion of Response Times Reveals Cognitive Dynamics

    ERIC Educational Resources Information Center

    Holden, John G.; Van Orden, Guy C.; Turvey, Michael T.

    2009-01-01

    Trial-to-trial variation in word-pronunciation times exhibits 1/f scaling. One explanation is that human performances are consequent on multiplicative interactions among interdependent processes-interaction dominant dynamics. This article describes simulated distributions of pronunciation times in a further test for multiplicative interactions and…

  6. Experimental verification of dynamic simulation

    NASA Technical Reports Server (NTRS)

    Yae, K. Harold; Hwang, Howyoung; Chern, Su-Tai

    1989-01-01

    The dynamics model here is a backhoe, which is a four degree of freedom manipulator from the dynamics standpoint. Two types of experiment are chosen that can also be simulated by a multibody dynamics simulation program. In the experiment, recorded were the configuration and force histories; that is, velocity and position, and force output and differential pressure change from the hydraulic cylinder, in the time domain. When the experimental force history is used as driving force in the simulation model, the forward dynamics simulation produces a corresponding configuration history. Then, the experimental configuration history is used in the inverse dynamics analysis to generate a corresponding force history. Therefore, two sets of configuration and force histories--one set from experiment, and the other from the simulation that is driven forward and backward with the experimental data--are compared in the time domain. More comparisons are made in regard to the effects of initial conditions, friction, and viscous damping.

  7. Remote manipulator dynamic simulation

    NASA Technical Reports Server (NTRS)

    Wild, E. C.; Donges, P. K.; Garand, W. A.

    1972-01-01

    A simulator to generate the real time visual scenes required to perform man in the loop investigations of remote manipulator application and design concepts for the space shuttle is described. The simulated remote manipulator consists of a computed display system that uses a digital computer, the electronic scene generator, an operator's station, and associated interface hardware. A description of the capabilities of the implemented simulation is presented. The mathematical models and programs developed for the simulation are included.

  8. Molecular Dynamics Simulations of Polymers

    NASA Astrophysics Data System (ADS)

    Han, Jie

    1995-01-01

    Molecular dynamics (MD) simulations have been undertaken in this work to explore structures and properties of polyethylene (PE), polyisobutylene (PIB), atactic polypropylene (aPP) and atactic polystyrene (aPS). This work has not only demonstrated the reliability of MD simulations by comparing results with available experiments, but more importantly has revealed structure-property relationships on a molecular level for these selected polymers. Structures of these amorphous polymers were characterized by radial distribution functions (RDFs) or scattering profiles, and properties of the polymers studied were pressure-volume -temperature (PVT) equation of state, enthalpy, cohesive energy, the diffusion coefficient of methane in the polymer, and glass transition temperature. Good agreement was found for these structures and properties between simulation and experiment. More importantly, the scientific understanding of structure-property relationships was established on a molecular level. In the order of aPP (PE), PIB and aPS, with the chain surface separation or free volume decreasing, the density increases and the diffusion coefficient decreases. Therefore, the effects of changes or modifications in the chemical structure of monomer molecules (substituting pendent hydrogen with methyl or phenyl) on polymeric materials performance were attributed to the effects of molecular chain structure on packing structure, which, in turn, affects the properties of these polymers. Local chain dynamics and relaxation have been studied for bulk PE and aPS. Cooperative transitions occur at second-neighbor bonds for PE, and first-neighbor bonds for aPS due to the role of side groups. The activation energy is a single torsional barrier for overall conformational transitions, and is single torsional barrier plus locally "trapped" barrier for relaxation. Temperature dependence is Arrhenius for transition time, and is WLF for relaxation time. The mean correlation times derived from

  9. Dynamic Power Grid Simulation

    Energy Science and Technology Software Center (ESTSC)

    2015-09-14

    GridDyn is a part of power grid simulation toolkit. The code is designed using modern object oriented C++ methods utilizing C++11 and recent Boost libraries to ensure compatibility with multiple operating systems and environments.

  10. Dynamic Environmental Photosynthetic Imaging Reveals Emergent Phenotypes.

    PubMed

    Cruz, Jeffrey A; Savage, Linda J; Zegarac, Robert; Hall, Christopher C; Satoh-Cruz, Mio; Davis, Geoffry A; Kovac, William Kent; Chen, Jin; Kramer, David M

    2016-06-22

    Understanding and improving the productivity and robustness of plant photosynthesis requires high-throughput phenotyping under environmental conditions that are relevant to the field. Here we demonstrate the dynamic environmental photosynthesis imager (DEPI), an experimental platform for integrated, continuous, and high-throughput measurements of photosynthetic parameters during plant growth under reproducible yet dynamic environmental conditions. Using parallel imagers obviates the need to move plants or sensors, reducing artifacts and allowing simultaneous measurement on large numbers of plants. As a result, DEPI can reveal phenotypes that are not evident under standard laboratory conditions but emerge under progressively more dynamic illumination. We show examples in mutants of Arabidopsis of such "emergent phenotypes" that are highly transient and heterogeneous, appearing in different leaves under different conditions and depending in complex ways on both environmental conditions and plant developmental age. These emergent phenotypes appear to be caused by a range of phenomena, suggesting that such previously unseen processes are critical for plant responses to dynamic environments. PMID:27336966

  11. Dynamic simulation of voltage collapses

    SciTech Connect

    Deuse, J.; Stubbe, M. )

    1993-08-01

    Most of the time the voltage collapse phenomena are studied by means of computer programs designed for the calculation of steady state conditions. But in the real world, the simultaneous occurrences of losses of synchronism, of AVR dynamics or of transformer tap changes call for a full dynamic simulation of voltage phenomena. The present paper shows some examples of dynamic simulations of voltage phenomena using a new general purpose stability program (EUROSTAG), covering in a continuous way the classical fields of transient, mid-term and long-term stability, and also the quasi steady state conditions of a power system.

  12. Floating orbital molecular dynamics simulations.

    PubMed

    Perlt, Eva; Brüssel, Marc; Kirchner, Barbara

    2014-04-21

    We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated. PMID:24600690

  13. Neutron Imaging Reveals Internal Plant Hydraulic Dynamics

    SciTech Connect

    Warren, Jeffrey; Bilheux, Hassina Z; Kang, Misun; Voisin, Sophie; Cheng, Chu-Lin; Horita, Jusuke; Perfect, Edmund

    2013-01-01

    Many terrestrial ecosystem processes are constrained by water availability and transport within the soil. Knowledge of plant water fluxes is thus critical for assessing mechanistic processes linked to biogeochemical cycles, yet resolution of root structure and xylem water transport dynamics has been a particularly daunting task for the ecologist. Through neutron imaging, we demonstrate the ability to non-invasively monitor individual root functionality and water fluxes within Zea mays L. (maize) and Panicum virgatum L. (switchgrass) seedlings growing in a sandy medium. Root structure and growth were readily imaged by neutron radiography and neutron computed tomography. Seedlings were irrigated with water or deuterium oxide and imaged through time as a growth lamp was cycled on to alter leaf demand for water. Sub-millimeter scale resolution reveals timing and magnitudes of root water uptake, redistribution within the roots, and root-shoot hydraulic linkages, relationships not well characterized by other techniques.

  14. Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations

    PubMed Central

    Verma, Sharad; Grover, Sonam; Tyagi, Chetna; Goyal, Sukriti; Jamal, Salma; Singh, Aditi; Grover, Abhinav

    2016-01-01

    p53, a tumor suppressor protein, has been proven to regulate the cell cycle, apoptosis, and DNA repair to prevent malignant transformation. MDM2 regulates activity of p53 and inhibits its binding to DNA. In the present study, we elucidated the MDM2 inhibition potential of polyphenols (Apigenin, Fisetin, Galangin and Luteolin) by MD simulation and MM/PBSA free energy calculations. All polyphenols bind to hydrophobic groove of MDM2 and the binding was found to be stable throughout MD simulation. Luteolin showed the highest negative binding free energy value of -173.80 kJ/mol followed by Fisetin with value of -172.25 kJ/mol. It was found by free energy calculations, that hydrophobic interactions (vdW energy) have major contribution in binding free energy. PMID:26863418

  15. Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations.

    PubMed

    Verma, Sharad; Grover, Sonam; Tyagi, Chetna; Goyal, Sukriti; Jamal, Salma; Singh, Aditi; Grover, Abhinav

    2016-01-01

    p53, a tumor suppressor protein, has been proven to regulate the cell cycle, apoptosis, and DNA repair to prevent malignant transformation. MDM2 regulates activity of p53 and inhibits its binding to DNA. In the present study, we elucidated the MDM2 inhibition potential of polyphenols (Apigenin, Fisetin, Galangin and Luteolin) by MD simulation and MM/PBSA free energy calculations. All polyphenols bind to hydrophobic groove of MDM2 and the binding was found to be stable throughout MD simulation. Luteolin showed the highest negative binding free energy value of -173.80 kJ/mol followed by Fisetin with value of -172.25 kJ/mol. It was found by free energy calculations, that hydrophobic interactions (vdW energy) have major contribution in binding free energy. PMID:26863418

  16. Tree Modeling and Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Tian-shuang, Fu; Yi-bing, Li; Dong-xu, Shen

    This paper introduces the theory about tree modeling and dynamic movements simulation in computer graphics. By comparing many methods we choose Geometry-based rendering as our method. The tree is decomposed into branches and leaves, under the rotation and quaternion methods we realize the tree animation and avoid the Gimbals Lock in Euler rotation. We take Orge 3D as render engine, which has good graphics programming ability. By the end we realize the tree modeling and dynamic movements simulation, achieve realistic visual quality with little computation cost.

  17. DNA sequencing with MspA: Molecular Dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants.

    PubMed

    Manara, Richard M A; Wallace, E Jayne; Khalid, Syma

    2015-01-01

    MspA has been identified as a promising candidate protein as a component of a nanopore-based DNA-sequencing device. However the wildtype protein must be engineered to incorporate all of the features desirable for an accurate and efficient device. In the present study we have utilized atomistic molecular dynamics to perform umbrella-sampling calculations to calculate the potential of mean force (PMF) profiles for translocation of the four DNA nucleotides through MspA. We show there is an energetic barrier to translocation of individual nucleotides through a mutant that closely resembles the wildtype protein, but not through a mutant engineered for the purpose of sequencing. Crucially we are able to quantify the change in free energy for mutating key residues. Thus providing a quantitative characterisation of the energetic impact of individual amino acid sidechains on nucleotide translocation through the pore of MspA. PMID:26255609

  18. DNA sequencing with MspA: Molecular Dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants

    PubMed Central

    Manara, Richard M.A.; Jayne Wallace, E.; Khalid, Syma

    2015-01-01

    MspA has been identified as a promising candidate protein as a component of a nanopore-based DNA-sequencing device. However the wildtype protein must be engineered to incorporate all of the features desirable for an accurate and efficient device. In the present study we have utilized atomistic molecular dynamics to perform umbrella-sampling calculations to calculate the potential of mean force (PMF) profiles for translocation of the four DNA nucleotides through MspA. We show there is an energetic barrier to translocation of individual nucleotides through a mutant that closely resembles the wildtype protein, but not through a mutant engineered for the purpose of sequencing. Crucially we are able to quantify the change in free energy for mutating key residues. Thus providing a quantitative characterisation of the energetic impact of individual amino acid sidechains on nucleotide translocation through the pore of MspA. PMID:26255609

  19. Nanoindentation of Zr by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Lu (芦子哲), Zizhe; Chernatynskiy, Aleksandr; Noordhoek, Mark J.; Sinnott, Susan B.; Phillpot, Simon R.

    2015-12-01

    Molecular dynamics simulations of nanoindentation are used to study the deformation behaviors of single crystal Zr for four different surface orientations. The comparison of results for two different potentials, an embedded atom method potential and a charged optimized many body potential, reveals the influence of stable and unstable stacking fault energy on dislocation behaviors under nanoindentation. The load-displacement curve, hardness and deformation behaviors of the various surface orientations Zr are compared and the elastic and plastic deformation behaviors are analyzed.

  20. Simulation visualization through dynamic instrumentation

    SciTech Connect

    Bisset, K.R.

    1998-09-01

    The goal of the instrument composition system is to allow a simulation user to dynamically create instruments as a simulation executes. Instruments can include graphical displays, data collectors, and debugging aides. Instruments are made up of small building blocks which can be easily combined into larger, more complex instruments. Through the sue of an Attribute Server (a distributed publication/subscription mechanism), the actors and instruments in a simulation can interact without direct knowledge of each other. Instead, each actor publishes the attributes which it has available. An instrument subscribes to the attributes in which it is interested, and is notified whenever the value of one of these attribute changes. An instrument can also publish attributes for use by other instruments. Since the Attribute Server is distributed, the publisher of an attribute need not execute on the same machine as the subscriber. This allows CPU intensive data visualization to execute on separate machines from the simulation, minimizing the impact on the simulation.

  1. Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA

    PubMed Central

    Kogut, Mateusz; Kleist, Cyprian; Czub, Jacek

    2016-01-01

    G-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully understood at the molecular level. Here, we used all-atom molecular dynamics to probe the microscopic origin of the G4 motif stability. By computing the free energy profiles governing the dissociation of the 3′-terminal G-tetrad in the telomeric parallel-stranded G4, we examined the thermodynamic and kinetic stability of a single G-tetrad, as a common structural unit of G4 DNA. Our results indicate that the energetics of guanine association alone does not explain the overall stability of the G-tetrad and that interactions involving sugar–phosphate backbone, in particular, the constrained minimization of the phosphate–phosphate repulsion energy, are crucial in providing the observed enthalpic stabilization. This enthalpic gain is largely compensated by the unfavorable entropy change due to guanine association and optimization of the backbone topology. PMID:26980278

  2. Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad-a common structural unit of G-quadruplex DNA.

    PubMed

    Kogut, Mateusz; Kleist, Cyprian; Czub, Jacek

    2016-04-20

    G-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs formin vivoand are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully understood at the molecular level. Here, we used all-atom molecular dynamics to probe the microscopic origin of the G4 motif stability. By computing the free energy profiles governing the dissociation of the 3'-terminal G-tetrad in the telomeric parallel-stranded G4, we examined the thermodynamic and kinetic stability of a single G-tetrad, as a common structural unit of G4 DNA. Our results indicate that the energetics of guanine association alone does not explain the overall stability of the G-tetrad and that interactions involving sugar-phosphate backbone, in particular, the constrained minimization of the phosphate-phosphate repulsion energy, are crucial in providing the observed enthalpic stabilization. This enthalpic gain is largely compensated by the unfavorable entropy change due to guanine association and optimization of the backbone topology. PMID:26980278

  3. Dynamic Simulation Nuclear Power Plants

    Energy Science and Technology Software Center (ESTSC)

    1992-03-03

    DSNP (Dynamic Simulator for Nuclear Power-Plants) is a system of programs and data files by which a nuclear power plant, or part thereof, can be simulated. The acronym DSNP is used interchangeably for the DSNP language, the DSNP libraries, the DSNP precompiler, and the DSNP document generator. The DSNP language is a special-purpose, block-oriented, digital-simulation language developed to facilitate the preparation of dynamic simulations of a large variety of nuclear power plants. It is amore » user-oriented language that permits the user to prepare simulation programs directly from power plant block diagrams and flow charts by recognizing the symbolic DSNP statements for the appropriate physical components and listing these statements in a logical sequence according to the flow of physical properties in the simulated power plant. Physical components of nuclear power plants are represented by functional blocks, or modules. Many of the more complex components are represented by several modules. The nuclear reactor, for example, has a kinetic module, a power distribution module, a feedback module, a thermodynamic module, a hydraulic module, and a radioactive heat decay module. These modules are stored in DSNP libraries in the form of a DSNP subroutine or function, a block of statements, a macro, or a combination of the above. Basic functional blocks such as integrators, pipes, function generators, connectors, and many auxiliary functions representing properties of materials used in nuclear power plants are also available. The DSNP precompiler analyzes the DSNP simulation program, performs the appropriate translations, inserts the requested modules from the library, links these modules together, searches necessary data files, and produces a simulation program in FORTRAN.« less

  4. Accelerated dynamics simulations of nanotubes.

    SciTech Connect

    Uberuaga, B. P.; Stuart, S. J.; Voter, A. F.

    2002-01-01

    We report on the application of accelerated dynamics techniques to the study of carbon nanotubes. We have used the parallel replica method and temperature accelerated dynamics simulations are currently in progress. In the parallel replica study, we have stretched tubes at a rate significantly lower than that used in previous studies. In these preliminary results, we find that there are qualitative differences in the rupture of the nanotubes at different temperatures. We plan on extending this investigation to include nanotubes of various chiralities. We also plan on exploring unique geometries of nanotubes.

  5. Radiation in molecular dynamic simulations

    SciTech Connect

    Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M

    2008-10-13

    Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.

  6. Neutron Imaging Reveals Internal Plant Hydraulic Dynamics

    NASA Astrophysics Data System (ADS)

    Warren, J.; Bilheux, H.; Kang, M.; Voisin, S.; Cheng, C.; Horita, J.; Perfect, E.

    2011-12-01

    In situ quantification of soil-plant water fluxes have not been fully successful due to a lack of non-destructive techniques capable of revealing roots or water fluxes at relevant spatial scales. Neutron imaging is a unique non-invasive tool that can assess sub-millimeter scale material properties and transport in situ, and which has been successfully applied to characterize soil and plant water status. Here, we have applied neutron radiography and tomography to quantify water transport through individual maize roots in response to internal plant demand. Zea mays seedlings were grown for 10 days in Flint silica sand within 2.6 cm diameter Al chambers. Using a reactor-based neutron source at Oak Ridge National Laboratory (HFIR), water fluxes were tracked through the maize soil-root systems by collecting consecutive neutron radiographs over a 12 h period following irrigation with D2O. D has a much lower neutron attenuation than H, thus D2O displacement of existing H2O within the plant vascular system, or influx of D2O into previously dry tissue or soil is readily tracked by changes in image intensity through time. Plant water release and uptake was regulated by periodically cycling on a high-intensity grow light. From each maize replicate, selected regions of interest (ROI) were delineated around individual roots, root free soil, stem and leaf segments. Changes in ROI were tracked through time to reveal patterns of water flux. The hydration of root and stem tissue cycled in response to illumination; root water content often increased during darkness, then decreased with illumination as water was transported from the root into the stem. Relative root-shoot hydration through time illustrates the balance between demand, storage capacity and uptake, which varies depending on root characteristics and its localized soil environment. The dynamic transport of water between soil, individual roots, stems and leaves was readily visualized and quantified illustrating the value

  7. Stochastic heart-rate model can reveal pathologic cardiac dynamics

    NASA Astrophysics Data System (ADS)

    Kuusela, Tom

    2004-03-01

    A simple one-dimensional Langevin-type stochastic difference equation can simulate the heart-rate fluctuations in a time scale from minutes to hours. The model consists of a deterministic nonlinear part and a stochastic part typical of Gaussian noise, and both parts can be directly determined from measured heart-rate data. Data from healthy subjects typically exhibit the deterministic part with two or more stable fixed points. Studies of 15 congestive heart-failure subjects reveal that the deterministic part of pathologic heart dynamics has no clear stable fixed points. Direct simulations of the stochastic model for normal and pathologic cases can produce statistical parameters similar to those of real subjects. Results directly indicate that pathologic situations simplify the heart-rate control system.

  8. Molecular dynamics simulation of benzene

    NASA Astrophysics Data System (ADS)

    Trumpakaj, Zygmunt; Linde, Bogumił B. J.

    2016-03-01

    Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.

  9. Dynamic simulations of tissue welding

    SciTech Connect

    Maitland, D.J.; Eder, D.C.; London, R.A.; Glinsky, M.E.

    1996-02-01

    The exposure of human skin to near-infrared radiation is numerically simulated using coupled laser, thermal transport and mass transport numerical models. The computer model LATIS is applied in both one-dimensional and two-dimensional geometries. Zones within the skin model are comprised of a topical solder, epidermis, dermis, and fatty tissue. Each skin zone is assigned initial optical, thermal and water density properties consistent with values listed in the literature. The optical properties of each zone (i.e. scattering, absorption and anisotropy coefficients) are modeled as a kinetic function of the temperature. Finally, the water content in each zone is computed from water diffusion where water losses are accounted for by evaporative losses at the air-solder interface. The simulation results show that the inclusion of water transport and evaporative losses in the model are necessary to match experimental observations. Dynamic temperature and damage distributions are presented for the skin simulations.

  10. Rotational Brownian Dynamics simulations of clathrin cage formation

    SciTech Connect

    Ilie, Ioana M.; Briels, Wim J.; Otter, Wouter K. den

    2014-08-14

    The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage.

  11. Molecular Dynamics Simulations of Graphene Oxide Frameworks

    SciTech Connect

    Zhu, Pan; Sumpter, Bobby G; Meunier, V.; Nicolai, Adrien

    2013-01-01

    We use quantum mechanical calculations to develop a full set of force field parameters in order to perform molecular dynamics simulations to understand and optimize the molecular storage properties inside Graphene Oxide Frameworks (GOFs). A set of boron-related parameters for commonly used empirical force fields is determined to describe the non-bonded and bonded interactions between linear boronic acid linkers and graphene sheets of GOF materials. The transferability of the parameters is discussed and their validity is quantified by comparing quantum mechanical and molecular mechanical structural and vibrational properties. The application of the model to the dynamics of water inside the GOFs reveals significant variations in structural flexibility of GOF depending on the linker density, which is shown to be usable as a tuning parameter for desired diffusion properties.

  12. Simulation of Fault Zone Dynamics

    NASA Astrophysics Data System (ADS)

    Mora, P.; Abe, S.; Place, D.

    2002-12-01

    Particle models such as the discrete element model for granular assemblies and the lattice solid model provide a means to study the dynamics of fault zones. The lattice solid model was developed with the aim of progressively building up the capacity to simulate all relevent physical processes in fault zones. The present implementation of the model is able to simulate the dynamics of a granular lattice consisting of bonded or unbonded circular (2D) or spherical (3D) particles. Thermal effects (frictional hear generation, thermal expansion, heat flow) and pore fluid effects (heat induced pore pressure gradients and the consequent Darcian flow and impact on effective friction) can be modelled. Past work involving both circular particles and non-circular grains constructed as groups of bonded particles have demonstrated that grain shape has a fundamental impact on zero-th order behaviour. When circular particles are used, rolling is the most efficient means to accomodate slip of a simulated fault gouge layer leading to unrealistically low friction, typically around 0.2. This is consistent with laboratory results by Mair and Marone which have demonstrated that gouge consisting entirely of spherical beads shows a lower coefficient of friction than gouge containing irregular shaped particles. Recent work comparing quasi-2D laboratory results using pasta (Marone) with 2D numerical results (Morgan) have confirmed that numerical and laboratory results with circular ``particles'' are in agreement. When irregular grains are modelled at the lowest scale, the friction of simulated gouge layers matches with laboratory observations of rock friction (μ ~ 0.6) and is insentitive to the value used for interparticle friction (Mora et al, 2000). This indicates a self-regulation mechanism is occurring in which the group behaviour of the gouge layer remains constant at around 0.6 by balancing the amount of slip and rolling of grains within the gouge layer. A limitation of these studies

  13. AVHRR imagery reveals Antarctic ice dynamics

    SciTech Connect

    Bindschadler, R.A.; Vornberger, P.L. STX Corp., Lanham, MD )

    1990-06-01

    A portion of AVHRR data taken on December 5, 1987 at 06:15 GMT over a part of Antarctica is used here to show that many of the most significant dynamic features of ice sheets can be identified by a careful examination of AVHRR imagery. The relatively low resolution of this instrument makes it ideal for obtaining a broad view of the ice sheets, while its wide swath allows coverage of areas beyond the reach of high-resolution imagers either currently in orbit or planned. An interpretation is given of the present data, which cover the area of ice streams that drain the interior of the West Antarctic ice sheet into the Ross Ice Shelf. 21 refs.

  14. Revealing protein dynamics by photobleaching techniques.

    PubMed

    van Drogen, Frank; Peter, Matthias

    2004-01-01

    Green fluorescent proteins (GFPs) are widely used tools to visualize proteins and study their intracellular distribution. One feature of working with GFP variants, photobleaching, has recently been combined with an older technique known as fluorescence recovery after photobleaching (FRAP) to study protein kinetics in vivo. During photobleaching, fluorochromes get destroyed irreversibly by repeated excitation with an intensive light source. When the photobleaching is applied to a restricted area or structure, recovery of fluorescence will be the result of active or passive diffusion from fluorescent molecules from unbleached surrounding areas. Fluorescence loss in photobleaching (FLIP) is a variant of FRAP where an area is bleached, and loss of fluorescence in surrounding areas is observed. FLIP can be used to study the dynamics of different pools of a protein or can show how a protein diffuses, or is transported through a cell or cellular structure. Here, we discuss these photobleaching fluorescent imaging techniques, illustrated with examples of these techniques applied to proteins of the Saccharomyces cerevisiae pheromone response MAPK pathway. PMID:15173624

  15. Dynamics of riboswitches: Molecular simulations.

    PubMed

    Sanbonmatsu, Karissa Y

    2014-10-01

    Riboswitch RNAs play key roles in bacterial metabolism and represent a promising new class of antibiotic targets for treatment of infectious disease. While many studies of riboswitches have been performed, the exact mechanism of riboswitch operation is still not fully understood at the atomistic level of detail. Molecular dynamics simulations are useful for interpreting existing experimental data and producing predictions for new experiments. Here, a wide range of computational studies on riboswitches is reviewed. By elucidating the key principles of riboswitch operation, computation may aid in the effort to design more specific antibiotics with affinities greater than those of the native ligand. Such a detailed understanding may be required to improve efficacy and reduce side effects. These studies are laying the groundwork for understanding the action mechanism of new compounds that inhibit riboswitch activity. Future directions such as magnesium effects, large-scale conformational changes, expression platforms and co-transcriptional folding are also discussed. This article is part of a Special Issue entitled: Riboswitches. PMID:24953187

  16. Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics.

    PubMed

    Tan, Cheng; Terakawa, Tsuyoshi; Takada, Shoji

    2016-07-13

    Protein binding to DNA changes the DNA's structure, and altered DNA structure can, in turn, modulate the dynamics of protein binding. This mutual dependency is poorly understood. Here we investigated dynamic couplings among protein binding to DNA, protein sliding on DNA, and DNA bending by applying a coarse-grained simulation method to the bacterial architectural protein HU and 14 other DNA-binding proteins. First, we verified our method by showing that the simulated HU exhibits a weak preference for A/T-rich regions of DNA and a much higher affinity for gapped and nicked DNA, consistent with biochemical experiments. The high affinity was attributed to a local DNA bend, but not the specific chemical moiety of the gap/nick. The long-time dynamic analysis revealed that HU sliding is associated with the movement of the local DNA bending site. Deciphering single sliding steps, we found the coupling between HU sliding and DNA bending is akin to neither induced-fit nor population-shift; instead they moved concomitantly. This is reminiscent of a cation transfer on DNA and can be viewed as a protein version of polaron-like sliding. Interestingly, on shorter time scales, HU paused when the DNA was highly bent at the bound position and escaped from pauses once the DNA spontaneously returned to a less bent structure. The HU sliding is largely regulated by DNA bending dynamics. With 14 other proteins, we explored the generality and versatility of the dynamic coupling and found that 6 of the 15 assayed proteins exhibit the polaron-like sliding. PMID:27309278

  17. Substrate Channel in Nitrogenase Revealed by a Molecular Dynamics Approach

    SciTech Connect

    Smith, Dayle; Danyal, Karamatullah; Raugei, Simone; Seefeldt, Lance C.

    2014-03-22

    Mo-dependent nitrogenase catalyzes the biological reduction of N2 to 2NH3 at the FeMo-cofactor buried deep inside the MoFe protein. Access of substrates, such as N2, to the active site is likely restricted by the surrounding protein, requiring substrate channels that lead from the surface to the active site. Earlier studies on crystallographic structures of the MoFe protein have suggested three putative substrate channels. Here, we have utilized sub-microsecond atomistic molecular dynamics simulations to allow the nitrogenase MoFe protein to explore its conformational space in an aqueous solution at physiological ionic strength, revealing a putative substrate channel not previously reported. The viability of the proposed channel was tested by examining the free energy of passage of N2 from the surface through the channel to FeMo-cofactor, with discovery of a very low energy barrier. These studies point to a viable substrate channel in nitrogenase that appears during thermal motions of the protein in an aqueous environment that approaches a face of FeMo-cofactor earlier implicated in substrate binding.

  18. Molecular dynamics simulations of large macromolecular complexes

    PubMed Central

    Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

    2015-01-01

    Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. PMID:25845770

  19. Coarse grained simulation reveals antifreeze properties of hyperactive antifreeze protein from Antarctic bacterium Colwellia sp.

    NASA Astrophysics Data System (ADS)

    Nguyen, Hung; Van, Thanh Dac; Le, Ly

    2015-10-01

    The novel hyperactive antifreeze protein (AFP) of Antarctic sea ice bacterium Colwellia sp. provides a target for studying the protection of psychrophilic microgoranisms against freezing environment. Interestingly, the Colwellia sp. hyperactive antifreeze protein (ColAFP) was crystallized without the structural dynamic characteristics. Here, the result indicated, through coarse grained simulation of ColAFP under various subfreezing temperature, that ColAFP remains active at temperature of equal and greater than 275 K (∼2 °C). Extensive simulation analyses also revealed the adaptive mechanism of ColAFP in subfreezing environment. Our result provides a structural dynamic understanding of the ColAFP.

  20. Computational Models of Protein Kinematics and Dynamics: Beyond Simulation

    PubMed Central

    Gipson, Bryant; Hsu, David; Kavraki, Lydia E.; Latombe, Jean-Claude

    2016-01-01

    Physics-based simulation represents a powerful method for investigating the time-varying behavior of dynamic protein systems at high spatial and temporal resolution. Such simulations, however, can be prohibitively difficult or lengthy for large proteins or when probing the lower-resolution, long-timescale behaviors of proteins generally. Importantly, not all questions about a protein system require full space and time resolution to produce an informative answer. For instance, by avoiding the simulation of uncorrelated, high-frequency atomic movements, a larger, domain-level picture of protein dynamics can be revealed. The purpose of this review is to highlight the growing body of complementary work that goes beyond simulation. In particular, this review focuses on methods that address kinematics and dynamics, as well as those that address larger organizational questions and can quickly yield useful information about the long-timescale behavior of a protein. PMID:22524225

  1. Charge-dependent conformations and dynamics of pamam dendrimers revealed by neutron scattering and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Wu, Bin

    spatial instrumental scales, understanding experimental results involves extensive and difficult data analysis based on liquid theory and condensed matter physics. Therefore, a model that successfully describes the inter- and intra-dendrimer correlations is crucial in obtaining and delivering reliable information. On the other hand, making meaningful comparisons between molecular dynamics and neutron scattering is a fundamental challenge to link simulations and experiments at the nano-scale. This challenge stems from our approach to utilize MD simulation to explain the underlying mechanism of experimental observation. The SANS measurements were conducted on a series of SANS spectrometers including the Extended Q-Range Small-Angle Neutron Scattering Diffractometer (EQ-SANS) and the General-Purpose Small-Angle Neutron Scattering Diffractometer (GP-SANS) at the Oak Ridge National Laboratory (ORNL), and NG7 Small Angle Neutron Scattering Spectrometer at National Institute of Standards (NIST) and Technology in U.S.A., large dynamic range small-angle diffractometer D22 at Institut Laue-Langevin (ILL) in France, and 40m-SANS Spectrometer at Korea Atomic Energy Research Institute (KAERI) in Korea. On the other hand, the Amber molecular dynamics simulation package is utilized to carry out the computational study. In this dissertation, the following observations have been revealed. The previously developed theoretical model for polyelectrolyte dendrimers are adopted to analyze SANS measurements and superb model fitting quality is found. Coupling with advanced contrast variation small angle neutron scattering (CVSANS) data analysis scheme reported recently, the intra-dendrimer hydration and hydrocarbon components distributions are revealed experimentally. The results indeed indicate that the maximum density is located in the molecular center rather than periphery, which is consistent to previous SANS studies and the back-folding picture of PAMAM dendrimers. According to this picture

  2. Brownian Dynamics Simulations of Dispersed Graphene Sheets

    NASA Astrophysics Data System (ADS)

    Xu, Yueyi; Green, Micah

    2013-03-01

    Past simulations of the dynamics of dispersed graphene sheets are limited to static fluids on small timescales, with little attention devoted to flow dynamics. To address this need, we investigated how flow fields affect graphene morphology dynamics using a coarse-grained model; this relatively untouched area is critical given the importance of graphene solution-processing of multifunctional devices and materials. In particular, we developed a Brownian Dynamics (BD) algorithm to study the morphology of sheetlike macromolecules in dilute, flowing solutions. We used a bead-rod lattice to represent the mesoscopic conformation of individual two dimensional sheets. We then analyzed the morphology dynamic modes (stretching, tumbling, crumpling) of these molecules as a function of sheet size, Weissenberg number, and bending stiffness. Our results indicate the model can successfully simulate a range of dynamic modes in a given flow field and yield fundamental insight into the flow processing of graphene sheets.

  3. The "Collisions Cube" Molecular Dynamics Simulator.

    ERIC Educational Resources Information Center

    Nash, John J.; Smith, Paul E.

    1995-01-01

    Describes a molecular dynamics simulator that employs ping-pong balls as the atoms or molecules and is suitable for either large lecture halls or small classrooms. Discusses its use in illustrating many of the fundamental concepts related to molecular motion and dynamics and providing a three-dimensional perspective of molecular motion. (JRH)

  4. Simulating Flexible-Spacecraft Dynamics and Control

    NASA Technical Reports Server (NTRS)

    Fedor, Joseph

    1987-01-01

    Versatile program applies to many types of spacecraft and dynamical problems. Flexible Spacecraft Dynamics and Control program (FSD) developed to aid in simulation of large class of flexible and rigid spacecraft. Extremely versatile and used in attitude dynamics and control analysis as well as in-orbit support of deployment and control of spacecraft. Applicable to inertially oriented spinning, Earth-oriented, or gravity-gradient-stabilized spacecraft. Written in FORTRAN 77.

  5. Molecular Dynamics Simulations of Simple Liquids

    ERIC Educational Resources Information Center

    Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.

    2004-01-01

    An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.

  6. Observing dynamical SUSY breaking with lattice simulation

    SciTech Connect

    Kanamori, Issaku

    2008-11-23

    On the basis of the recently developed lattice formulation of supersymmetric theories which keeps a part of the supersymmetry, we propose a method of observing dynamical SUSY breaking with lattice simulation. We use Hamiltonian as an order parameter and measure the ground state energy as a zero temperature limit of the finite temperature simulation. Our method provides a way of obtaining a physical result from the lattice simulation for supersymmetric theories.

  7. Simulation of liquid dynamics onboard Sloshsat FLEVO

    NASA Astrophysics Data System (ADS)

    Vreeburg, J. P. B.

    1999-01-01

    The Sloshsat FLEVO project has an Investigators Working Group which prepared orbital experiments on the behavior of liquid in spacecraft. These are to be performed with a dedicated small satellite, of about 90 kg empty weight and about 34 kg of water in a 87 litre tank. The spacecraft dynamics are simulated by SMS, the Sloshsat Motion Simulator. SMS predictions and those generated by a CFD simulation are compared for an example.

  8. Molecular dynamics simulations: advances and applications

    PubMed Central

    Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L

    2015-01-01

    Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.

  9. Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations

    NASA Astrophysics Data System (ADS)

    Vijaykumar, Adithya; Bolhuis, Peter G.; ten Wolde, Pieter Rein

    2015-12-01

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

  10. Structure and dynamics of complex liquid water: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    S, Indrajith V.; Natesan, Baskaran

    2015-06-01

    We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

  11. DUVFEL PHOTOINJECTOR DYNAMICS: MEASUREMENT AND SIMULATION.

    SciTech Connect

    GRAVES, W.S.; DIMAURO, L.F.; HEESE, R.; JOHNSON, E.D.; ROSE, J.; RUDATI, J.; SHAFTAN, T.; SHEEHY, B.; YU, L.H.; DOWELL, D.H.

    2001-06-18

    The DUVFEL photoinjector consists of a 1.6 cell BNL gun IV with copper cathode, variable pulse length Ti:Sapp and solenoid magnet. The beam dynamics and the electromagnetic fields in the photoinjector have been characterized by producing a short electron beam with very low charge that is used as a field probe. Transverse beam size and divergence are measured as a function of initial RF phase and initial spot size and compared with simulations using the code HOMDYN. The electromagnetic fields used in the simulations are produced by SUPERFISH, and have been verified with RF measurements. The simulations and measurements of beam dynamics are presented.

  12. Simulation of wetlands forest vegetation dynamics

    USGS Publications Warehouse

    Phipps, R.L.

    1979-01-01

    A computer program, SWAMP, was designed to simulate the effects of flood frequency and depth to water table on southern wetlands forest vegetation dynamics. By incorporating these hydrologic characteristics into the model, forest vegetation and vegetation dynamics can be simulated. The model, based on data from the White River National Wildlife Refuge near De Witt, Arkansas, "grows" individual trees on a 20 x 20-m plot taking into account effects on the tree growth of flooding, depth to water table, shade tolerance, overtopping and crowding, and probability of death and reproduction. A potential application of the model is illustrated with simulations of tree fruit production following flood-control implementation and lumbering. ?? 1979.

  13. Dynamic system simulation of small satellite projects

    NASA Astrophysics Data System (ADS)

    Raif, Matthias; Walter, Ulrich; Bouwmeester, Jasper

    2010-11-01

    A prerequisite to accomplish a system simulation is to have a system model holding all necessary project information in a centralized repository that can be accessed and edited by all parties involved. At the Institute of Astronautics of the Technische Universitaet Muenchen a modular approach for modeling and dynamic simulation of satellite systems has been developed called dynamic system simulation (DySyS). DySyS is based on the platform independent description language SysML to model a small satellite project with respect to the system composition and dynamic behavior. A library of specific building blocks and possible relations between these blocks have been developed. From this library a system model of the satellite of interest can be created. A mapping into a C++ simulation allows the creation of an executable system model with which simulations are performed to observe the dynamic behavior of the satellite. In this paper DySyS is used to model and simulate the dynamic behavior of small satellites, because small satellite projects can act as a precursor to demonstrate the feasibility of a system model since they are less complex compared to a large scale satellite project.

  14. Discrete dislocation dynamics simulations in a cylinder

    NASA Astrophysics Data System (ADS)

    Li, Maosheng; Gao, Chan; Xu, Jianing

    2015-02-01

    Mechanical properties of material are closely related to the motion of dislocations, and predicting the interactions and resulting collective motion of dislocations is a major task in understanding and modelling plastically deforming materials. A discrete dislocation dynamics model is used to describe the orientation substructure within the microstructure. Discrete dislocation dynamics simulations in three dimensions have been used to examine the role of dislocation multiplication and mobility on the plasticity in small samples under uniaxial compression. In this paper we describe the application of the dislocation dynamics simulations in a cylindrical geometry. The boundary conditions for the simulation were estimated from the distribution of the geometrically necessary dislocation density which was obtained from the orientation map. Numerical studies benchmark could validate the accuracy of the algorithms and the importance of handling the singularity correctly. The results of the simulation explain the formation of the experimentally observed substructure.

  15. Spin dynamics simulations at AGS

    SciTech Connect

    Huang, H.; MacKay, W.W.; Meot, F.; Roser, T.

    2010-05-23

    To preserve proton polarization through acceleration, it is important to have a correct model of the process. It has been known that with the insertion of the two helical partial Siberian snakes in the Alternating Gradient Synchrotron (AGS), the MAD model of AGS can not deal with a field map with offset orbit. The stepwise ray-tracing code Zgoubi provides a tool to represent the real electromagnetic fields in the modeling of the optics and spin dynamics for the AGS. Numerical experiments of resonance crossing, including spin dynamics in presence of the snakes and Q-jump, have been performed in AGS lattice models, using Zgoubi. This contribution reports on various results so obtained.

  16. Multibody dynamic simulation of knee contact mechanics

    PubMed Central

    Bei, Yanhong; Fregly, Benjamin J.

    2006-01-01

    Multibody dynamic musculoskeletal models capable of predicting muscle forces and joint contact pressures simultaneously would be valuable for studying clinical issues related to knee joint degeneration and restoration. Current three-dimensional multi-body knee models are either quasi-static with deformable contact or dynamic with rigid contact. This study proposes a computationally efficient methodology for combining multibody dynamic simulation methods with a deformable contact knee model. The methodology requires preparation of the articular surface geometry, development of efficient methods to calculate distances between contact surfaces, implementation of an efficient contact solver that accounts for the unique characteristics of human joints, and specification of an application programming interface for integration with any multibody dynamic simulation environment. The current implementation accommodates natural or artificial tibiofemoral joint models, small or large strain contact models, and linear or nonlinear material models. Applications are presented for static analysis (via dynamic simulation) of a natural knee model created from MRI and CT data and dynamic simulation of an artificial knee model produced from manufacturer’s CAD data. Small and large strain natural knee static analyses required 1 min of CPU time and predicted similar contact conditions except for peak pressure, which was higher for the large strain model. Linear and nonlinear artificial knee dynamic simulations required 10 min of CPU time and predicted similar contact force and torque but different contact pressures, which were lower for the nonlinear model due to increased contact area. This methodology provides an important step toward the realization of dynamic musculoskeletal models that can predict in vivo knee joint motion and loading simultaneously. PMID:15564115

  17. Buckybomb: Reactive Molecular Dynamics Simulation.

    PubMed

    Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V

    2015-03-01

    Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material. PMID:26262672

  18. Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA

    PubMed Central

    Mitchell, J. S.; Laughton, C. A.; Harris, Sarah A.

    2011-01-01

    Although DNA is frequently bent and supercoiled in the cell, much of the available information on DNA structure at the atomistic level is restricted to short linear sequences. We report atomistic molecular dynamics (MD) simulations of a series of DNA minicircles containing between 65 and 110 bp which we compare with a recent biochemical study of structural distortions in these tight DNA loops. We have observed a wealth of non-canonical DNA structures such as kinks, denaturation bubbles and wrinkled conformations that form in response to bending and torsional stress. The simulations show that bending alone is sufficient to induce the formation of kinks in circles containing only 65 bp, but we did not observe any defects in simulations of larger torsionally relaxed circles containing 110 bp over the same MD timescales. We also observed that under-winding in minicircles ranging in size from 65 to 110 bp leads to the formation of single stranded bubbles and wrinkles. These calculations are used to assess the ability of atomistic MD simulations to determine the structure of bent and supercoiled DNA. PMID:21247872

  19. Topological structure dynamics revealing collective evolution in active nematics

    PubMed Central

    Shi, Xia-qing; Ma, Yu-qiang

    2013-01-01

    Topological defects frequently emerge in active matter like bacterial colonies, cytoskeleton extracts on substrates, self-propelled granular or colloidal layers and so on, but their dynamical properties and the relations to large-scale organization and fluctuations in these active systems are seldom touched. Here we reveal, through a simple model for active nematics using self-driven hard elliptic rods, that the excitation, annihilation and transportation of topological defects differ markedly from those in non-active media. These dynamical processes exhibit strong irreversibility in active nematics in the absence of detailed balance. Moreover, topological defects are the key factors in organizing large-scale dynamic structures and collective flows, resulting in multi-spatial temporal effects. These findings allow us to control the self-organization of active matter through topological structures. PMID:24346733

  20. Dynamic procedure for filtered gyrokinetic simulations

    SciTech Connect

    Morel, P.; Banon Navarro, A.; Albrecht-Marc, M.; Carati, D.; Merz, F.; Goerler, T.; Jenko, F.

    2012-01-15

    Large eddy simulations (LES) of gyrokinetic plasma turbulence are investigated as interesting candidates to decrease the computational cost. A dynamic procedure is implemented in the gene code, allowing for dynamic optimization of the free parameters of the LES models (setting the amplitudes of dissipative terms). Employing such LES methods, one recovers the free energy and heat flux spectra obtained from highly resolved direct numerical simulations. Systematic comparisons are performed for different values of the temperature gradient and magnetic shear, parameters which are of prime importance in ion temperature gradient driven turbulence. Moreover, the degree of anisotropy of the problem, which can vary with parameters, can be adapted dynamically by the method that shows gyrokinetic large eddy simulation to be a serious candidate to reduce numerical cost of gyrokinetic solvers.

  1. Computer simulation of microstructural dynamics

    SciTech Connect

    Grest, G.S.; Anderson, M.P.; Srolovitz, D.J.

    1985-01-01

    Since many of the physical properties of materials are determined by their microstructure, it is important to be able to predict and control microstructural development. A number of approaches have been taken to study this problem, but they assume that the grains can be described as spherical or hexagonal and that growth occurs in an average environment. We have developed a new technique to bridge the gap between the atomistic interactions and the macroscopic scale by discretizing the continuum system such that the microstructure retains its topological connectedness, yet is amenable to computer simulations. Using this technique, we have studied grain growth in polycrystalline aggregates. The temporal evolution and grain morphology of our model are in excellent agreement with experimental results for metals and ceramics.

  2. Distortion and flow of nematics simulated by dissipative particle dynamics.

    PubMed

    Zhao, Tongyang; Wang, Xiaogong

    2014-05-14

    In this study, we simulated distortion and flow of nematics by dissipative particle dynamics (DPD). The nematics were modeled by a binary mixture that contained rigid rods composed of DPD particles as mesogenic units and normal DPD particles as solvent. Elastic distortions were investigated by monitoring director orientation in space under influences of boundary anchoring and external fields. Static distortion demonstrated by the simulation is consistent with the prediction of Frank elastic theory. Spatial distortion profile of the director was examined to obtain static elastic constants. Rotational motions of the director under influence of the external field were simulated to understand the dynamic process. The rules revealed by the simulation are in a good agreement with those obtained from dynamical experiments and classical theories for nematics. Three Miesowicz viscosities were obtained by using external fields to hold the orientation of the rods in shear flows. The simulation showed that the Miesowicz viscosities have the order of ηc > ηa > ηb and the rotational viscosity γ1 is about two orders larger than the Miesowicz viscosity ηb. The DPD simulation correctly reproduced the non-monotonic concentration dependence of viscosity, which is a unique property of lyotropic nematic fluids. By comparing simulation results with classical theories for nematics and experiments, the DPD nematic fluids are proved to be a valid model to investigate the distortion and flow of lyotropic nematics. PMID:24832301

  3. Distortion and flow of nematics simulated by dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Zhao, Tongyang; Wang, Xiaogong

    2014-05-01

    In this study, we simulated distortion and flow of nematics by dissipative particle dynamics (DPD). The nematics were modeled by a binary mixture that contained rigid rods composed of DPD particles as mesogenic units and normal DPD particles as solvent. Elastic distortions were investigated by monitoring director orientation in space under influences of boundary anchoring and external fields. Static distortion demonstrated by the simulation is consistent with the prediction of Frank elastic theory. Spatial distortion profile of the director was examined to obtain static elastic constants. Rotational motions of the director under influence of the external field were simulated to understand the dynamic process. The rules revealed by the simulation are in a good agreement with those obtained from dynamical experiments and classical theories for nematics. Three Miesowicz viscosities were obtained by using external fields to hold the orientation of the rods in shear flows. The simulation showed that the Miesowicz viscosities have the order of ηc > ηa > ηb and the rotational viscosity γ1 is about two orders larger than the Miesowicz viscosity ηb. The DPD simulation correctly reproduced the non-monotonic concentration dependence of viscosity, which is a unique property of lyotropic nematic fluids. By comparing simulation results with classical theories for nematics and experiments, the DPD nematic fluids are proved to be a valid model to investigate the distortion and flow of lyotropic nematics.

  4. Dynamic Fracture Simulations of Explosively Loaded Cylinders

    SciTech Connect

    Arthur, Carly W.; Goto, D. M.

    2015-11-30

    This report documents the modeling results of high explosive experiments investigating dynamic fracture of steel (AerMet® 100 alloy) cylinders. The experiments were conducted at Lawrence Livermore National Laboratory (LLNL) during 2007 to 2008 [10]. A principal objective of this study was to gain an understanding of dynamic material failure through the analysis of hydrodynamic computer code simulations. Two-dimensional and three-dimensional computational cylinder models were analyzed using the ALE3D multi-physics computer code.

  5. Dynamic simulation recalls condensate piping event

    SciTech Connect

    Farrell, R.J.; Reneberg, K.O. ); Moy, H.C. )

    1994-05-01

    This article describes how experience gained from simulating and reconstructing a condensate piping event will be used by Consolidated Edison to analyze control system problems. A cooperative effort by Con Edison and the Chemical Engineering Department at Polytechnic University used modular modeling system to investigate the probable cause of a Con Edison condensate piping event. Con Edison commissioned the work to serve as a case study for the more general problem of control systems analysis using dynamic simulation and MMS.

  6. Fluctuation power spectra reveal dynamical heterogeneity of peptides

    NASA Astrophysics Data System (ADS)

    Khatri, Bhavin; Yew, Zu Thur; Krivov, Sergei; McLeish, Tom; Paci, Emanuele

    2010-07-01

    Characterizing the conformational properties and dynamics of biopolymers and their relation to biological activity and function is an ongoing challenge. Single molecule techniques have provided a rich experimental window on these properties, yet they have often relied on simple one-dimensional projections of a multidimensional free energy landscape for a practical interpretation of the results. Here, we study three short peptides with different structural propensity (α helical, β hairpin, and random coil) in the presence (or absence) of a force applied to their ends using Langevin dynamics simulation and an all-atom model with implicit solvation. Each peptide produces fluctuation power spectra with a characteristic dynamic fingerprint consistent with persistent structural motifs of helices, hairpins, and random coils. The spectra for helix formation shows two well-defined relaxation modes, corresponding to local relaxation and cooperative coil to uncoil interconversion. In contrast, both the hairpin and random coil are polymerlike, showing a broad and continuous range of relaxation modes giving characteristic power laws of ω-5/4 and ω-3/2, respectively; the -5/4 power law for hairpins is robust and has not been previously observed. Langevin dynamics simulations of diffusers on a potential of mean force derived from the atomistic simulations fail to reproduce the fingerprints of each peptide motif in the power spectral density, demonstrating explicitly that such information is lacking in such one-dimensional projections. Our results demonstrate the yet unexploited potential of single molecule fluctuation spectroscopy to probe more fine scaled properties of proteins and biological macromolecules and how low dimensional projections may cause the loss of relevant information.

  7. Molecular dynamic simulations of ocular tablet dissolution.

    PubMed

    Ru, Qian; Fadda, Hala M; Li, Chung; Paul, Daniel; Khaw, Peng T; Brocchini, Steve; Zloh, Mire

    2013-11-25

    Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies. PMID:24073784

  8. Airborne Simulation of Launch Vehicle Dynamics

    NASA Technical Reports Server (NTRS)

    Miller, Christopher J.; Orr, Jeb S.; Hanson, Curtis E.; Gilligan, Eric T.

    2015-01-01

    In this paper we present a technique for approximating the short-period dynamics of an exploration-class launch vehicle during flight test with a high-performance surrogate aircraft in relatively benign endoatmospheric flight conditions. The surrogate vehicle relies upon a nonlinear dynamic inversion scheme with proportional-integral feedback to drive a subset of the aircraft states into coincidence with the states of a time-varying reference model that simulates the unstable rigid body dynamics, servodynamics, and parasitic elastic and sloshing dynamics of the launch vehicle. The surrogate aircraft flies a constant pitch rate trajectory to approximate the boost phase gravity turn ascent, and the aircraft's closed-loop bandwidth is sufficient to simulate the launch vehicle's fundamental lateral bending and sloshing modes by exciting the rigid body dynamics of the aircraft. A novel control allocation scheme is employed to utilize the aircraft's relatively fast control effectors in inducing various failure modes for the purposes of evaluating control system performance. Sufficient dynamic similarity is achieved such that the control system under evaluation is configured for the full-scale vehicle with no changes to its parameters, and pilot-control system interaction studies can be performed to characterize the effects of guidance takeover during boost. High-fidelity simulation and flight-test results are presented that demonstrate the efficacy of the design in simulating the Space Launch System (SLS) launch vehicle dynamics using the National Aeronautics and Space Administration (NASA) Armstrong Flight Research Center Fullscale Advanced Systems Testbed (FAST), a modified F/A-18 airplane (McDonnell Douglas, now The Boeing Company, Chicago, Illinois), over a range of scenarios designed to stress the SLS's Adaptive Augmenting Control (AAC) algorithm.

  9. Airborne Simulation of Launch Vehicle Dynamics

    NASA Technical Reports Server (NTRS)

    Gilligan, Eric T.; Miller, Christopher J.; Hanson, Curtis E.; Orr, Jeb S.

    2014-01-01

    In this paper we present a technique for approximating the short-period dynamics of an exploration-class launch vehicle during flight test with a high-performance surrogate aircraft in relatively benign endoatmospheric flight conditions. The surrogate vehicle relies upon a nonlinear dynamic inversion scheme with proportional-integral feedback to drive a subset of the aircraft states into coincidence with the states of a time-varying reference model that simulates the unstable rigid body dynamics, servodynamics, and parasitic elastic and sloshing dynamics of the launch vehicle. The surrogate aircraft flies a constant pitch rate trajectory to approximate the boost phase gravity-turn ascent, and the aircraft's closed-loop bandwidth is sufficient to simulate the launch vehicle's fundamental lateral bending and sloshing modes by exciting the rigid body dynamics of the aircraft. A novel control allocation scheme is employed to utilize the aircraft's relatively fast control effectors in inducing various failure modes for the purposes of evaluating control system performance. Sufficient dynamic similarity is achieved such that the control system under evaluation is optimized for the full-scale vehicle with no changes to its parameters, and pilot-control system interaction studies can be performed to characterize the effects of guidance takeover during boost. High-fidelity simulation and flight test results are presented that demonstrate the efficacy of the design in simulating the Space Launch System (SLS) launch vehicle dynamics using NASA Dryden Flight Research Center's Full-scale Advanced Systems Testbed (FAST), a modified F/A-18 airplane, over a range of scenarios designed to stress the SLS's adaptive augmenting control (AAC) algorithm.

  10. Fully dynamical simulation of central nuclear collisions.

    PubMed

    van der Schee, Wilke; Romatschke, Paul; Pratt, Scott

    2013-11-27

    We present a fully dynamical simulation of central nuclear collisions around midrapidity at LHC energies. Unlike previous treatments, we simulate all phases of the collision, including the equilibration of the system. For the simulation, we use numerical relativity solutions to anti-de Sitter space/conformal field theory for the preequilibrium stage, viscous hydrodynamics for the plasma equilibrium stage, and kinetic theory for the low-density hadronic stage. Our preequilibrium stage provides initial conditions for hydrodynamics, resulting in sizable radial flow. The resulting light particle spectra reproduce the measurements from the ALICE experiment at all transverse momenta. PMID:24329444

  11. Molecular dynamics simulation of ice XII

    NASA Astrophysics Data System (ADS)

    Borzsák, István; Cummings, Peter T.

    1999-02-01

    Molecular dynamics simulations have been performed on the newly discovered metastable ice XII. This new crystalline ice phase [C. Lobban, J.L. Finney, W.F. Kuhs, Nature (London) 391 (1998) 268] is proton-disordered. Thus 90 possible configurations of the unit cell can be constructed which differ only in the orientations of the water molecules. The simulation used the TIP4P potential model for water at constant temperature and density. About one-quarter of the initial configurations did not melt in the course of the simulation. This result is supportive of the experimental structure and also demonstrates the ability of this water model to study ice phases.

  12. Reactive Molecular Dynamics Simulations at the Petascale (Invited)

    NASA Astrophysics Data System (ADS)

    Nakano, A.

    2013-12-01

    We are developing a divide-conquer-recombine algorithmic framework into a metascalable (or 'design once, scale on new architectures') parallelization scheme to perform large spatiotemporal-scale reactive molecular dynamics simulations. The scheme has achieved parallel efficiency well over 0.9 on 786,432 IBM BlueGene/Q processors for 8.5 trillion-atom molecular dynamics and 1.9 trillion electronic degrees-of-freedom quantum molecular dynamics in the framework of density functional theory. Simulation results reveal intricate interplay between photoexcitation, mechanics, flow, and chemical reactions at the nanoscale. Specifically, we will discuss atomistic mechanisms of: (1) rapid hydrogen production from water using metallic alloy nanoparticles; (2) molecular control of charge transfer, charge recombination, and singlet fission for efficient solar cells; and (3) mechanically enhanced reaction kinetics in nanobubbles and nanojets.

  13. Digital simulation of stiff linear dynamic systems.

    NASA Technical Reports Server (NTRS)

    Holland, L. D.; Walsh, J. R., Jr.; Kerr, J. H.

    1972-01-01

    A method is derived for digital computer simulation of linear time-invariant systems when the insignificant eigenvalues involved in such systems are eliminated by an ALSAP root removal technique. The method is applied to a thirteenth-order dynamic system representing a passive RLC network.

  14. Dynamic simulation of a reverse Brayton refrigerator

    SciTech Connect

    Peng, N.; Xiong, L. Y.; Dong, B.; Liu, L. Q.; Lei, L. L.; Tang, J. C.

    2014-01-29

    A test refrigerator based on the modified Reverse Brayton cycle has been developed in the Chinese Academy of Sciences recently. To study the behaviors of this test refrigerator, a dynamic simulation has been carried out. The numerical model comprises the typical components of the test refrigerator: compressor, valves, heat exchangers, expander and heater. This simulator is based on the oriented-object approach and each component is represented by a set of differential and algebraic equations. The control system of the test refrigerator is also simulated, which can be used to optimize the control strategies. This paper describes all the models and shows the simulation results. Comparisons between simulation results and experimental data are also presented. Experimental validation on the test refrigerator gives satisfactory results.

  15. Chain dynamics in a hexadecane melt as seen by neutron scattering and identified by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Morhenn, Humphrey; Busch, Sebastian; Unruh, Tobias

    2012-09-01

    Different local and global chain dynamics in a C16H34 melt could be revealed by resolution resolved time-of-flight quasielastic neutron scattering and complementary molecular dynamics simulations. Thereby it has been demonstrated that the measured intermediate scattering functions can validate the simulated data on the pico- to nanosecond timescale. Remarkably the shape of the experimentally measured intermediate scattering functions can be reproduced excellently by molecular dynamics simulations. It was found that although the extracted apparent activation energy corresponds to the long-range diffusion value, the molecular dynamics in this time range are mainly due to local bond rotations and the rotation of entire molecules.

  16. Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

    PubMed Central

    Chen, Rui; Mias, George I.; Li-Pook-Than, Jennifer; Jiang, Lihua; Lam, Hugo Y. K.; Chen, Rong; Miriami, Elana; Karczewski, Konrad J.; Hariharan, Manoj; Dewey, Frederick E.; Cheng, Yong; Clark, Michael J.; Im, Hogune; Habegger, Lukas; Balasubramanian, Suganthi; O'Huallachain, Maeve; Dudley, Joel T.; Hillenmeyer, Sara; Haraksingh, Rajini; Sharon, Donald; Euskirchen, Ghia; Lacroute, Phil; Bettinger, Keith; Boyle, Alan P.; Kasowski, Maya; Grubert, Fabian; Seki, Scott; Garcia, Marco; Whirl-Carrillo, Michelle; Gallardo, Mercedes; Blasco, Maria A.; Greenberg, Peter L.; Snyder, Phyllis; Klein, Teri E.; Altman, Russ B.; Butte, Atul; Ashley, Euan A.; Nadeau, Kari C.; Gerstein, Mark; Tang, Hua; Snyder, Michael

    2012-01-01

    SUMMARY Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here we present an integrative Personal Omics Profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14-month period. Our iPOP analysis revealed various medical risks, including Type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high coverage genomic and transcriptomic data, which provide the basis of our iPOP, discovered extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism. This study demonstrates that longitudinal iPOP can be used to interpret healthy and disease states by connecting genomic information with additional dynamic omics activity. PMID:22424236

  17. Ultrafast cooling reveals microsecond-scale biomolecular dynamics.

    PubMed

    Polinkovsky, Mark E; Gambin, Yann; Banerjee, Priya R; Erickstad, Michael J; Groisman, Alex; Deniz, Ashok A

    2014-01-01

    The temperature-jump technique, in which the sample is rapidly heated by a powerful laser pulse, has been widely used to probe the fast dynamics of folding of proteins and nucleic acids. However, the existing temperature-jump setups tend to involve sophisticated and expensive instrumentation, while providing only modest temperature changes of ~10-15 °C, and the temperature changes are only rapid for heating, but not cooling. Here we present a setup comprising a thermally conductive sapphire substrate with light-absorptive nano-coating, a microfluidic device and a rapidly switched moderate-power infrared laser with the laser beam focused on the nano-coating, enabling heating and cooling of aqueous solutions by ~50 °C on a 1-μs time scale. The setup is used to probe folding and unfolding dynamics of DNA hairpins after direct and inverse temperature jumps, revealing low-pass filter behaviour during periodic temperature variations. PMID:25517430

  18. ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS*

    PubMed Central

    Aristoff, David; Lelièvre, Tony; Mayne, Christopher G.; Teo, Ivan

    2014-01-01

    Adaptive Multilevel Splitting (AMS) is a replica-based rare event sampling method that has been used successfully in high-dimensional stochastic simulations to identify trajectories across a high potential barrier separating one metastable state from another, and to estimate the probability of observing such a trajectory. An attractive feature of AMS is that, in the limit of a large number of replicas, it remains valid regardless of the choice of reaction coordinate used to characterize the trajectories. Previous studies have shown AMS to be accurate in Monte Carlo simulations. In this study, we extend the application of AMS to molecular dynamics simulations and demonstrate its effectiveness using a simple test system. Our conclusion paves the way for useful applications, such as molecular dynamics calculations of the characteristic time of drug dissociation from a protein target. PMID:26005670

  19. Test of a flexible spacecraft dynamics simulator

    NASA Technical Reports Server (NTRS)

    Dichmann, Donald; Sedlak, Joseph

    1998-01-01

    There are a number of approaches one can take to modeling the dynamics of a flexible body. While one can attempt to capture the full dynamical behavior subject to disturbances from actuators and environmental torques, such a detailed description often is unnecessary. Simplification is possible either by limiting the amplitude of motion to permit linearization of the dynamics equations or by restricting the types of allowed motion. In this work, we study the nonlinear dynamics of bending deformations of wire booms on spinning spacecraft. The theory allows for large amplitude excursions from equilibrium while enforcing constraints on the dynamics to prohibit those modes that are physically less relevant or are expected to damp out fast. These constraints explicitly remove the acoustic modes (i.e., longitudinal sound waves and shear waves) while allowing for arbitrary bending and twisting, motions which typically are of lower frequency. As a test case, a spin axis reorientation maneuver by the Polar Plasma Laboratory (POLAR) spacecraft has been simulated. POLAR was chosen as a representative spacecraft because it has flexible wire antennas that extend to a length of 65 meters. Bending deformations in these antennas could be quite large and have a significant effect on the attitude dynamics of the spacecraft body. Summary results from the simulation are presented along, with a comparison with POLAR flight data.

  20. Dynamic changes in network synchrony reveal resting-state functional networks

    NASA Astrophysics Data System (ADS)

    Vuksanović, Vesna; Hövel, Philipp

    2015-02-01

    Experimental functional magnetic resonance imaging studies have shown that spontaneous brain activity, i.e., in the absence of any external input, exhibit complex spatial and temporal patterns of co-activity between segregated brain regions. These so-called large-scale resting-state functional connectivity networks represent dynamically organized neural assemblies interacting with each other in a complex way. It has been suggested that looking at the dynamical properties of complex patterns of brain functional co-activity may reveal neural mechanisms underlying the dynamic changes in functional interactions. Here, we examine how global network dynamics is shaped by different network configurations, derived from realistic brain functional interactions. We focus on two main dynamics measures: synchrony and variations in synchrony. Neural activity and the inferred hemodynamic response of the network nodes are simulated using a system of 90 FitzHugh-Nagumo neural models subject to system noise and time-delayed interactions. These models are embedded into the topology of the complex brain functional interactions, whose architecture is additionally reduced to its main structural pathways. In the simulated functional networks, patterns of correlated regional activity clearly arise from dynamical properties that maximize synchrony and variations in synchrony. Our results on the fast changes of the level of the network synchrony also show how flexible changes in the large-scale network dynamics could be.

  1. Observed and Simulated Regional North American Vegetation Dynamics: 1982- 2005

    NASA Astrophysics Data System (ADS)

    Neigh, C. S.; Tucker, C. J.; Townshend, J. R.; Collatz, G. J.

    2006-12-01

    Normalized difference vegetation index data from the NOAA series of Advanced Very High Resolution Radiometers (AVHRR) revealed regions in North America that experienced marked increases in annual photosynthetic capacity at various times from 1982 to 2005. Inspection of these anomalous areas with Landsat, Ikonos, aerial photography, and ancillary statistical datasets revealed a range of causes: climatic influences; drought and subsequent recovery; irrigated agriculture expansion; herbivores insect outbreaks followed by logging and subsequent regeneration; and forest fires with subsequent regeneration. We describe an efficient continental monitoring system that simulates biogeochemistry dynamics to quantify changing carbon content of ecosystems.

  2. Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

    SciTech Connect

    Noe, F; Diadone, Isabella; Lollmann, Marc; Sauer, Marcus; Chondera, John D; Smith, Jeremy C

    2011-01-01

    There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is dynamical fingerprints which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.

  3. Simulation studies using multibody dynamics code DART

    NASA Technical Reports Server (NTRS)

    Keat, James E.

    1989-01-01

    DART is a multibody dynamics code developed by Photon Research Associates for the Air Force Astronautics Laboratory (AFAL). The code is intended primarily to simulate the dynamics of large space structures, particularly during the deployment phase of their missions. DART integrates nonlinear equations of motion numerically. The number of bodies in the system being simulated is arbitrary. The bodies' interconnection joints can have an arbitrary number of degrees of freedom between 0 and 6. Motions across the joints can be large. Provision for simulating on-board control systems is provided. Conservation of energy and momentum, when applicable, are used to evaluate DART's performance. After a brief description of DART, studies made to test the program prior to its delivery to AFAL are described. The first is a large angle reorientating of a flexible spacecraft consisting of a rigid central hub and four flexible booms. Reorientation was accomplished by a single-cycle sine wave shape torque input. In the second study, an appendage, mounted on a spacecraft, was slewed through a large angle. Four closed-loop control systems provided control of this appendage and of the spacecraft's attitude. The third study simulated the deployment of the rim of a bicycle wheel configuration large space structure. This system contained 18 bodies. An interesting and unexpected feature of the dynamics was a pulsing phenomena experienced by the stays whole playout was used to control the deployment. A short description of the current status of DART is given.

  4. Mesoscopic Simulation Methods for Polymer Dynamics

    NASA Astrophysics Data System (ADS)

    Larson, Ronald

    2015-03-01

    We assess the accuracy and efficiency of mesoscopic simulation methods, namely Brownian Dynamics (BD), Stochastic Rotation Dynamics (SRD) and Dissipative Particle Dynamics (DPD), for polymers in solution at equilibrium and in flows in microfluidic geometries. Both SRD and DPD use solvent ``particles'' to carry momentum, and so account automatically for hydrodynamic interactions both within isolated polymer coils, and with other polymer molecules and with nearby solid boundaries. We assess quantitatively the effects of artificial particle inertia and fluid compressibility and show that they can be made small with appropriate choice of simulation parameters. We then use these methods to study flow-induced migration of polymer chains produced by: 1) hydrodynamic interactions, 2) streamline curvature or stress-gradients, and 3) convection of wall depletion zones. We show that huge concentration gradients can be produced by these mechanisms in microfluidic geometries that can be exploited for separation of polymers by size in periodic contraction-expansion geometries. We also assess the range of conditions for which BD, SRD or DPD is preferable for mesoscopic simulations. Finally, we show how such methods can be used to simulate quantitatively the swimming of micro-organisms such as E. coli. In collaboration with Lei Jiang and Tongyang Zhao, University of Michigan, Ann Arbor, MI.

  5. Dynamic simulation of the mastication muscles

    NASA Astrophysics Data System (ADS)

    Weingaertner, Tim; Albrecht, Jochen

    1998-05-01

    The purpose of a simulated operation system in craniofacial surgery is to evaluate and visualize the results of operations on the overall facial shape of the patient and on the functionality of his jaw. This paper presents the analyzation of muscle movements in the mastication system by applying real jaw movements to the simulation. With this method an accurate modeling of the mastication muscles can be performed which is a prerequisite for a realistic simulation and precise intra- operative registration. According to this results a large- scale musculoskeletal model of the mastication system is generated including kinematic and dynamic parameters. By integrating distance sensors in the simulation of a segmented CT (computer tomograph) image of the maxilla and mandible the motions of the masticatory muscles during different kinds of jaw movements have been analyzed. The data for this motions have been recorded by a commercial system (CONDYLOCOMP LR3) on a test person and transformed to the graphical simulation system. This method for the first time allows to observe the dynamics of the mastication muscles and their different parameters like muscle length ratio and velocity. The integration of a kinematic model for the jaw movement makes it possible to analyze non traced movements.

  6. Dynamic Simulation of a Helium Liquefier

    SciTech Connect

    Maekawa, R.; Ooba, K.; Mito, T.; Nobutoki, M.

    2004-06-23

    Dynamic behavior of a helium liquefier has been studied in detail with a Cryogenic Process REal-time SimulaTor (C-PREST) at the National Institute for Fusion Science (NIFS). The C-PREST is being developed to integrate large-scale helium cryogenic plant design, operation and maintenance for optimum process establishment. As a first step of simulations of cooldown to 4.5 K with the helium liquefier model is conducted, which provides a plant-process validation platform. The helium liquefier consists of seven heat exchangers, a liquid-nitrogen (LN2) precooler, two expansion turbines and a liquid-helium (LHe) reservoir. Process simulations are fulfilled with sequence programs, which were implemented with C-PREST based on an existing liquefier operation. The interactions of a JT valve, a JT-bypass valve and a reservoir-return valve have been dynamically simulated. The paper discusses various aspects of refrigeration process simulation, including its difficulties such as a balance between complexity of the adopted models and CPU time.

  7. Thermostability of Enzymes from Molecular Dynamics Simulations.

    PubMed

    Zeiske, Tim; Stafford, Kate A; Palmer, Arthur G

    2016-06-14

    Thermodynamic stability is a central requirement for protein function, and one goal of protein engineering is improvement of stability, particularly for applications in biotechnology. Herein, molecular dynamics simulations are used to predict in vitro thermostability of members of the bacterial ribonuclease HI (RNase H) family of endonucleases. The temperature dependence of the generalized order parameter, S, for four RNase H homologues, from psychrotrophic, mesophilic, and thermophilic organisms, is highly correlated with experimentally determined melting temperatures and with calculated free energies of folding at the midpoint temperature of the simulations. This study provides an approach for in silico mutational screens to improve thermostability of biologically and industrially relevant enzymes. PMID:27123810

  8. Dynamical transition of myoglobin revealed by inelastic neutron scattering

    NASA Astrophysics Data System (ADS)

    Doster, Wolfgang; Cusack, Stephen; Petry, Winfried

    1989-02-01

    Structural fluctuations in proteins on the picosecond timescale have been studied in considerable detail by theoretical methods such as molecular dynamics simulation1,2, but there exist very few experimental data with which to test the conclusions. We have used the technique of inelastic neutron scattering to investigate atomic motion in hydrated myoglobin over the temperature range 4 350 K and on the molecular dynamics timescale 0.1 100 ps. At temperatures below 180 K myglobin behaves as a harmonic solid, with essentially only vibrational motion. Above 180 K there is a striking dynamic transition arising from the excitation of non-vibrational motion, which we interpret as corresponding to tor-sional jumps between states of different energy, with a mean energy asymmetry of KJ mol -1. This extra mobility is reflected in a strong temperature dependence of the mean-square atomic displacements, a phenomenon previously observed specifically for the heme iron by Mossbauer spectroscopy3 5, but on a much slower timescale (10-7 s). It also correlates with a glass-like transition in the hydration shell of myoglobin6 and with the temperature-dependence of ligand-binding rates at the heme iron, as monitored by flash photolysis7. In contrast, the crystal structure of myoglobin determined down to 80 K shows no significant structural transition8 10. The dynamical behaviour we find for myoglobin (and other globular proteins) suggests a coupling of fast local motions to slower collective motions, which is a characteristic feature of other dense glass-forming systems.

  9. Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways

    PubMed Central

    Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.

    2014-01-01

    Simulations can provide tremendous insight into atomistic details of biological mechanisms, but micro- to milliseconds timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative, bringing long-timescale processes within reach of a broader community. We used Google's Exacycle cloud computing platform to simulate 2 milliseconds of dynamics of the β2 adrenergic receptor — a major drug target G protein-coupled receptor (GPCR). Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a GPCR, revealing multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design PMID:24345941

  10. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

    NASA Astrophysics Data System (ADS)

    Kohlhoff, Kai J.; Shukla, Diwakar; Lawrenz, Morgan; Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.

    2014-01-01

    Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.

  11. Numerical Simulations of Ion Cloud Dynamics

    NASA Astrophysics Data System (ADS)

    Sillitoe, Nicolas; Hilico, Laurent

    We explain how to perform accurate numerical simulations of ion cloud dynamics by discussing the relevant orders of magnitude of the characteristic times and frequencies involved in the problem and the computer requirement with respect to the ion cloud size. We then discuss integration algorithms and Coulomb force parallelization. We finally explain how to take into account collisions, cooling laser interaction and chemical reactions in a Monte Carlo approach and discuss how to use random number generators to that end.

  12. Multiscale Simulations of the Structure and Dynamics of the Magnetopause

    NASA Astrophysics Data System (ADS)

    Berchem, Jean; Lapenta, Giovanni; Ashour-Abdalla, Maha

    2016-04-01

    Ongoing observations by the spacecraft of NASA's Magnetospheric Multiscale Mission are revealing a very complex structure and dynamics of the low-latitude magnetopause. One of the main difficulties to comprehend physical processes occurring at the magnetopause is that it requires following both the evolution of the large-scale interaction of the solar wind with the dayside magnetosphere, and the details of the kinetic processes that enable transport of energy and mass in localized regions of the magnetospheric boundary. To address this multiscale problem, we have carried out particle-in-cell (PIC) simulations of the dayside magnetopause. These simulations employ domains that are large enough to include large-scale features of the solar wind interaction with the geomagnetic field (e.g., field curvature and plasma asymmetries). The numerical challenge is dealt with by using the implicit iPic3d simulation code together with the results of global magnetohydrodynamic (MHD) simulations. We discuss the results of the PIC simulations in the context of the global MHD states that provide initial and boundary conditions, and local spacecraft observations at the magnetopause. In particular, we analyze the evolution of electromagnetic fields and particle distributions in different regions of the simulations to determine how reconnection processes affect the structure and dynamics of the magnetospheric boundary.

  13. Simulation of counterflow pedestrian dynamics using spheropolygons

    NASA Astrophysics Data System (ADS)

    Alonso-Marroquín, Fernando; Busch, Jonathan; Chiew, Coraline; Lozano, Celia; Ramírez-Gómez, Álvaro

    2014-12-01

    Pedestrian dynamic models are typically designed for comfortable walking or slightly congested conditions and typically use a single disk or combination of three disks for the shape of a pedestrian. Under crowd conditions, a more accurate pedestrian shape has advantages over the traditional single or three-disks model. We developed a method for simulating pedestrian dynamics in a large dense crowd of spheropolygons adapted to the cross section of the chest and arms of a pedestrian. Our numerical model calculates pedestrian motion from Newton's second law, taking into account viscoelastic contact forces, contact friction, and ground-reaction forces. Ground-reaction torque was taken to arise solely from the pedestrians' orientation toward their preferred destination. Simulations of counterflow pedestrians dynamics in corridors were used to gain insight into a tragic incident at the Madrid Arena pavilion in Spain, where five girls were crushed to death. The incident took place at a Halloween Celebration in 2012, in a long, densely crowded hallway used as entrance and exit at the same time. Our simulations reconstruct the mechanism of clogging in the hallway. The hypothetical case of a total evacuation order was also investigated. The results highlights the importance of the pedestrians' density and the effect of counterflow in the onset of avalanches and clogging and provides an estimation of the number of injuries based on a calculation of the contact-force network between the pedestrians.

  14. Simulation of counterflow pedestrian dynamics using spheropolygons.

    PubMed

    Alonso-Marroquín, Fernando; Busch, Jonathan; Chiew, Coraline; Lozano, Celia; Ramírez-Gómez, Álvaro

    2014-12-01

    Pedestrian dynamic models are typically designed for comfortable walking or slightly congested conditions and typically use a single disk or combination of three disks for the shape of a pedestrian. Under crowd conditions, a more accurate pedestrian shape has advantages over the traditional single or three-disks model. We developed a method for simulating pedestrian dynamics in a large dense crowd of spheropolygons adapted to the cross section of the chest and arms of a pedestrian. Our numerical model calculates pedestrian motion from Newton's second law, taking into account viscoelastic contact forces, contact friction, and ground-reaction forces. Ground-reaction torque was taken to arise solely from the pedestrians' orientation toward their preferred destination. Simulations of counterflow pedestrians dynamics in corridors were used to gain insight into a tragic incident at the Madrid Arena pavilion in Spain, where five girls were crushed to death. The incident took place at a Halloween Celebration in 2012, in a long, densely crowded hallway used as entrance and exit at the same time. Our simulations reconstruct the mechanism of clogging in the hallway. The hypothetical case of a total evacuation order was also investigated. The results highlights the importance of the pedestrians' density and the effect of counterflow in the onset of avalanches and clogging and provides an estimation of the number of injuries based on a calculation of the contact-force network between the pedestrians. PMID:25615220

  15. Electronic continuum model for molecular dynamics simulations.

    PubMed

    Leontyev, I V; Stuchebrukhov, A A

    2009-02-28

    A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627

  16. Integrated computer simulation on FIR FEL dynamics

    SciTech Connect

    Furukawa, H.; Kuruma, S.; Imasaki, K.

    1995-12-31

    An integrated computer simulation code has been developed to analyze the RF-Linac FEL dynamics. First, the simulation code on the electron beam acceleration and transport processes in RF-Linac: (LUNA) has been developed to analyze the characteristics of the electron beam in RF-Linac and to optimize the parameters of RF-Linac. Second, a space-time dependent 3D FEL simulation code (Shipout) has been developed. The RF-Linac FEL total simulations have been performed by using the electron beam data from LUNA in Shipout. The number of particles using in a RF-Linac FEL total simulation is approximately 1000. The CPU time for the simulation of 1 round trip is about 1.5 minutes. At ILT/ILE, Osaka, a 8.5MeV RF-Linac with a photo-cathode RF-gun is used for FEL oscillation experiments. By using 2 cm wiggler, the FEL oscillation in the wavelength approximately 46 {mu}m are investigated. By the simulations using LUNA with the parameters of an ILT/ILE experiment, the pulse shape and the energy spectra of the electron beam at the end of the linac are estimated. The pulse shape of the electron beam at the end of the linac has sharp rise-up and it slowly decays as a function of time. By the RF-linac FEL total simulations with the parameters of an ILT/ILE experiment, the dependencies of the start up of the FEL oscillations on the pulse shape of the electron beam at the end of the linac are estimated. The coherent spontaneous emission effects and the quick start up of FEL oscillations have been observed by the RF-Linac FEL total simulations.

  17. Molecular dynamics simulation of liquid sulfur dioxide.

    PubMed

    Ribeiro, Mauro C C

    2006-05-01

    A previously proposed model for molecular dynamics (MD) simulation of liquid sulfur dioxide, SO(2), has been reviewed. Thermodynamic, structural, and dynamical properties were calculated for a large range of thermodynamic states. Predicted (P,V,T) of simulated system agrees with an elaborated equation of state recently proposed for liquid SO(2). Calculated heat capacity, expansion coefficient, and isothermal compressibility are also in good agreement with experimental data. Calculated equilibrium structure agrees with X-ray and neutron scattering measurements on liquid SO(2). The model also predicts the same (SO(2))(2) dimer structure as previously determined by ab initio calculations. Detailed analysis of equilibrium structure of liquid SO(2) is provided, indicating that, despite the rather large dipole moment of the SO(2) molecule, the structure is mainly determined by the Lennard-Jones interactions. Both single-particle and collective dynamics are investigated. Temperature dependency of dynamical properties is given. The MD results are compared with previous findings obtained from the analysis of inelastic neutron scattering spectra of liquid SO(2), including wave-vector dependent structural relaxation, tau(k), and viscosity, eta(k). PMID:16640437

  18. Simulating stochastic dynamics using large time steps.

    PubMed

    Corradini, O; Faccioli, P; Orland, H

    2009-12-01

    We present an approach to investigate the long-time stochastic dynamics of multidimensional classical systems, in contact with a heat bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short- and long-time scales and both molecular dynamics or Monte Carlo (MC) simulations are generally inefficient. Using a field theoretic approach, we perform analytically the average over the short-time stochastic fluctuations. This way, we obtain an effective theory, which generates the same long-time dynamics of the original theory, but has a lower time-resolution power. Such an approach is used to develop an improved version of the MC algorithm, which is particularly suitable to investigate the dynamics of rare conformational transitions. In the specific case of molecular systems at room temperature, we show that elementary integration time steps used to simulate the effective theory can be chosen a factor approximately 100 larger than those used in the original theory. Our results are illustrated and tested on a simple system, characterized by a rugged energy landscape. PMID:20365123

  19. Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Byutner, Oleksiy; Smith, Grant

    2001-03-01

    In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.

  20. Molecular dynamics simulation of radiation damage cascades in diamond

    SciTech Connect

    Buchan, J. T.; Robinson, M.; Christie, H. J.; Roach, D. L.; Ross, D. K.; Marks, N. A.

    2015-06-28

    Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.

  1. Annihilation of craters: Molecular dynamic simulations on a silver surface

    SciTech Connect

    Henriksson, K. O. E.; Nordlund, K.; Keinonen, J.

    2007-12-15

    The ability of silver cluster ions containing 13 atoms to fill in a preexisting crater with a radius of about 28 A ring on a silver (001) target has been investigated using molecular dynamics simulations and the molecular-dynamics-Monte Carlo corrected effective medium potential. The largest lateral distance r between crater and ion was about three times the radius of the preexisting crater, namely, 75 A ring . The results reveal that when r<20 A ring and r>60 A ring the preexisting crater is partially filled in, and for other distances there is a net growth of the crater. The lattice damage created by the cluster ions, the total sputtering yield, the cluster sputtering yield, and simulated transmission electron microscopy images of the irradiated targets are also presented.

  2. A review of the analytical simulation of aircraft crash dynamics

    NASA Technical Reports Server (NTRS)

    Fasanella, Edwin L.; Carden, Huey D.; Boitnott, Richard L.; Hayduk, Robert J.

    1990-01-01

    A large number of full scale tests of general aviation aircraft, helicopters, and one unique air-to-ground controlled impact of a transport aircraft were performed. Additionally, research was also conducted on seat dynamic performance, load-limiting seats, load limiting subfloor designs, and emergency-locator-transmitters (ELTs). Computer programs were developed to provide designers with methods for predicting accelerations, velocities, and displacements of collapsing structure and for estimating the human response to crash loads. The results of full scale aircraft and component tests were used to verify and guide the development of analytical simulation tools and to demonstrate impact load attenuating concepts. Analytical simulation of metal and composite aircraft crash dynamics are addressed. Finite element models are examined to determine their degree of corroboration by experimental data and to reveal deficiencies requiring further development.

  3. Simulating coronal condensation dynamics in 3D

    NASA Astrophysics Data System (ADS)

    Moschou, S. P.; Keppens, R.; Xia, C.; Fang, X.

    2015-12-01

    We present numerical simulations in 3D settings where coronal rain phenomena take place in a magnetic configuration of a quadrupolar arcade system. Our simulation is a magnetohydrodynamic simulation including anisotropic thermal conduction, optically thin radiative losses, and parametrised heating as main thermodynamical features to construct a realistic arcade configuration from chromospheric to coronal heights. The plasma evaporation from chromospheric and transition region heights eventually causes localised runaway condensation events and we witness the formation of plasma blobs due to thermal instability, that evolve dynamically in the heated arcade part and move gradually downwards due to interchange type dynamics. Unlike earlier 2.5D simulations, in this case there is no large scale prominence formation observed, but a continuous coronal rain develops which shows clear indications of Rayleigh-Taylor or interchange instability, that causes the denser plasma located above the transition region to fall down, as the system moves towards a more stable state. Linear stability analysis is used in the non-linear regime for gaining insight and giving a prediction of the system's evolution. After the plasma blobs descend through interchange, they follow the magnetic field topology more closely in the lower coronal regions, where they are guided by the magnetic dips.

  4. Oscillatory Enzyme Dynamics Revealed by Two-Dimensional Infrared Spectroscopy.

    PubMed

    Pagano, Philip; Guo, Qi; Kohen, Amnon; Cheatum, Christopher M

    2016-07-01

    Enzymes move on a variety of length and time scales. While much is known about large structural fluctuations that impact binding of the substrates and release of products, little is known about faster motions of enzymes and how these motions may influence enzyme-catalyzed reactions. This Letter reports frequency fluctuations of the azide anion bound to the active site of formate dehydrogenase measured via 2D IR spectroscopy. These measurements reveal an underdamped oscillatory component to the frequency-frequency correlation function when the azide is bound to the NAD(+) ternary complex. This oscillation disappears when the reduced cofactor is added, indicating that the oscillating contributions most likely come from the charged nicotinamide ring. These oscillatory motions may be relevant to donor-acceptor distance sampling of the catalyzed hydride transfer and therefore may give future insights into the dynamic behavior involved in enzyme catalysis. PMID:27305279

  5. Molecular Dynamics Simulation of Shock Induced Detonation

    NASA Astrophysics Data System (ADS)

    Tomar, Vikas; Zhou, Min

    2004-07-01

    This research focuses on molecular dynamics (MD) simulation of shock induced detonation in Fe2O3+Al thermite mixtures. A MD model is developed to simulate non-equilibrium stress-induced reactions. The focus is on establishing a criterion for reaction initiation, energy content and rate of energy release as functions of mixture and reinforcement characteristics. A cluster functional potential is proposed for this purpose. The potential uses the electronegativity equalization to account for changes in the charge of different species according to local environment. Parameters in the potential are derived to fit to the properties of Fe, Al, Fe2O3, and Al2O3. NPT MD simulations are carried out to qualitatively check the energetics of the forward (Fe2O3+Al) as well as backward (Al2O3+Fe) thermite reactions. The results show that the potential can account for the energetics of thermite reactions.

  6. Dynamic simulator for PEFC propulsion plant

    SciTech Connect

    Hiraide, Masataka; Kaneda, Eiichi; Sato, Takao

    1996-12-31

    This report covers part of a joint study on a PEFC propulsion system for surface ships, summarized in a presentation to this Seminar, entitled {open_quote}Study on a Polymer Electrolyte Fuel Cell (PEFC) Propulsion System for Surface Ships{close_quotes}, and which envisages application to a 1,500 DWT cargo vessel. The work presented here focuses on a simulation study on PEFC propulsion plant performance, and particularly on the system response to changes in load. Using a dynamic simulator composed of system components including fuel cell, various simulations were executed, to examine the performance of the system as a whole and of the individual system components under quick and large load changes such as occasioned by maneuvering operations and by racing when the propeller emerges above water in heavy sea.

  7. Molecular-dynamics simulations of lead clusters

    NASA Astrophysics Data System (ADS)

    Hendy, S. C.; Hall, B. D.

    2001-08-01

    Molecular-dynamics simulations of nanometer-sized lead clusters have been performed using the Lim-Ong-Ercolessi glue potential [Surf. Sci. 269/270, 1109 (1992)]. The binding energies of clusters forming crystalline (fcc), decahedron and icosahedron structures are compared, showing that fcc cuboctahedra are the most energetically favored of these polyhedral model structures. However, simulations of the freezing of liquid droplets produced a characteristic form of surface-reconstructed ``shaved'' icosahedron, in which atoms are absent at the edges and apexes of the polyhedron. This arrangement is energetically favored for 600-4000 atom clusters. Larger clusters favor crystalline structures. Indeed, simulated freezing of a 6525-atom liquid droplet produced an imperfect fcc Wulff particle, containing a number of parallel stacking faults. The effects of temperature on the preferred structure of crystalline clusters below the melting point have been considered. The implications of these results for the interpretation of experimental data is discussed.

  8. Genomic analysis of regulatory network dynamics reveals large topological changes

    NASA Astrophysics Data System (ADS)

    Luscombe, Nicholas M.; Madan Babu, M.; Yu, Haiyuan; Snyder, Michael; Teichmann, Sarah A.; Gerstein, Mark

    2004-09-01

    Network analysis has been applied widely, providing a unifying language to describe disparate systems ranging from social interactions to power grids. It has recently been used in molecular biology, but so far the resulting networks have only been analysed statically. Here we present the dynamics of a biological network on a genomic scale, by integrating transcriptional regulatory information and gene-expression data for multiple conditions in Saccharomyces cerevisiae. We develop an approach for the statistical analysis of network dynamics, called SANDY, combining well-known global topological measures, local motifs and newly derived statistics. We uncover large changes in underlying network architecture that are unexpected given current viewpoints and random simulations. In response to diverse stimuli, transcription factors alter their interactions to varying degrees, thereby rewiring the network. A few transcription factors serve as permanent hubs, but most act transiently only during certain conditions. By studying sub-network structures, we show that environmental responses facilitate fast signal propagation (for example, with short regulatory cascades), whereas the cell cycle and sporulation direct temporal progression through multiple stages (for example, with highly inter-connected transcription factors). Indeed, to drive the latter processes forward, phase-specific transcription factors inter-regulate serially, and ubiquitously active transcription factors layer above them in a two-tiered hierarchy. We anticipate that many of the concepts presented here-particularly the large-scale topological changes and hub transience-will apply to other biological networks, including complex sub-systems in higher eukaryotes.

  9. Spectrins in axonal cytoskeletons: Dynamics revealed by extensions and fluctuations

    NASA Astrophysics Data System (ADS)

    Lai, Lipeng; Cao, Jianshu

    2014-07-01

    The macroscopic properties, the properties of individual components, and how those components interact with each other are three important aspects of a composited structure. An understanding of the interplay between them is essential in the study of complex systems. Using axonal cytoskeleton as an example system, here we perform a theoretical study of slender structures that can be coarse-grained as a simple smooth three-dimensional curve. We first present a generic model for such systems based on the fundamental theorem of curves. We use this generic model to demonstrate the applicability of the well-known worm-like chain (WLC) model to the network level and investigate the situation when the system is stretched by strong forces (weakly bending limit). We specifically studied recent experimental observations that revealed the hitherto unknown periodic cytoskeleton structure of axons and measured the longitudinal fluctuations. Instead of focusing on single molecules, we apply analytical results from the WLC model to both single molecule and network levels and focus on the relations between extensions and fluctuations. We show how this approach introduces constraints to possible local dynamics of the spectrin tetramers in the axonal cytoskeleton and finally suggests simple but self-consistent dynamics of spectrins in which the spectrins in one spatial period of axons fluctuate in-sync.

  10. INCORPORATING DYNAMIC 3D SIMULATION INTO PRA

    SciTech Connect

    Steven R Prescott; Curtis Smith

    2011-07-01

    provide superior results and insights. We also couple the state model with the dynamic 3D simulation analysis representing events (such as flooding) to determine which (if any) components fail. Not only does the simulation take into account any failed items from the state model, but any failures caused by the simulation are incorporated back into the state model and factored into the overall results. Using this method we incorporate accurate 3D simulation results, eliminate static-based PRA issues, and have time ordered failure information.

  11. Circulating protein synthesis rates reveal skeletal muscle proteome dynamics.

    PubMed

    Shankaran, Mahalakshmi; King, Chelsea L; Angel, Thomas E; Holmes, William E; Li, Kelvin W; Colangelo, Marc; Price, John C; Turner, Scott M; Bell, Christopher; Hamilton, Karyn L; Miller, Benjamin F; Hellerstein, Marc K

    2016-01-01

    Here, we have described and validated a strategy for monitoring skeletal muscle protein synthesis rates in rodents and humans over days or weeks from blood samples. We based this approach on label incorporation into proteins that are synthesized specifically in skeletal muscle and escape into the circulation. Heavy water labeling combined with sensitive tandem mass spectrometric analysis allowed integrated synthesis rates of proteins in muscle tissue across the proteome to be measured over several weeks. Fractional synthesis rate (FSR) of plasma creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3) in the blood, more than 90% of which is derived from skeletal muscle, correlated closely with FSR of CK-M, CA-3, and other proteins of various ontologies in skeletal muscle tissue in both rodents and humans. Protein synthesis rates across the muscle proteome generally changed in a coordinate manner in response to a sprint interval exercise training regimen in humans and to denervation or clenbuterol treatment in rodents. FSR of plasma CK-M and CA-3 revealed changes and interindividual differences in muscle tissue proteome dynamics. In human subjects, sprint interval training primarily stimulated synthesis of structural and glycolytic proteins. Together, our results indicate that this approach provides a virtual biopsy, sensitively revealing individualized changes in proteome-wide synthesis rates in skeletal muscle without a muscle biopsy. Accordingly, this approach has potential applications for the diagnosis, management, and treatment of muscle disorders. PMID:26657858

  12. Circulating protein synthesis rates reveal skeletal muscle proteome dynamics

    PubMed Central

    Shankaran, Mahalakshmi; King, Chelsea L.; Angel, Thomas E.; Holmes, William E.; Li, Kelvin W.; Colangelo, Marc; Price, John C.; Turner, Scott M.; Bell, Christopher; Hamilton, Karyn L.; Miller, Benjamin F.; Hellerstein, Marc K.

    2015-01-01

    Here, we have described and validated a strategy for monitoring skeletal muscle protein synthesis rates in rodents and humans over days or weeks from blood samples. We based this approach on label incorporation into proteins that are synthesized specifically in skeletal muscle and escape into the circulation. Heavy water labeling combined with sensitive tandem mass spectrometric analysis allowed integrated synthesis rates of proteins in muscle tissue across the proteome to be measured over several weeks. Fractional synthesis rate (FSR) of plasma creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3) in the blood, more than 90% of which is derived from skeletal muscle, correlated closely with FSR of CK-M, CA-3, and other proteins of various ontologies in skeletal muscle tissue in both rodents and humans. Protein synthesis rates across the muscle proteome generally changed in a coordinate manner in response to a sprint interval exercise training regimen in humans and to denervation or clenbuterol treatment in rodents. FSR of plasma CK-M and CA-3 revealed changes and interindividual differences in muscle tissue proteome dynamics. In human subjects, sprint interval training primarily stimulated synthesis of structural and glycolytic proteins. Together, our results indicate that this approach provides a virtual biopsy, sensitively revealing individualized changes in proteome-wide synthesis rates in skeletal muscle without a muscle biopsy. Accordingly, this approach has potential applications for the diagnosis, management, and treatment of muscle disorders. PMID:26657858

  13. REVEAL: An Extensible Reduced Order Model Builder for Simulation and Modeling

    SciTech Connect

    Agarwal, Khushbu; Sharma, Poorva; Ma, Jinliang; Lo, Chaomei; Gorton, Ian; Liu, Yan

    2013-04-30

    Many science domains need to build computationally efficient and accurate representations of high fidelity, computationally expensive simulations. These computationally efficient versions are known as reduced-order models. This paper presents the design and implementation of a novel reduced-order model (ROM) builder, the REVEAL toolset. This toolset generates ROMs based on science- and engineering-domain specific simulations executed on high performance computing (HPC) platforms. The toolset encompasses a range of sampling and regression methods that can be used to generate a ROM, automatically quantifies the ROM accuracy, and provides support for an iterative approach to improve ROM accuracy. REVEAL is designed to be extensible in order to utilize the core functionality with any simulator that has published input and output formats. It also defines programmatic interfaces to include new sampling and regression techniques so that users can ‘mix and match’ mathematical techniques to best suit the characteristics of their model. In this paper, we describe the architecture of REVEAL and demonstrate its usage with a computational fluid dynamics model used in carbon capture.

  14. Molecular Dynamics Simulation of Iron — A Review

    NASA Astrophysics Data System (ADS)

    Chui, C. P.; Liu, Wenqing; Xu, Yongbing; Zhou, Yan

    2015-12-01

    Molecular dynamics (MD) is a technique of atomistic simulation which has facilitated scientific discovery of interactions among particles since its advent in the late 1950s. Its merit lies in incorporating statistical mechanics to allow for examination of varying atomic configurations at finite temperatures. Its contributions to materials science from modeling pure metal properties to designing nanowires is also remarkable. This review paper focuses on the progress of MD in understanding the behavior of iron — in pure metal form, in alloys, and in composite nanomaterials. It also discusses the interatomic potentials and the integration algorithms used for simulating iron in the literature. Furthermore, it reveals the current progress of MD in simulating iron by exhibiting some results in the literature. Finally, the review paper briefly mentions the development of the hardware and software tools for such large-scale computations.

  15. Monoamine transporters: insights from molecular dynamics simulations

    PubMed Central

    Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit

    2015-01-01

    The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185

  16. Local Refinements in Classical Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Fackeldey, Konstantin; Weber, Marcus

    2014-03-01

    Quantum mechanics provide a detailed description of the physical and chemical behavior of molecules. However, with increasing size of the system the complexity rises exponentially, which is prohibitive for efficient dynamical simulation. In contrast, classical molecular dynamics procure a coarser description by using less degrees of freedom. Thus, it seems natural to seek for an adequate trade-off between accurateness and computational feasibility in the simulation of molecules. Here, we propose a novel method, which combines classical molecular simulations with quantum mechanics for molecular systems. For this we decompose the state space of the respective molecule into subsets, by employing a meshfree partition of unity. We show, that this partition allows us to localize an empirical force field and to run locally constrained classical trajectories. Within each subset, we compute the energy on the quantum level for a fixed number of spatial states (ab initio points). With these energy values from the ab initio points we have a local scattered data problem, which can be solved by the moving least squares method.

  17. Dynamic transitions in molecular dynamics simulations of supercooled silicon

    NASA Astrophysics Data System (ADS)

    Mei, Xiaojun; Eapen, Jacob

    2013-04-01

    Two dynamic transitions or crossovers, one at a low temperature (T* ≈ 1006 K) and the other at a high temperature (T0 ≈ 1384 K), are shown to emerge in supercooled liquid silicon using molecular dynamics simulations. The high-temperature transition (T0) marks the decoupling of stress, density, and energy relaxation mechanisms. At the low-temperature transition (T*), depending on the cooling rate, supercooled silicon can either undergo a high-density-liquid to low-density-liquid (HDL-LDL) phase transition or experience an HDL-HDL crossover. Dynamically heterogeneous domains that emerge with supercooling become prominent across the HDL-HDL transition at 1006 K, with well-separated mobile and immobile regions. Interestingly, across the HDL-LDL transition, the most mobile atoms form large prominent aggregates while the least mobile atoms get spatially dispersed akin to that in a crystalline state. The attendant partial return to spatial uniformity with the HDL-LDL phase transition indicates a dynamic mechanism for relieving the frustration in supercooled states.

  18. Dynamical simulation of dipolar Janus colloids: Dynamical properties

    NASA Astrophysics Data System (ADS)

    Hagy, Matthew C.; Hernandez, Rigoberto

    2013-05-01

    The dynamical properties of dipolar Janus particles are studied through simulation using our previously-developed detailed pointwise (PW) model and an isotropically coarse-grained (CG) model [M. C. Hagy and R. Hernandez, J. Chem. Phys. 137, 044505 (2012), 10.1063/1.4737432]. The CG model is found to have accelerated dynamics relative to the PW model over a range of conditions for which both models have near identical static equilibrium properties. Physically, this suggests dipolar Janus particles have slower transport properties (such as diffusion) in comparison to isotropically attractive particles. Time rescaling and damping with Langevin friction are explored to map the dynamics of the CG model to that of the PW model. Both methods map the diffusion constant successfully and improve the velocity autocorrelation function and the mean squared displacement of the CG model. Neither method improves the distribution of reversible bond durations f(tb) observed in the CG model, which is found to lack the longer duration reversible bonds observed in the PW model. We attribute these differences in f(tb) to changes in the energetics of multiple rearrangement mechanisms. This suggests a need for new methods that map the coarse-grained dynamics of such systems to the true time scale.

  19. Unsupervised Deconvolution of Dynamic Imaging Reveals Intratumor Vascular Heterogeneity and Repopulation Dynamics

    PubMed Central

    Chen, Li; Choyke, Peter L.; Wang, Niya; Clarke, Robert; Bhujwalla, Zaver M.; Hillman, Elizabeth M. C.; Wang, Ge; Wang, Yue

    2014-01-01

    With the existence of biologically distinctive malignant cells originated within the same tumor, intratumor functional heterogeneity is present in many cancers and is often manifested by the intermingled vascular compartments with distinct pharmacokinetics. However, intratumor vascular heterogeneity cannot be resolved directly by most in vivo dynamic imaging. We developed multi-tissue compartment modeling (MTCM), a completely unsupervised method of deconvoluting dynamic imaging series from heterogeneous tumors that can improve vascular characterization in many biological contexts. Applying MTCM to dynamic contrast-enhanced magnetic resonance imaging of breast cancers revealed characteristic intratumor vascular heterogeneity and therapeutic responses that were otherwise undetectable. MTCM is readily applicable to other dynamic imaging modalities for studying intratumor functional and phenotypic heterogeneity, together with a variety of foreseeable applications in the clinic. PMID:25379705

  20. Finite element simulation of pipe dynamic response

    SciTech Connect

    Slagis, G.C.; Litton, R.W.

    1996-12-01

    Nonlinear finite element dynamic analyses of the response of a pipe span to controlled-displacement, sinusoidal vibration have been performed. The objective of this preliminary study is to compare strain and acceleration response data to those generated by Beaney in the Berkeley Nuclear Laboratories experiments. Results for an unpressurized, 5 Hz, carbon steel pipe are in good agreement with the experiments. Hence, it appears that analytical simulation will be useful to assess seismic margins. Recommendations for additional studies are provided. The analyses confirm the test results--dynamic response is greatly attenuated by material plasticity. Analytical strains and accelerations are about 30% higher than test data. There are several possible explanations for the differences. To assess the effect of frequency on response, the length of the pipe span was increased. Analysis of the longer, 2 Hz, pipe span shows significantly greater cyclic strains than the 5 Hz span at the same input excitation levels.

  1. Molecular dynamics simulations of weak detonations.

    PubMed

    Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie

    2011-12-01

    Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal. PMID:22304055

  2. Dynamic simulations of membranes with cytoskeletal interactions

    NASA Astrophysics Data System (ADS)

    Lin, Lawrence C.-L.; Brown, Frank L. H.

    2005-07-01

    We describe a simulation algorithm for the dynamics of elastic membrane sheets over long length and time scales. Our model includes implicit hydrodynamic coupling between membrane and surrounding solvent and allows for arbitrary external forces acting on the membrane surface. In particular, the methodology is well suited to studying membranes in interaction with cytoskeletal filaments. We present results for the thermal undulations of a lipid bilayer attached to a regular network of spectrin filaments as a model for the red blood cell membrane. The dynamic fluctuations of the bilayer over the spectrin network are quantified and used to predict the macroscopic diffusion constant of band 3 on the surface of the red blood cell. We find that thermal undulations likely play a role in the mobility of band 3 in the plane of the erythrocyte membrane.

  3. Osmosis : a molecular dynamics computer simulation study

    NASA Astrophysics Data System (ADS)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  4. Isotropic MD simulations of dynamic brittle fracture

    SciTech Connect

    Espanol, P.; Rubio, M.A.; Zuniga, I.

    1996-12-01

    The authors present results obtained by molecular dynamics simulations on the propagation of fast cracks in triangular 2D lattices. Their aim is to simulate Mode 1 fracture of brittle isotropic materials. They propose a force law that respects the isotropy of the material. The code yields the correct imposed sound c{sub {parallel}}, shear c{sub {perpendicular}} and surface V{sub R} wave speeds. Different notch lengths are systematically studied. They observed that initially the cracks are linear and always branch at a particular critical velocity c* {approx} 0.8V{sub R} and that this occurs when the crack tip reaches the position of a front emitted from the initial crack tip and propagating at a speed c = 0.68V{sub R}.

  5. Dynamic Curving Simulation of Tilting Train

    NASA Astrophysics Data System (ADS)

    Zeng, Jing; Luo, Ren

    The application of carbody tilting technology is the most efficient way to raise train speed during curve negotiations. This paper mainly deals with the dynamic performance simulation of the tilting train. Through the establishment of the nonlinear mathematical model for the titling train electromechanical coupled system, the carbody tilting control law, bogie radial steering mechanism, and titling train curving performance are investigated. The effect of time delay caused by the sensing and control system on the tilting performance of the train is analyzed, and the compensation methods for the time delay effect are studied.

  6. Molecular dynamics simulations of dense plasmas

    SciTech Connect

    Collins, L.A.; Kress, J.D.; Kwon, I.; Lynch, D.L.; Troullier, N.

    1993-12-31

    We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.

  7. Dynamic Deployment Simulations of Inflatable Space Structures

    NASA Technical Reports Server (NTRS)

    Wang, John T.

    2005-01-01

    The feasibility of using Control Volume (CV) method and the Arbitrary Lagrangian Eulerian (ALE) method in LSDYNA to simulate the dynamic deployment of inflatable space structures is investigated. The CV and ALE methods were used to predict the inflation deployments of three folded tube configurations. The CV method was found to be a simple and computationally efficient method that may be adequate for modeling slow inflation deployment sine the inertia of the inflation gas can be neglected. The ALE method was found to be very computationally intensive since it involves the solving of three conservative equations of fluid as well as dealing with complex fluid structure interactions.

  8. Molecular dynamics simulation of bicrystalline metal surface treatment

    SciTech Connect

    Nikonov, A. Yu.

    2015-10-27

    The paper reports the molecular dynamics simulation results on the behavior of a copper crystallite in local frictional contact. The crystallite has a perfect defect-free structure and contains a high-angle grain boundary of type Σ5. The influence of the initial structure on the specimen behavior under loading was analyzed. It is shown that nanoblocks are formed in the subsurface layer. The atomic mechanism of nanofragmentation was studied. A detailed analysis of atomic displacements in the blocks showed that the displacements are rotational. Calculations revealed that the misorientation angle of formed nanoblocks along different directions does not exceed 2 degrees.

  9. Phase Resetting Reveals Network Dynamics Underlying a Bacterial Cell Cycle

    PubMed Central

    Lin, Yihan; Li, Ying; Crosson, Sean; Dinner, Aaron R.; Scherer, Norbert F.

    2012-01-01

    Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In this work we introduce an approach that provides this complementary information and apply it to the bacterium Caulobacter crescentus, a paradigm for cell-cycle control. Operationally, we use an inducible promoter to express the essential transcriptional regulatory gene ctrA in a periodic, pulsed fashion. This chemical perturbation causes the population of cells to divide synchronously, and we use the resulting advance or delay of the division times of single cells to construct a phase resetting curve. We find that delay is strongly favored over advance. This finding is surprising since it does not follow from the temporal expression profile of CtrA and, in turn, simulations of existing network models. We propose a phenomenological model that suggests that the cell-cycle network comprises two distinct functional modules that oscillate autonomously and couple in a highly asymmetric fashion. These features collectively provide a new mechanism for tight temporal control of the cell cycle in C. crescentus. We discuss how the procedure can serve as the basis for a general approach for probing network dynamics, which we term chemical perturbation spectroscopy (CPS). PMID:23209388

  10. Cytoplasmic Dynamics Reveals Two Modes of Nucleoid-Dependent Mobility

    PubMed Central

    Stylianidou, Stella; Kuwada, Nathan J.; Wiggins, Paul A.

    2014-01-01

    It has been proposed that forces resulting from the physical exclusion of macromolecules from the bacterial nucleoid play a central role in organizing the bacterial cell, yet this proposal has not been quantitatively tested. To investigate this hypothesis, we mapped the generic motion of large protein complexes in the bacterial cytoplasm through quantitative analysis of thousands of complete cell-cycle trajectories of fluorescently tagged ectopic MS2-mRNA complexes. We find the motion of these complexes in the cytoplasm is strongly dependent on their spatial position along the long axis of the cell, and that their dynamics are consistent with a quantitative model that requires only nucleoid exclusion and membrane confinement. This analysis also reveals that the nucleoid increases the mobility of MS2-mRNA complexes, resulting in a fourfold increase in diffusion coefficients between regions of the lowest and highest nucleoid density. These data provide strong quantitative support for two modes of nucleoid action: the widely accepted mechanism of nucleoid exclusion in organizing the cell and a newly proposed mode, in which the nucleoid facilitates rapid motion throughout the cytoplasm. PMID:25468347

  11. How to identify dislocations in molecular dynamics simulations?

    NASA Astrophysics Data System (ADS)

    Li, Duo; Wang, FengChao; Yang, ZhenYu; Zhao, YaPu

    2014-12-01

    Dislocations are of great importance in revealing the underlying mechanisms of deformed solid crystals. With the development of computational facilities and technologies, the observations of dislocations at atomic level through numerical simulations are permitted. Molecular dynamics (MD) simulation suggests itself as a powerful tool for understanding and visualizing the creation of dislocations as well as the evolution of crystal defects. However, the numerical results from the large-scale MD simulations are not very illuminating by themselves and there exist various techniques for analyzing dislocations and the deformed crystal structures. Thus, it is a big challenge for the beginners in this community to choose a proper method to start their investigations. In this review, we summarized and discussed up to twelve existing structure characterization methods in MD simulations of deformed crystal solids. A comprehensive comparison was made between the advantages and disadvantages of these typical techniques. We also examined some of the recent advances in the dynamics of dislocations related to the hydraulic fracturing. It was found that the dislocation emission has a significant effect on the propagation and bifurcation of the crack tip in the hydraulic fracturing.

  12. Massively Parallel Reactive and Quantum Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Vashishta, Priya

    2015-03-01

    In this talk I will discuss two simulations: Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near silica surface. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. Quantum molecular dynamics (QMD) simulations are performed on 786,432-processor Blue Gene/Q to study on-demand production of hydrogen gas from water using Al nanoclusters. QMD simulations reveal rapid hydrogen production from water by an Al nanocluster. We find a low activation-barrier mechanism, in which a pair of Lewis acid and base sites on the Aln surface preferentially catalyzes hydrogen production. I will also discuss on-demand production of hydrogen gas from water using and LiAl alloy particles. Research reported in this lecture was carried in collaboration with Rajiv Kalia, Aiichiro Nakano and Ken-ichi Nomura from the University of Southern California, and Fuyuki Shimojo and Kohei Shimamura from Kumamoto University, Japan.

  13. Dynamic stiffness removal for direct numerical simulations

    SciTech Connect

    Lu, Tianfeng; Law, Chung K.; Yoo, Chun Sang; Chen, Jacqueline H.

    2009-08-15

    A systematic approach was developed to derive non-stiff reduced mechanisms for direct numerical simulations (DNS) with explicit integration solvers. The stiffness reduction was achieved through on-the-fly elimination of short time-scales induced by two features of fast chemical reactivity, namely quasi-steady-state (QSS) species and partial-equilibrium (PE) reactions. The sparse algebraic equations resulting from QSS and PE approximations were utilized such that the efficiency of the dynamic stiffness reduction is high compared with general methods of time-scale reduction based on Jacobian decomposition. Using the dimension reduction strategies developed in our previous work, a reduced mechanism with 52 species was first derived from a detailed mechanism with 561 species. The reduced mechanism was validated for ignition and extinction applications over the parameter range of equivalence ratio between 0.5 and 1.5, pressure between 10 and 50 atm, and initial temperature between 700 and 1600 K for ignition, and worst-case errors of approximately 30% were observed. The reduced mechanism with dynamic stiffness removal was then applied in homogeneous and 1-D ignition applications, as well as a 2-D direct numerical simulation of ignition with temperature inhomogeneities at constant volume with integration time-steps of 5-10 ns. The integration was numerically stable and good accuracy was achieved. (author)

  14. Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.

    PubMed

    Kalescky, Robert; Zhou, Hongyu; Liu, Jin; Tao, Peng

    2016-04-01

    Intra-protein information is transmitted over distances via allosteric processes. This ubiquitous protein process allows for protein function changes due to ligand binding events. Understanding protein allostery is essential to understanding protein functions. In this study, allostery in the second PDZ domain (PDZ2) in the human PTP1E protein is examined as model system to advance a recently developed rigid residue scan method combining with configurational entropy calculation and principal component analysis. The contributions from individual residues to whole-protein dynamics and allostery were systematically assessed via rigid body simulations of both unbound and ligand-bound states of the protein. The entropic contributions of individual residues to whole-protein dynamics were evaluated based on covariance-based correlation analysis of all simulations. The changes of overall protein entropy when individual residues being held rigid support that the rigidity/flexibility equilibrium in protein structure is governed by the La Châtelier's principle of chemical equilibrium. Key residues of PDZ2 allostery were identified with good agreement with NMR studies of the same protein bound to the same peptide. On the other hand, the change of entropic contribution from each residue upon perturbation revealed intrinsic differences among all the residues. The quasi-harmonic and principal component analyses of simulations without rigid residue perturbation showed a coherent allosteric mode from unbound and bound states, respectively. The projection of simulations with rigid residue perturbation onto coherent allosteric modes demonstrated the intrinsic shifting of ensemble distributions supporting the population-shift theory of protein allostery. Overall, the study presented here provides a robust and systematic approach to estimate the contribution of individual residue internal motion to overall protein dynamics and allostery. PMID:27115535

  15. Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery

    PubMed Central

    Liu, Jin

    2016-01-01

    Intra-protein information is transmitted over distances via allosteric processes. This ubiquitous protein process allows for protein function changes due to ligand binding events. Understanding protein allostery is essential to understanding protein functions. In this study, allostery in the second PDZ domain (PDZ2) in the human PTP1E protein is examined as model system to advance a recently developed rigid residue scan method combining with configurational entropy calculation and principal component analysis. The contributions from individual residues to whole-protein dynamics and allostery were systematically assessed via rigid body simulations of both unbound and ligand-bound states of the protein. The entropic contributions of individual residues to whole-protein dynamics were evaluated based on covariance-based correlation analysis of all simulations. The changes of overall protein entropy when individual residues being held rigid support that the rigidity/flexibility equilibrium in protein structure is governed by the La Châtelier’s principle of chemical equilibrium. Key residues of PDZ2 allostery were identified with good agreement with NMR studies of the same protein bound to the same peptide. On the other hand, the change of entropic contribution from each residue upon perturbation revealed intrinsic differences among all the residues. The quasi-harmonic and principal component analyses of simulations without rigid residue perturbation showed a coherent allosteric mode from unbound and bound states, respectively. The projection of simulations with rigid residue perturbation onto coherent allosteric modes demonstrated the intrinsic shifting of ensemble distributions supporting the population-shift theory of protein allostery. Overall, the study presented here provides a robust and systematic approach to estimate the contribution of individual residue internal motion to overall protein dynamics and allostery. PMID:27115535

  16. Molecular dynamics simulation of amorphous indomethacin.

    PubMed

    Xiang, Tian-Xiang; Anderson, Bradley D

    2013-01-01

    Molecular dynamics (MD) simulations have been conducted using an assembly consisting of 105 indomethacin (IMC) molecules and 12 water molecules to investigate the underlying dynamic (e.g., rotational and translational diffusivities and conformation relaxation rates) and structural properties (e.g., conformation, hydrogen-bonding distributions, and interactions of water with IMC) of amorphous IMC. These properties may be important in predicting physical stability of this metastable material. The IMC model was constructed using X-ray diffraction data with the force-field parameters mostly assigned by analogy with similar groups in Amber-ff03 and atomic charges calculated with the B3LYP/ccpVTZ30, IEFPCM, and RESP models. The assemblies were initially equilibrated in their molten state and cooled through the glass transition temperature to form amorphous solids. Constant temperature dynamic runs were then carried out above and below the T(g) (i.e., at 600 K (10 ns), 400 K (350 ns), and 298 K (240 ns)). The density (1.312 ± 0.003 g/cm(3)) of the simulated amorphous solid at 298 K was close to the experimental value (1.32 g/cm(3)) while the estimated T(g) (384 K) was ~64 degrees higher than the experimental value (320 K) due to the faster cooling rate. Due to the hindered rotation of its amide bond, IMC can exist in different diastereomeric states. Different IMC conformations were sufficiently sampled in the IMC melt or vapor, but transitions occurred rarely in the glass. The hydrogen-bonding patterns in amorphous IMC are more complex in the amorphous state than in the crystalline polymorphs. Carboxylic dimers that are dominant in α- and γ-crystals were found to occur at a much lower probability in the simulated IMC glasses while hydrogen-bonded IMC chains were more easily identified patterns in the simulated amorphous solids. To determine molecular diffusivity, a novel analytical method is proposed to deal with the non-Einsteinian behavior, in which the temporal

  17. Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations.

    PubMed

    Li, Chun-Xiang; Guo, Wei-Wei; Xie, Bin-Bin; Cui, Ganglong

    2016-08-21

    Herein we have used combined static electronic structure calculations and "on-the-fly" global-switching trajectory surface-hopping dynamics simulations to explore the photochemical mechanism of oxybenzone sunscreen. We have first employed the multi-configurational CASSCF method to optimize minima, conical intersections, and minimum-energy reaction paths related to excited-state intramolecular proton transfer (ESIPT) and excited-state decays in the (1)ππ(∗), (1)nπ(∗), and S0 states (energies are refined at the higher MS-CASPT2 level). According to the mapped potential energy profiles, we have identified two ultrafast excited-state deactivation pathways for the initially populated (1)ππ(∗) system. The first is the diabatic ESIPT process along the (1)ππ(∗) potential energy profile. The generated (1)ππ(∗) keto species then decays to the S0 state via the keto (1)ππ(∗)/gs conical intersection. The second is internal conversion to the dark (1)nπ(∗) state near the (1)ππ(∗) /(1)nπ(∗) crossing point in the course of the diabatic (1)ππ(∗) ESIPT process. Our following dynamics simulations have shown that the ESIPT and (1)ππ(∗) → S0 internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the (1)ππ(∗) → S0 internal conversion in the keto region, the (1)ππ(∗) → (1)nπ(∗) internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone. PMID:27544106

  18. Atomistic molecular dynamic simulations of multiferroics.

    PubMed

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L

    2012-08-10

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings. PMID:23006300

  19. Atomistic Molecular Dynamic Simulations of Multiferroics

    NASA Astrophysics Data System (ADS)

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L.

    2012-08-01

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings.

  20. Dynamical simulations of vesicle growth and division

    NASA Astrophysics Data System (ADS)

    Ruiz-Herrero, Teresa; Mahadevan, L.

    2015-03-01

    Prebiotic cells constitute a beautiful and intriguing example of self-replicating vesicles. How these cells managed to grow and divide without sophisticated machinery is still an open question. The properties of these primitive vesicles can shed light on the ways modern cells have evolved by exploiting those characteristics to develop their replication mechanisms. The equilibrium configurations of elastic shells are well understood, however the dynamical behavior during growth still lacks of a deep theoretical understanding. To study vesicle growth from a general perspective, we have developed a minimal generic model where vesicles are represented by a 2D spring network and characterized by a minimum set of magnitudes: growth rate, permeability, bending stiffness, viscosity and temperature. We have performed hybrid molecuar dynamic simulations as a function of a reduced set of dimensionless parameters. Three main outcomes were observed: vesicles that grow without division, vesicles that divide symmetrically, and vesicles that act as generators of daughter vesicles. The type of outcome depends on the system parameters and specifically on its dynamics via two timescales. Furthermore, we found sets of parameters where the system shows size homeostasis. TRH was supported by Ramon Areces Foundation.

  1. Quantum molecular dynamics simulations of dense matter

    SciTech Connect

    Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I.

    1997-12-31

    The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.

  2. Digital system for structural dynamics simulation

    NASA Technical Reports Server (NTRS)

    Krauter, A. I.; Lagace, L. J.; Wojnar, M. K.; Glor, C.

    1982-01-01

    State-of-the-art digital hardware and software for the simulation of complex structural dynamic interactions, such as those which occur in rotating structures (engine systems). System were incorporated in a designed to use an array of processors in which the computation for each physical subelement or functional subsystem would be assigned to a single specific processor in the simulator. These node processors are microprogrammed bit-slice microcomputers which function autonomously and can communicate with each other and a central control minicomputer over parallel digital lines. Inter-processor nearest neighbor communications busses pass the constants which represent physical constraints and boundary conditions. The node processors are connected to the six nearest neighbor node processors to simulate the actual physical interface of real substructures. Computer generated finite element mesh and force models can be developed with the aid of the central control minicomputer. The control computer also oversees the animation of a graphics display system, disk-based mass storage along with the individual processing elements.

  3. Dynamics simulations for engineering macromolecular interactions

    NASA Astrophysics Data System (ADS)

    Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey

    2013-06-01

    The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could

  4. Dynamics simulations for engineering macromolecular interactions

    PubMed Central

    Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey

    2013-01-01

    The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could

  5. The study of dynamics heterogeneity and slow down of silica by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    San, L. T.; Hung, P. K.; Hue, H. V.

    2016-06-01

    We have numerically studied the diffusion in silica liquids via the SiOx → SiOx±1, OSiy → OSiy±1 reactions and coordination cells (CC). Five models with temperatures from 1000 to 3500 K have been constructed by molecular dynamics simulation. We reveal that the reactions happen not randomly in the space. In addition, the reactions correlated strongly with the mobility of CC atom. Further we examine the clustering of atoms having unbroken bonds and restored bonds. The time evolution of these clusters under temperature is also considered. The simulation shows that both slow down and dynamic heterogeneity (DH) is related not only to the percolation of restored-rigid clusters near glass transition but also to their long lifetime.

  6. Molecular Dynamics Simulations of Homogeneous Crystallization in Polymer Melt

    NASA Astrophysics Data System (ADS)

    Kong, Bin

    2015-03-01

    Molecular mechanisms of homogeneous nucleation and crystal growth from the melt of polyethylene-like polymer were investigated by molecular dynamics simulations. The crystallinity was determined by using the site order parameter method (SOP), which described local order degree around an atom. Snapshots of the simulations showed evolution of the nucleation and the crystal growth through SOP images clearly. The isothermal crystallization kinetics was determined at different temperatures. The rate of crystallization, Kc, and the Avrami exponents, n, were determined as a function of temperature. The forming of nucleis was traced to reveal that the nucleis were formed with more ordered cores and less ordered shells. A detailed statistical analysis of the MD snapshots and trajectories suggested conformations of the polymer chains changed smoothly from random coil to chain folded lamella in the crystallization processes.

  7. Active microrheology of Brownian suspensions via Accelerated Stokesian Dynamics simulations

    NASA Astrophysics Data System (ADS)

    Chu, Henry; Su, Yu; Gu, Kevin; Hoh, Nicholas; Zia, Roseanna

    2015-11-01

    The non-equilibrium rheological response of colloidal suspensions is studied via active microrheology utilizing Accelerated Stokesian Dynamics simulations. In our recent work, we derived the theory for micro-diffusivity and suspension stress in dilute suspensions of hydrodynamically interacting colloids. This work revealed that force-induced diffusion is anisotropic, with qualitative differences between diffusion along the line of the external force and that transverse to it, and connected these effects to the role of hydrodynamic, interparticle, and Brownian forces. This work also revealed that these forces play a similar qualitative role in the anisotropy of the stress and in the evolution of the non-equilibrium osmotic pressure. Here, we show that theoretical predictions hold for suspensions ranging from dilute to near maximum packing, and for a range of flow strengths from near-equilibrium to the pure-hydrodynamic limit.

  8. Revealing the morphological architecture of a shape memory polyurethane by simulation.

    PubMed

    Hu, Jinlian; Zhang, Cuili; Ji, Fenglong; Li, Xun; Han, Jianping; Wu, You

    2016-01-01

    The lack of specific knowledge of the network structure in shape memory polymers (SMPs) has prevented us from gaining an in-depth understanding of their mechanisms and limited the potential for materials innovation. This paper firstly reveals the unit-cell nanoscale morphological architecture of SMPs by simulation. The phase separated architecture of a segmented shape memory polyurethane (SMPU) with a 30 wt% hard segment content (HSC, 4,4'-diphenylmethane diisocyanate (MDI) and 1,4-butanediol (BDO)) showing good shape memory properties was investigated by dissipative particle dynamics (DPD) simulations. A linked-spherical netpoint-frame phase of MDI, a matrix-switch phase of polycaprolactone (PCL) and a connected-spider-like interphase for BDO were obtained for this SMPU. The BDO interphase can reinforce the MDI network. Based on these simulation results, a three-dimensional (3D) overall morphological architectural model of the SMPU can be established. This theoretical study has verified, enriched and integrated two existing schematic models: one being the morphological model deduced from experiments and the other the frame model for SMPs reported before. It can serve as a theoretical guide for smart polymeric materials design. This method for the simulation of polymer structure at the nanoscale can be extended to many areas such as photonic crystals where nanoscale self-assembly plays a vital role. PMID:27373495

  9. Revealing the morphological architecture of a shape memory polyurethane by simulation

    NASA Astrophysics Data System (ADS)

    Hu, Jinlian; Zhang, Cuili; Ji, Fenglong; Li, Xun; Han, Jianping; Wu, You

    2016-07-01

    The lack of specific knowledge of the network structure in shape memory polymers (SMPs) has prevented us from gaining an in-depth understanding of their mechanisms and limited the potential for materials innovation. This paper firstly reveals the unit-cell nanoscale morphological architecture of SMPs by simulation. The phase separated architecture of a segmented shape memory polyurethane (SMPU) with a 30 wt% hard segment content (HSC, 4,4’-diphenylmethane diisocyanate (MDI) and 1,4-butanediol (BDO)) showing good shape memory properties was investigated by dissipative particle dynamics (DPD) simulations. A linked-spherical netpoint-frame phase of MDI, a matrix-switch phase of polycaprolactone (PCL) and a connected-spider-like interphase for BDO were obtained for this SMPU. The BDO interphase can reinforce the MDI network. Based on these simulation results, a three-dimensional (3D) overall morphological architectural model of the SMPU can be established. This theoretical study has verified, enriched and integrated two existing schematic models: one being the morphological model deduced from experiments and the other the frame model for SMPs reported before. It can serve as a theoretical guide for smart polymeric materials design. This method for the simulation of polymer structure at the nanoscale can be extended to many areas such as photonic crystals where nanoscale self-assembly plays a vital role.

  10. Revealing the morphological architecture of a shape memory polyurethane by simulation

    PubMed Central

    Hu, Jinlian; Zhang, Cuili; Ji, Fenglong; Li, Xun; Han, Jianping; Wu, You

    2016-01-01

    The lack of specific knowledge of the network structure in shape memory polymers (SMPs) has prevented us from gaining an in-depth understanding of their mechanisms and limited the potential for materials innovation. This paper firstly reveals the unit-cell nanoscale morphological architecture of SMPs by simulation. The phase separated architecture of a segmented shape memory polyurethane (SMPU) with a 30 wt% hard segment content (HSC, 4,4’-diphenylmethane diisocyanate (MDI) and 1,4-butanediol (BDO)) showing good shape memory properties was investigated by dissipative particle dynamics (DPD) simulations. A linked-spherical netpoint-frame phase of MDI, a matrix-switch phase of polycaprolactone (PCL) and a connected-spider-like interphase for BDO were obtained for this SMPU. The BDO interphase can reinforce the MDI network. Based on these simulation results, a three-dimensional (3D) overall morphological architectural model of the SMPU can be established. This theoretical study has verified, enriched and integrated two existing schematic models: one being the morphological model deduced from experiments and the other the frame model for SMPs reported before. It can serve as a theoretical guide for smart polymeric materials design. This method for the simulation of polymer structure at the nanoscale can be extended to many areas such as photonic crystals where nanoscale self-assembly plays a vital role. PMID:27373495

  11. Revealing the dynamic heterogeneity of PMMA/PVDF blends: from microscopic dynamics to macroscopic properties.

    PubMed

    Lu, Bo; Lamnawar, Khalid; Maazouz, Abderrahim; Zhang, Huagui

    2016-04-01

    An effort was made to demonstrate the dynamic heterogeneity of poly(methyl methacrylate) (PMMA)/poly(vinylidene fluoride) (PVDF) blends, where its composition dependence and the role of interphase were probed. Firstly, the composition dependence of thermorheological complexity of PMMA/PVDF blends in the melt was revealed. The molecular entanglement state involving intra- and interchain entanglements was found to govern the scenario of thermorheological complexity. Intriguingly, local heterogeneity was further demonstrated to exist in the melt-state blends with intermediate compositions, and its origin was depicted to be the interphase. The interphase, coupled with unfavourable interchain entanglements in those blends, could explain the reduced viscosity and speed-up relaxations, contributing to the overall thermorheological complexity. Besides, two experimental glass transition temperatures of blends were resolved in view of segment motions in the miscible phase and the crystal-amorphous interphase, and further assessed via the "self-concentration" concept. The presence of a crystal-amorphous interphase, likely leading to three distinct dynamics of segments in blends, was supposed to contribute to the dynamic heterogeneity in segment relaxations for PMMA/PVDF blends in the solid state. Lastly, effects of dynamic heterogeneity on dynamic mechanical properties were also evaluated. PMID:26932245

  12. Magnetotail dynamics: MHD simulations of driven and spontaneous dynamic changes

    SciTech Connect

    Birn, J.; Schindler, K.; Hesse, M.

    1994-05-01

    The dynamic evolution of the magnetotail during growth phase and expansion phase of a substorm is studied through threedimensional time-dependent MHD simulations. To model growth phase effects, an external electric field with an equatorward inflow is applied at the boundaries over a finite time period. This leads to the formation of a thin current sheet with greatly enhanced current density in the near tail, embedded in the wider plasma/current sheet, which becomes diminished in strength. A faster, spontaneous current sheet formation occurs when entropy conservation is released in an isobaric model, while the ideal MHD constraint persists. This may be a suitable model for the late, explosive part of the growth phase. The transition to the substorm expansive phase is modeled by an increase in anomalous resistivity, using either uniform resistivity or a current density dependent resistivity which is turned on when the current density exceeds a certain threshold. In both cases the violation of ideal MHD leads to resistive instability and the formation of a near-Earth neutral line, fast flow, and plasmoid ejection, together with the dipolarization and current reduction in the region further earthward. The spontaneous increase in total region 1 type field-aligned currents associated with the disruptions of the thin current sheets is less significant than that found in earlier simulations of the disruption of a wider current sheet, whereas the driven increase in the region 1 type current is substantial. The results demonstrate that the same dynamic process which appears spontaneous in the behavior of some quantities might be interpreted as entirely driven from the observation of others.

  13. Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.

    PubMed

    Schwabe, Tobias

    2015-08-20

    For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273

  14. CADS:Cantera Aerosol Dynamics Simulator.

    SciTech Connect

    Moffat, Harry K.

    2007-07-01

    This manual describes a library for aerosol kinetics and transport, called CADS (Cantera Aerosol Dynamics Simulator), which employs a section-based approach for describing the particle size distributions. CADS is based upon Cantera, a set of C++ libraries and applications that handles gas phase species transport and reactions. The method uses a discontinuous Galerkin formulation to represent the particle distributions within each section and to solve for changes to the aerosol particle distributions due to condensation, coagulation, and nucleation processes. CADS conserves particles, elements, and total enthalpy up to numerical round-off error, in all of its formulations. Both 0-D time dependent and 1-D steady state applications (an opposing-flow flame application) have been developed with CADS, with the initial emphasis on developing fundamental mechanisms for soot formation within fires. This report also describes the 0-D application, TDcads, which models a time-dependent perfectly stirred reactor.

  15. Molecular Dynamics Simulations of Water Evaporation

    NASA Astrophysics Data System (ADS)

    Wen, Chengyuan; Grest, Gary; Cheng, Shengfeng

    2015-03-01

    The evaporation of water from the liquid/vapor interface is studied via large-scale molecular dynamics simulations for systems of more than a million atoms at 550K and 600K. The TIP4P-2005 water model whose liquid/vapor surface tension is in excellent agreement with experiments is used. Evaporative cooling at the interface is observed from temperature profiles determined from both translational and rotational kinetic energy. During evaporation, the density of water is slightly enhanced near the liquid-vapor interface. The velocity distribution of water molecules in the vapor phase during evaporation at various distances relative to the interface fit a Maxwell-Boltzmann distribution. While our results indicate an imbalance between evaporating and condensing water molecules, local thermal equilibrium is found to hold in addition to mechanical equilibrium. Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.

  16. Mathematical simulation of Earth system dynamics

    NASA Astrophysics Data System (ADS)

    Dymnikov, V. P.; Lykosov, V. N.; Volodin, E. M.

    2015-05-01

    The mathematical simulation of the Earth system, the dynamics of which depends on physical, chemical, biological, and other processes and which requires interdisciplinary approaches to studying this problem, is considered. The term "the Earth system" extends the concept "the climatic system," since additional geospheres (lithosphere, heliosphere, etc.) are taken into account and a wider range of physical, chemical, biological, and social interactions is described. The present-day level of climate modeling is discussed, and some data obtained at the Institute of Numerical Mathematics, Russian Academy of Sciences (INM RAS), are presented for this purpose. The prospects for further development of climate models toward the creation of the Earth system models based on a seamless approach, according to which a unified model is used to make short-term (several days) and long-term (climatic) prediction, are considered.

  17. Fiber lubrication: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Liu, Hongyi

    Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence

  18. In silico FRET from simulated dye dynamics

    NASA Astrophysics Data System (ADS)

    Hoefling, Martin; Grubmüller, Helmut

    2013-03-01

    Single molecule fluorescence resonance energy transfer (smFRET) experiments probe molecular distances on the nanometer scale. In such experiments, distances are recorded from FRET transfer efficiencies via the Förster formula, E=1/(1+(). The energy transfer however also depends on the mutual orientation of the two dyes used as distance reporter. Since this information is typically inaccessible in FRET experiments, one has to rely on approximations, which reduce the accuracy of these distance measurements. A common approximation is an isotropic and uncorrelated dye orientation distribution. To assess the impact of such approximations, we present the algorithms and implementation of a computational toolkit for the simulation of smFRET on the basis of molecular dynamics (MD) trajectory ensembles. In this study, the dye orientation dynamics, which are used to determine dynamic FRET efficiencies, are extracted from MD simulations. In a subsequent step, photons and bursts are generated using a Monte Carlo algorithm. The application of the developed toolkit on a poly-proline system demonstrated good agreement between smFRET simulations and experimental results and therefore confirms our computational method. Furthermore, it enabled the identification of the structural basis of measured heterogeneity. The presented computational toolkit is written in Python, available as open-source, applicable to arbitrary systems and can easily be extended and adapted to further problems. Catalogue identifier: AENV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv3, the bundled SIMD friendly Mersenne twister implementation [1] is provided under the SFMT-License. No. of lines in distributed program, including test data, etc.: 317880 No. of bytes in distributed program, including test data, etc.: 54774217 Distribution format: tar.gz Programming language

  19. Numerical simulations of Modified Newtonian Dynamics

    NASA Astrophysics Data System (ADS)

    Candlish, G. N.; Smith, R.; Fellhauer, M.

    2016-05-01

    The ΛCDM standard cosmological model is strongly supported by multiple lines of evidence, particularly from observations at large scales such as the CMB and large scale structure. There are some indications, however, of problems at smaller scales. An alternative to the CDM approach is to modify the gravitational force, as exemplified by the MOdified Newtonian Dynamics (MOND) idea. While evidence suggests MOND cannot account for dynamics at all scales without dark matter, it has been successful at galactic scales. Due to the complexity of the theory, however, most tests of MOND have extended no further than using a simple scaling relation to determine rotation curves or velocity dispersions. Therefore, to test the concept more thoroughly we require numerical simulations. We discuss the development and testing of a new N-body solver, using two distinct formulations of MOND, that is incorporated into the RAMSES code. The theory of MOND as a modification of Newtonian gravity is briefly summarised. We then show how it is implemented in the code, providing an example of an idealised test case and future applications.

  20. Numerical simulation of tulip flame dynamics

    SciTech Connect

    Cloutman, L.D.

    1991-11-30

    A finite difference reactive flow hydrodynamics program based on the full Navier-Stokes equations was used to simulate the combustion process in a homogeneous-charge, constant-volume combustion bomb in which an oddly shaped flame, known as a ``tulip flame`` in the literature, occurred. The ``tulip flame`` was readily reproduced in the numerical simulations, producing good agreement with the experimental flame shapes and positions at various times. The calculations provide sufficient detail about the dynamics of the experiment to provide some insight into the physical mechanisms responsible for the peculiar flame shape. Several factors seem to contribute to the tulip formation. The most important process is the baroclinic production of vorticity by the flame front, and this rate of production appears to be dramatically increased by the nonaxial flow generated when the initial semicircular flame front burns out along the sides of the chamber. The vorticity produces a pair of vortices behind the flame that advects the flame into the tulip shape. Boundary layer effects contribute to the details of the flame shape next to the walls of the chamber, but are otherwise not important. 24 refs.

  1. Numerical simulation of tulip flame dynamics

    SciTech Connect

    Cloutman, L.D.

    1991-11-30

    A finite difference reactive flow hydrodynamics program based on the full Navier-Stokes equations was used to simulate the combustion process in a homogeneous-charge, constant-volume combustion bomb in which an oddly shaped flame, known as a tulip flame'' in the literature, occurred. The tulip flame'' was readily reproduced in the numerical simulations, producing good agreement with the experimental flame shapes and positions at various times. The calculations provide sufficient detail about the dynamics of the experiment to provide some insight into the physical mechanisms responsible for the peculiar flame shape. Several factors seem to contribute to the tulip formation. The most important process is the baroclinic production of vorticity by the flame front, and this rate of production appears to be dramatically increased by the nonaxial flow generated when the initial semicircular flame front burns out along the sides of the chamber. The vorticity produces a pair of vortices behind the flame that advects the flame into the tulip shape. Boundary layer effects contribute to the details of the flame shape next to the walls of the chamber, but are otherwise not important. 24 refs.

  2. Molecular dynamics simulations of microscale fluid transport

    SciTech Connect

    Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.

    1998-02-01

    Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.

  3. Consequence modeling using the fire dynamics simulator.

    PubMed

    Ryder, Noah L; Sutula, Jason A; Schemel, Christopher F; Hamer, Andrew J; Van Brunt, Vincent

    2004-11-11

    The use of Computational Fluid Dynamics (CFD) and in particular Large Eddy Simulation (LES) codes to model fires provides an efficient tool for the prediction of large-scale effects that include plume characteristics, combustion product dispersion, and heat effects to adjacent objects. This paper illustrates the strengths of the Fire Dynamics Simulator (FDS), an LES code developed by the National Institute of Standards and Technology (NIST), through several small and large-scale validation runs and process safety applications. The paper presents two fire experiments--a small room fire and a large (15 m diameter) pool fire. The model results are compared to experimental data and demonstrate good agreement between the models and data. The validation work is then extended to demonstrate applicability to process safety concerns by detailing a model of a tank farm fire and a model of the ignition of a gaseous fuel in a confined space. In this simulation, a room was filled with propane, given time to disperse, and was then ignited. The model yields accurate results of the dispersion of the gas throughout the space. This information can be used to determine flammability and explosive limits in a space and can be used in subsequent models to determine the pressure and temperature waves that would result from an explosion. The model dispersion results were compared to an experiment performed by Factory Mutual. Using the above examples, this paper will demonstrate that FDS is ideally suited to build realistic models of process geometries in which large scale explosion and fire failure risks can be evaluated with several distinct advantages over more traditional CFD codes. Namely transient solutions to fire and explosion growth can be produced with less sophisticated hardware (lower cost) than needed for traditional CFD codes (PC type computer verses UNIX workstation) and can be solved for longer time histories (on the order of hundreds of seconds of computed time) with

  4. Dynamic Shade and Irradiance Simulation of Aquatic Landscapes and Watersheds

    EPA Science Inventory

    Penumbra is a landscape shade and irradiance simulation model that simulates how solar energy spatially and temporally interacts within dynamic ecosystems such as riparian zones, forests, and other terrain that cast topological shadows. Direct and indirect solar energy accumulate...

  5. Validation of vehicle dynamics simulation models - a review

    NASA Astrophysics Data System (ADS)

    Kutluay, Emir; Winner, Hermann

    2014-02-01

    In this work, a literature survey on the validation of vehicle dynamics simulation models is presented. Estimating the dynamic responses of existing or proposed vehicles has a wide array of applications in the development of vehicle technologies, e.g. active suspensions, controller design, driver assistance systems, etc. Although simulation environments, measurement tools and mathematical theories on vehicle dynamics are well established, the methodical link between the experimental test data and validity analysis of the simulation model is still lacking. This report presents different views on the definition of validation, and its usage in vehicle dynamics simulation models.

  6. Laser altimetry reveals complex pattern of Greenland Ice Sheet dynamics.

    PubMed

    Csatho, Beata M; Schenk, Anton F; van der Veen, Cornelis J; Babonis, Gregory; Duncan, Kyle; Rezvanbehbahani, Soroush; van den Broeke, Michiel R; Simonsen, Sebastian B; Nagarajan, Sudhagar; van Angelen, Jan H

    2014-12-30

    We present a new record of ice thickness change, reconstructed at nearly 100,000 sites on the Greenland Ice Sheet (GrIS) from laser altimetry measurements spanning the period 1993-2012, partitioned into changes due to surface mass balance (SMB) and ice dynamics. We estimate a mean annual GrIS mass loss of 243 ± 18 Gt ⋅ y(-1), equivalent to 0.68 mm ⋅ y(-1) sea level rise (SLR) for 2003-2009. Dynamic thinning contributed 48%, with the largest rates occurring in 2004-2006, followed by a gradual decrease balanced by accelerating SMB loss. The spatial pattern of dynamic mass loss changed over this time as dynamic thinning rapidly decreased in southeast Greenland but slowly increased in the southwest, north, and northeast regions. Most outlet glaciers have been thinning during the last two decades, interrupted by episodes of decreasing thinning or even thickening. Dynamics of the major outlet glaciers dominated the mass loss from larger drainage basins, and simultaneous changes over distances up to 500 km are detected, indicating climate control. However, the intricate spatiotemporal pattern of dynamic thickness change suggests that, regardless of the forcing responsible for initial glacier acceleration and thinning, the response of individual glaciers is modulated by local conditions. Recent projections of dynamic contributions from the entire GrIS to SLR have been based on the extrapolation of four major outlet glaciers. Considering the observed complexity, we question how well these four glaciers represent all of Greenland's outlet glaciers. PMID:25512537

  7. Studying Interactions by Molecular Dynamics Simulations at High Concentration

    PubMed Central

    Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C. E.; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro

    2012-01-01

    Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. PMID:22500085

  8. Eye Movements Reveal the Dynamic Simulation of Speed in Language

    ERIC Educational Resources Information Center

    Speed, Laura J.; Vigliocco, Gabriella

    2014-01-01

    This study investigates how speed of motion is processed in language. In three eye-tracking experiments, participants were presented with visual scenes and spoken sentences describing fast or slow events (e.g., "The lion ambled/dashed to the balloon"). Results showed that looking time to relevant objects in the visual scene was affected…

  9. Analysis & Simulation of Dynamics in Supercooled Liquids

    NASA Astrophysics Data System (ADS)

    Elmatad, Yael Sarah

    2011-12-01

    The nature of supercooled liquids and the glass transition has been debated by many scientists. Several theories have been put forth to describe the remarkable properties of this out-of-equilibrium material. Each of these theories makes specific predictions as to how the scaling of various transport properties in supercooled materials should behave. Given access to a large pool of high-quality supercooled liquid data we seek to compare these theories to one another. Moreover, we explore properties of a pair of models which are the basis for one particularly attractive theory---Chandler-Garrahan theory---and discuss the models' behavior in space-time and possible implications to the behavior of experimental supercooled liquids. Here we investigate the nature of dynamics in supercooled liquids using a two pronged approach. First we analyze the transport properties found in experiments and simulations of supercooled liquids. Then, we analyze simulation trajectories for lattice models which reproduce many of the interesting properties of supercooled liquids. In doing so, we illuminate several glass universalities, common properties of a wide variety of glass formers. By analyzing relaxation time and viscosity data for over 50 data sets and 1200 points, we find that relaxation time can be collapsed onto a single, parabolic curve. This collapse supports a theory of universal glass behavior based on facilitated models proposed by David Chandler and Juan Garrahan in 2003. We then show that the parabolic fit parameters for any particular liquid are a material property: they converge fast and are capable of predicting behavior in regions beyond the included data sets. We compare this property to other popular fitting schemes such as the Vogel-Fulcher, double exponential, and fractional exponential forms and conclude that these three forms result in parameters which are non predictive and therefore not material properties. Additionally, we examine the role of attractive

  10. Simulations reveal the role of composition into the atomic-level flexibility of bioactive glass cements.

    PubMed

    Tian, Kun Viviana; Chass, Gregory A; Di Tommaso, Devis

    2016-01-14

    Bioactive glass ionomer cements (GICs), the reaction product of a fluoro-alumino-silicate glass and polyacrylic acid, have been in effective use in dentistry for over 40 years and more recently in orthopaedics and medical implantation. Their desirable properties have affirmed GIC's place in the medical materials community, yet are limited to non-load bearing applications due to the brittle nature of the hardened composite cement, thought to arise from the glass component and the interfaces it forms. Towards helping resolve the fundamental bases of the mechanical shortcomings of GICs, we report the 1st ever computational models of a GIC-relevant component. Ab initio molecular dynamics simulations were employed to generate and characterise three fluoro-alumino-silicate glasses of differing compositions with focus on resolving the atomic scale structural and dynamic contributions of aluminium, phosphorous and fluorine. Analyses of the glasses revealed rising F-content leading to the expansion of the glass network, compression of Al-F bonding, angular constraint at Al-pivots, localisation of alumino-phosphates and increased fluorine diffusion. Together, these changes to the structure, speciation and dynamics with raised fluorine content impart an overall rigidifying effect on the glass network, and suggest a predisposition to atomic-level inflexibility, which could manifest in the ionomer cements they form. PMID:26646505

  11. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

    PubMed Central

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-01-01

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

  12. Accurate Langevin approaches to simulate Markovian channel dynamics

    NASA Astrophysics Data System (ADS)

    Huang, Yandong; Rüdiger, Sten; Shuai, Jianwei

    2015-12-01

    The stochasticity of ion-channels dynamic is significant for physiological processes on neuronal cell membranes. Microscopic simulations of the ion-channel gating with Markov chains can be considered to be an accurate standard. However, such Markovian simulations are computationally demanding for membrane areas of physiologically relevant sizes, which makes the noise-approximating or Langevin equation methods advantageous in many cases. In this review, we discuss the Langevin-like approaches, including the channel-based and simplified subunit-based stochastic differential equations proposed by Fox and Lu, and the effective Langevin approaches in which colored noise is added to deterministic differential equations. In the framework of Fox and Lu’s classical models, several variants of numerical algorithms, which have been recently developed to improve accuracy as well as efficiency, are also discussed. Through the comparison of different simulation algorithms of ion-channel noise with the standard Markovian simulation, we aim to reveal the extent to which the existing Langevin-like methods approximate results using Markovian methods. Open questions for future studies are also discussed.

  13. High frequency dynamic engine simulation. [TF-30 engine

    NASA Technical Reports Server (NTRS)

    Schuerman, J. A.; Fischer, K. E.; Mclaughlin, P. W.

    1977-01-01

    A digital computer simulation of a mixed flow, twin spool turbofan engine was assembled to evaluate and improve the dynamic characteristics of the engine simulation to disturbance frequencies of at least 100 Hz. One dimensional forms of the dynamic mass, momentum and energy equations were used to model the engine. A TF30 engine was simulated so that dynamic characteristics could be evaluated against results obtained from testing of the TF30 engine at the NASA Lewis Research Center. Dynamic characteristics of the engine simulation were improved by modifying the compression system model. Modifications to the compression system model were established by investigating the influence of size and number of finite dynamic elements. Based on the results of this program, high frequency engine simulations using finite dynamic elements can be assembled so that the engine dynamic configuration is optimum with respect to dynamic characteristics and computer execution time. Resizing of the compression systems finite elements improved the dynamic characteristics of the engine simulation but showed that additional refinements are required to obtain close agreement simulation and actual engine dynamic characteristics.

  14. Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

    SciTech Connect

    Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto; Shimojo, Fuyuki

    2015-08-17

    The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)

  15. Nanoscale deicing by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-07-01

    Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice

  16. Molecular Dynamics Simulation of Disordered Zircon

    SciTech Connect

    Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin

    2004-02-27

    The melting of zircon and the amorphous state produced by quenching from the melt were simulated by molecular dynamics using a new partial charge model combined with the Ziegler-Biersack-Littmark potential. The model has been established for the description of the crystalline and aperiodic structures of zircon in order to be used for the simulation of displacement cascades. It provides an excellent fit to the structure, and accounts with convenient precision the mechanical and thermodynamic properties of zircon. The calculated melting temperature is about 2100 K. The activation energy for self-diffusion of ions in the liquid state was determined to be 190-200 kJ/mole. Melt quenching was employed to produce two different disordered states with distinct densities and structures. In the high density disordered state, the zircon structure is intact but the bond angle distributions are broader, 4% of the Si units are polymerized, and the volume swelling is about 8%. In the low density amorphous state, the Zr and Si coordination numbers are lower, and the Zr-O and Si-O bond lengths are shorter than corresponding values for the crystal. In addition, a highly polymerized Si network, with average connectivity of two, is observed in the low density amorphous state. These features have all been experimentally observed in natural metamict zircon. The present findings, when considered in light of experimental radiation effects studies, suggest that the swelling in zircon arises initially from disorder in the zircon crystal, and at high doses the disordered crystal is unable to accommodate the volume expansion and transforms to the amorphous state.

  17. Molecular dynamics simulations of supramolecular polymer rheology

    NASA Astrophysics Data System (ADS)

    Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E.

    2010-11-01

    Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate β and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.

  18. Numerical simulation of magma chamber dynamics.

    NASA Astrophysics Data System (ADS)

    Longo, Antonella; Papale, Paolo; Montagna, Chiara Paola; Vassalli, Melissa; Giudice, Salvatore; Cassioli, Andrea

    2010-05-01

    Magma chambers are characterized by periodic arrivals of deep magma batches that give origin to complex patterns of magma convection and mixing, and modify the distribution of physical quantities inside the chamber. We simulate the transient, 2D, multi-component homogeneous dynamics in geometrically complex dyke+chamber systems, by means of GALES, a finite element parallel C++ code solving mass, momentum and energy equations for multi-component homogeneous gas-liquid (± crystals) mixtures in compressible-to-incompressible flow conditions. Code validation analysis includes several cases from the classical engineering literature, corresponding to a variety of subsonic to supersonic gas-liquid flow regimes (see http://www.pi.ingv.it/~longo/gales/gales.html). The model allows specification of the composition of the different magmas in the domain, in terms of ten major oxides plus the two volatile species H2O and CO2. Gas-liquid thermodynamics are modeled by using the compositional dependent, non-ideal model in Papale et al. (Chem.. Geol., 2006). Magma properties are defined in terms of local pressure, temperature, and composition including volatiles. Several applications are performed within domains characterized by the presence of one or more magma chambers and one or more dykes, with different geometries and characteristic size from hundreds of m to several km. In most simulations an initial compositional interface is placed at the top of a feeding dyke, or at larger depth, with the deeper magma having a lower density as a consequence of larger volatile content. The numerical results show complex patterns of magma refilling in the chamber, with alternating phases of magma ingression and magma sinking from the chamber into the feeding dyke. Intense mixing takes place in feeding dykes, so that the new magma entering the chamber is always a mixture of the deep and the initially resident magma. Buoyant plume rise occurs through the formation of complex convective

  19. Simulation of chemical isomerization reaction dynamics on a NMR quantum simulator.

    PubMed

    Lu, Dawei; Xu, Nanyang; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng

    2011-07-01

    Quantum simulation can beat current classical computers with minimally a few tens of qubits. Here we report an experimental demonstration that a small nuclear-magnetic-resonance quantum simulator is already able to simulate the dynamics of a prototype laser-driven isomerization reaction using engineered quantum control pulses. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future. PMID:21797586

  20. Staggered solution procedures for multibody dynamics simulation

    NASA Technical Reports Server (NTRS)

    Park, K. C.; Chiou, J. C.; Downer, J. D.

    1990-01-01

    The numerical solution procedure for multibody dynamics (MBD) systems is termed a staggered MBD solution procedure that solves the generalized coordinates in a separate module from that for the constraint force. This requires a reformulation of the constraint conditions so that the constraint forces can also be integrated in time. A major advantage of such a partitioned solution procedure is that additional analysis capabilities such as active controller and design optimization modules can be easily interfaced without embedding them into a monolithic program. After introducing the basic equations of motion for MBD system in the second section, Section 3 briefly reviews some constraint handling techniques and introduces the staggered stabilized technique for the solution of the constraint forces as independent variables. The numerical direct time integration of the equations of motion is described in Section 4. As accurate damping treatment is important for the dynamics of space structures, we have employed the central difference method and the mid-point form of the trapezoidal rule since they engender no numerical damping. This is in contrast to the current practice in dynamic simulations of ground vehicles by employing a set of backward difference formulas. First, the equations of motion are partitioned according to the translational and the rotational coordinates. This sets the stage for an efficient treatment of the rotational motions via the singularity-free Euler parameters. The resulting partitioned equations of motion are then integrated via a two-stage explicit stabilized algorithm for updating both the translational coordinates and angular velocities. Once the angular velocities are obtained, the angular orientations are updated via the mid-point implicit formula employing the Euler parameters. When the two algorithms, namely, the two-stage explicit algorithm for the generalized coordinates and the implicit staggered procedure for the constraint Lagrange

  1. System dynamic simulation of precision segmented reflector

    NASA Technical Reports Server (NTRS)

    Shih, Choon-Foo; Lou, Michael C.

    1991-01-01

    A joint effort was undertaken on a Precision Segmented Reflector (PSR) Project. The missions in which the PSR is to be used will use large (up to 20 m in diameter) telescopes. The essential requirement for the telescopes is that the reflector surface of the primary mirror must be made extremely precise to allow no more than a few microns of errors and, additionally, this high surface precision must be maintained when the telescope is subjected to on-orbital mechanical and thermal disturbances. Based on the mass, size, and stability considerations, reflector surface formed by segmented, probably actively or passively controlled, composite panels are regarded as most suitable for future space based astronomical telescope applications. In addition to the design and fabrication of composite panels with a surface error of less than 3 microns RMS, PSR also develops related reflector structures, materials, control, and sensing technologies. As part of the planning effort for PSR Technology Demonstration, a system model which couples the reflector, consisting of panels, support truss and actuators, and the optical bench was assembled for dynamic simulations. Random vibration analyses using seismic data obtained from actual measurements at the test site designated for PSR Technology Demonstration are described.

  2. Kinetic simulations of plasmoid chain dynamics

    SciTech Connect

    Markidis, S.; Henri, P.; Lapenta, G.; Divin, A.; Goldman, M.; Newman, D.; Laure, E.

    2013-08-15

    The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The plasmoid chain forms by spontaneous magnetic reconnection: the tearing instability rapidly disrupts the initial current sheet generating several small-scale plasmoids that rapidly grow in size coalescing and kinking. The plasmoid kink is mainly driven by the coalescence process. It is found that the presence of guide field strongly influences the evolution of the plasmoid chain. Without a guide field, a main reconnection site dominates and smaller reconnection regions are included in larger ones, leading to an hierarchical structure of the plasmoid-dominated current sheet. On the contrary in presence of a guide field, plasmoids have approximately the same size and the hierarchical structure does not emerge, a strong core magnetic field develops in the center of the plasmoid in the direction of the existing guide field, and bump-on-tail instability, leading to the formation of electron holes, is detected in proximity of the plasmoids.

  3. Molecular Dynamics Simulations of Coulomb Explosion

    SciTech Connect

    Bringa, E M

    2002-05-17

    A swift ion creates a track of electronic excitations in the target material. A net repulsion inside the track can cause a ''Coulomb Explosion'', which can lead to damage and sputtering of the material. Here we report results from molecular-dynamics (MD) simulations of Coulomb explosion for a cylindrical track as a function of charge density and neutralization/quenching time, {tau}. Screening by the free electrons is accounted for using a screened Coulomb potential for the interaction among charges. The yield exhibits a prompt component from the track core and a component, which dominates at higher excitation density, from the heated region produced. For the cases studied, the number of atoms ejected per incident ion, i.e. the sputtering yield Y, is quadratic with charge density along the track as suggested by simple models. Y({tau} = 0.2 Debye periods) is nearly 20% of the yield when there is no neutralization ({tau} {yields} {infinity}). The connections between ''Coulomb explosions'', thermal spikes and measurements of electronic sputtering are discussed.

  4. Annual Report 1999 Environmental Dynamics and Simulation

    SciTech Connect

    NS Foster-Mills

    2000-06-28

    This annual report describes selected 1999 research accomplishments for the Environmental Dynamics and Simulation (ED and S) directorate, one of six research organizations in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). These accomplishments are representative of the different lines of research underway in the ED and S directorate. EMSL is one of US Department of Energy's (DOE) national scientific user facilities and is the centerpiece of DOE's commitment to providing world-class experimental, theoretical, and computational capabilities for solving the nation's environmental problems. Capabilities in the EMSL include over 100 major instrument systems for use by the resident research staff, their collaborators, and users of the EMSL. These capabilities are used to address the fundamental science that will be the basis for finding solutions to national environmental issues such as cleaning up contamianted areas at DOE sites across the country and developing green technologies that will reduce or eliminate future pollution production. The capabilities are also used to further the understanding of global climate change and environmental issues relevant to energy production and use and health effects resulting from exposure to contaminated environments.

  5. Expansion techniques for collisionless stellar dynamical simulations

    SciTech Connect

    Meiron, Yohai; Li, Baile; Holley-Bockelmann, Kelly; Spurzem, Rainer

    2014-09-10

    We present graphics processing unit (GPU) implementations of two fast force calculation methods based on series expansions of the Poisson equation. One method is the self-consistent field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other method is the multipole expansion (MEX) method, which is a Taylor-like expansion of the Green's function. MEX, which has been advocated in the past, has not gained as much popularity as SCF. Both are particle-field methods and optimized for collisionless galactic dynamics, but while SCF is a 'pure' expansion, MEX is an expansion in just the angular part; thus, MEX is capable of capturing radial structure easily, while SCF needs a large number of radial terms. We show that despite the expansion bias, these methods are more accurate than direct techniques for the same number of particles. The performance of our GPU code, which we call ETICS, is profiled and compared to a CPU implementation. On the tested GPU hardware, a full force calculation for one million particles took ∼0.1 s (depending on expansion cutoff), making simulations with as many as 10{sup 8} particles fast for a comparatively small number of nodes.

  6. Nanoscale deicing by molecular dynamics simulation.

    PubMed

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-08-14

    Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion. PMID:27431975

  7. Dynamic Simulation over Long Time Periods with 100% Solar Generation.

    SciTech Connect

    Concepcion, Ricky James; Elliott, Ryan Thomas

    2015-12-01

    This project aimed to identify the path forward for dynamic simulation tools to accommodate these needs by characterizing the properties of power systems (with high PV penetration), analyzing how these properties affect dynamic simulation software, and offering solutions for potential problems.

  8. Application of control theory to dynamic systems simulation

    NASA Technical Reports Server (NTRS)

    Auslander, D. M.; Spear, R. C.; Young, G. E.

    1982-01-01

    The application of control theory is applied to dynamic systems simulation. Theory and methodology applicable to controlled ecological life support systems are considered. Spatial effects on system stability, design of control systems with uncertain parameters, and an interactive computing language (PARASOL-II) designed for dynamic system simulation, report quality graphics, data acquisition, and simple real time control are discussed.

  9. Rhodopsin Photoactivation Dynamics Revealed by Quasi-Elastic Neutron Scattering

    NASA Astrophysics Data System (ADS)

    Bhowmik, Debsindhu; Shrestha, Utsab; Perera, Suchhithranga M. C. D.; Chawla, Udeep; Mamontov, Eugene; Brown, Michael; Chu, Xiang-Qiang

    2015-03-01

    Rhodopsin is a G-protein-coupled receptor (GPCR) responsible for vision. During photoactivation, the chromophore retinal dissociates from protein yielding the opsin apoprotein. What are the changes in protein dynamics that occur during the photoactivation process? Here, we studied the microscopic dynamics of dark-state rhodopsin and the ligand-free opsin using quasielastic neutron scattering (QENS). The QENS technique tracks individual hydrogen atom motion because of the much higher neutron scattering cross-section of hydrogen than other atoms. We used protein with CHAPS detergent hydrated with heavy water. The activation of proteins is confirmed at low temperatures up to 300 K by mean-square displacement (MSD) analysis. The QENS experiments at temperatures ranging from 220 K to 300 K clearly indicate an increase in protein dynamic behavior with temperature. The relaxation time for the ligand-bound protein rhodopsin is faster compared to opsin, which can be correlated with the photoactivation. Moreover, the protein dynamics are orders of magnitude slower than the accompanying CHAPS detergent, which unlike protein, manifests localized motions.

  10. OLIGOMERIZATION STATE OF RUBISCO ACTIVASE REVEALED BY DYNAMIC LIGHT SCATTERING

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The self-association of Rubisco activase has been suggested to be required for Rubisco activation via ATP hydrolysis. To study the oligmerization patterns in detail, we initially measured the size of each isoform (42 KDa and 45 KDa) of recombinant spinach activase using dynamic light scattering spec...

  11. Structure and Dynamics of Four-way DNA Junctions Dynamics Revealed by Single-Molecule AFM

    NASA Astrophysics Data System (ADS)

    Lyubchenko, Yuri

    2004-03-01

    For-way DNA junctions (Holliday junctions) are critical intermediates for homologous, site-specific recombination, DNA repair and replication. A wealth of structural information is available for immobile four-way junctions. However, these data cannot give the answer on the mechanism of branch migration, the major property of the Holliday junction. Two models for the mechanism of branch migration were suggested. According to the early model of Alberts-Meselson-Sigal, exchanging DNA strands around the junction remain parallel during branch migration. Kinetic studies of branch migration suggest an alternative model in which the junction adopts an extended conformation. We tested these models using a Holliday junction undergoing branch migration. Note that it was the first time when the dynamics of the four-way DNA junction capable of branch migration had been analyzed. We applied time-lapse atomic force microscopy (single molecule dynamics AFM) to image directly loosely bound DNA at liquid-surface interface. These experiments show that mobile Holliday junctions adopt an unfolded conformation during branch migration. This conformation of the junction remains unchanged until strand separation. The data obtained support the model for branch migration having the extended conformation of the Holliday junction. The analysis of the Holliday junctions dynamics at conditions limiting branch migration revealed a broad movement of the arms suggesting that the range of mobility of these junctions is much wider than detected before. Further applications of the time-lapse AFM approach in attempt to resolve the subpopulations of the junctions conformers and the prospects for analyses of dynamics of complex biological systems will be discussed.

  12. Reaction ensemble molecular dynamics: Direct simulation of the dynamic equilibrium properties of chemically reacting mixtures

    NASA Astrophysics Data System (ADS)

    Brennan, John K.; Lísal, Martin; Gubbins, Keith E.; Rice, Betsy M.

    2004-12-01

    A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is formulated upon the reaction ensemble Monte Carlo (RxMC) method, hence the term reaction ensemble molecular dynamics. Thermodynamic and transport properties are calculated in the dynamic cell by using a constant-temperature molecular dynamics simulation method. RxMC forward and reverse reaction steps are performed in the control cell only, while molecular dynamics steps are performed in both the dynamic cell and the control cell. The control cell, which acts as a sink and source reservoir, is maintained at reaction equilibrium conditions via the RxMC algorithm. The reaction ensemble molecular dynamics method is analogous to the grand canonical ensemble molecular dynamics technique, while using some elements of the osmotic molecular dynamics method, and so simulates conditions that directly relate to real, open systems. The accuracy and stability of the method is assessed by considering the ammonia synthesis reaction N2+3H2⇔2NH3 . It is shown to be a viable method for predicting the effects of nonideal environments on the dynamic properties (particularly diffusion) as well as reaction equilibria for chemically reacting mixtures.

  13. Swimming patterns and dynamics of simulated Escherichia coli bacteria

    PubMed Central

    Zonia, Laura; Bray, Dennis

    2009-01-01

    A spatially and temporally realistic simulation of Escherichia coli chemotaxis was used to investigate the swimming patterns of wild-type and mutant bacteria within a rectangular arena in response to chemoattractant gradients. Swimming dynamics were analysed during long time series with phase-space trajectories, power spectra and estimations of fractal dimensions (FDs). Cell movement displayed complex trajectories in the phase space owing to interaction of multiple attractors that captured runs and tumbles. Deletion of enzymes responsible for adaptation (CheR and CheB) restricted the pattern of bacterial swimming in the absence of a gradient. In the presence of a gradient, there was a strong increase in trajectories arising from runs and attenuation of those arising from tumbles. Similar dynamics were observed for mutants lacking CheY, which are unable to tumble. The deletion of CheR, CheB and CheY also caused significant shifts in chemotaxis spectral frequencies. Rescaled range analysis and estimation of FD suggest that wild-type bacteria display characteristics of fractional Brownian motion with positive correlation between past and future events. These results reveal an underlying order in bacterial swimming dynamics, which enables a chemotactic search strategy conforming to a fractal walk. PMID:19324687

  14. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

    PubMed Central

    Sun, Jian; Zhang, Qing; Schlick, Tamar

    2005-01-01

    Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended “beads-on-a-string” conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA–nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt. PMID:15919827

  15. iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.

    PubMed

    Musselman, Catherine; Al-Hashimi, Hashim M; Andricioaei, Ioan

    2007-07-15

    The HIV-1 transactivation response RNA element (TAR), which is essential to the lifecycle of the virus, has been suggested, based on NMR and hydrodynamic measurements, to undergo substantial, collective, structural dynamics that are important for its function. To deal with the significant coupling between overall diffusional rotation and internal motion expected to exist in TAR, here we utilize an isotropic reorientational eigenmode dynamics analysis of simulated molecular trajectories to obtain a detailed description of TAR dynamics and an accurately quantified pattern of dynamical correlations. The analysis demonstrates the inseparability of internal and overall motional modes, confirms the existence and reveals the nature of collective domain dynamics, and additionally reveals that the hinge for these motions is centered on residues U23, C24, and C41. Results also indicate the existence of long-range communication between the loop and the core of the RNA, and between the loop and the bulge. Additionally, the isotropic reorientational eigenmode dynamics analysis explains, from a dynamical perspective, several existing biochemical mutational studies and suggests new mutations for future structural dynamics studies. PMID:17449677

  16. Controlled multibody dynamics simulation for large space structures

    NASA Technical Reports Server (NTRS)

    Housner, J. M.; Wu, S. C.; Chang, C. W.

    1989-01-01

    Multibody dynamics discipline, and dynamic simulation in control structure interaction (CSI) design are discussed. The use, capabilities, and architecture of the Large Angle Transient Dynamics (LATDYN) code as a simulation tool are explained. A generic joint body with various types of hinge connections; finite element and element coordinate systems; results of a flexible beam spin-up on a plane; mini-mast deployment; space crane and robotic slewing manipulations; a potential CSI test article; and multibody benchmark experiments are also described.

  17. A note on simulation and dynamical hierarchies

    SciTech Connect

    Rasmussen, S.; Barrett, C.L. |; Baas, N.A.; Olesen, M.W.

    1996-02-22

    This paper summarizes some of the problems associated with the generation of higher order emergent structures in formal dynamical systems as well as some of the formal properties of dynamical systems capable of generating higher order structures.

  18. Physical Properties of GaN Nanotubes as Revealed by Computer Simulation

    SciTech Connect

    Wang, Zhiguo; Gao, Fei; Zu, Xiaotao; Weber, William J.

    2008-07-25

    Single-crystalline wurtzite GaN nanotubes have been synthesized recently with proposed applications in nanoscale electronics, optoelectronics and the biochemical-sensing field. Molecular dynamics methods with a Stillinger-Weber potential are used to investigate the melting behavior, thermal conductivity and mechanical properties of these wurtzite-type single crystalline GaN nanotubes. Four major topical areas are summarized in this chapter. (1) The melting temperature of the GaN nanotubes increases with the thickness of the nanotubes to a saturation value, which is close to the melting temperature of bulk GaN. The simulations result reveal that the nanotubes begin to melt at the surface, and then the melting rapidly extends to the interior of the nanotubes as the temperature increases. (2) The thermal conductivity of nanotubes is smaller than that of the bulk GaN single crystal. The thermal conductivity is also found to decrease with temperature and increase with increasing wall thickness of the nanotubes. The change of phonon spectrum and surface inelastic scattering may account for the reduction of thermal conductivity in the nanotubes, while thermal softening and high frequency phonon interactions at high temperatures may provide an explanation for its decrease with increasing temperature. (3) At low temperatures, the simulation results show that the nanotubes exhibit brittle properties; whereas at high temperatures, they behave as ductile materials. The brittle to ductile transition temperature generally increases with increasing wall thickness of the nanotubes and increasing strain rate. (4) The simulation temperature, tube length and strain rate affect the buckling behavior of GaN nanotubes. The critical stress decreases with the increase of simulation temperature and tube length. The dependence of buckling on tube length is consistent with the analysis of equivalent continuum structures using Euler buckling theory.

  19. Molecular dynamics simulation of graphene bombardment with Si ion

    NASA Astrophysics Data System (ADS)

    Qin, Xin-Mao; Gao, Ting-Hong; Yan, Wan-Jun; Guo, Xiao-Tian; Xie, Quan

    2014-03-01

    Molecular dynamics simulations with Tersoff-Ziegler-Biersack-Littmark (Tersoff-ZBL) potential and adaptive intermolecular reactive empirical bond order (AIREBO) potential are performed to study the effect of irradiated graphene with silicon ion at several positions and energy levels of 0.1-1000 eV. The simulations reveal four processes: absorption, replacement, transmission and damage. At energies below 110 eV, the dominant process is absorption. For atom in group (a), the process that takes place is replacement, in which the silicon ion removes one carbon atom and occupies the place of the eliminated atom at the incident energy of 72-370 eV. Transmission is present at energies above 100 eV for atom in group (d). Damage is a very important process in current bombardment, and there are four types of defects: single vacancy, replacement-single vacancy, double vacancy and nanopore. The simulations provide a fundamental understanding of the silicon bombardment of graphene, and the parameters required to develop graphene-based devices by controlling defect formation.

  20. Optogenetic perturbations reveal the dynamics of an oculomotor integrator

    PubMed Central

    Gonçalves, Pedro J.; Arrenberg, Aristides B.; Hablitzel, Bastian; Baier, Herwig; Machens, Christian K.

    2014-01-01

    Many neural systems can store short-term information in persistently firing neurons. Such persistent activity is believed to be maintained by recurrent feedback among neurons. This hypothesis has been fleshed out in detail for the oculomotor integrator (OI) for which the so-called “line attractor” network model can explain a large set of observations. Here we show that there is a plethora of such models, distinguished by the relative strength of recurrent excitation and inhibition. In each model, the firing rates of the neurons relax toward the persistent activity states. The dynamics of relaxation can be quite different, however, and depend on the levels of recurrent excitation and inhibition. To identify the correct model, we directly measure these relaxation dynamics by performing optogenetic perturbations in the OI of zebrafish expressing halorhodopsin or channelrhodopsin. We show that instantaneous, inhibitory stimulations of the OI lead to persistent, centripetal eye position changes ipsilateral to the stimulation. Excitatory stimulations similarly cause centripetal eye position changes, yet only contralateral to the stimulation. These results show that the dynamics of the OI are organized around a central attractor state—the null position of the eyes—which stabilizes the system against random perturbations. Our results pose new constraints on the circuit connectivity of the system and provide new insights into the mechanisms underlying persistent activity. PMID:24616666

  1. Research on hyperspectral dynamic infrared scene simulation technology

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Hu, Yu; Ding, Na; Sun, Kefeng; Sun, Dandan; Xie, Junhu; Wu, Wenli; Gao, Jiaobo

    2015-02-01

    The paper presents a hardware in loop dynamic IR scene simulation technology for IR hyperspectral imaging system. Along with fleetly development of new type EO detecting, remote sensing and hyperspectral imaging technique, not only static parameters' calibration of hyperspectral IR imaging system but also dynamic parameters' testing and evaluation are required, thus hyperspectral dynamic IR simulation and evaluation become more and more important. Hyperspectral dynamic IR scene projector utilizes hyperspectral space and time domain features controlling spectrum and time synchronously to realize hardware in loop simulation. Hyperspectral IR target and background simulating image can be gained by the accomplishment of 3D model and IR characteristic romancing, hyperspectral dynamic IR scene is produced by image converting device. The main parameters of a developed hyperspectral dynamic IR scene projector: wave band range is 3~5μm, 8~12μm Field of View (FOV) is 8°; spatial resolution is 1024×768 spectrum resolution is 1%~2%. IR source and simulating scene features should be consistent with spectrum characters of target, and different spectrum channel's images can be gotten from calibration. A hyperspectral imaging system splits light with dispersing type grating, pushbrooms and collects the output signal of dynamic IR scene projector. With hyperspectral scene spectrum modeling, IR features romancing, atmosphere transmission feature modeling and IR scene projecting, target and scene in outfield can be simulated ideally, simulation and evaluation of IR hyperspectral imaging system's dynamic features are accomplished in laboratory.

  2. Dynamic Monitoring Reveals Motor Task Characteristics in Prehistoric Technical Gestures

    PubMed Central

    Pfleging, Johannes; Stücheli, Marius; Iovita, Radu; Buchli, Jonas

    2015-01-01

    Reconstructing ancient technical gestures associated with simple tool actions is crucial for understanding the co-evolution of the human forelimb and its associated control-related cognitive functions on the one hand, and of the human technological arsenal on the other hand. Although the topic of gesture is an old one in Paleolithic archaeology and in anthropology in general, very few studies have taken advantage of the new technologies from the science of kinematics in order to improve replicative experimental protocols. Recent work in paleoanthropology has shown the potential of monitored replicative experiments to reconstruct tool-use-related motions through the study of fossil bones, but so far comparatively little has been done to examine the dynamics of the tool itself. In this paper, we demonstrate that we can statistically differentiate gestures used in a simple scraping task through dynamic monitoring. Dynamics combines kinematics (position, orientation, and speed) with contact mechanical parameters (force and torque). Taken together, these parameters are important because they play a role in the formation of a visible archaeological signature, use-wear. We present our new affordable, yet precise methodology for measuring the dynamics of a simple hide-scraping task, carried out using a pull-to (PT) and a push-away (PA) gesture. A strain gage force sensor combined with a visual tag tracking system records force, torque, as well as position and orientation of hafted flint stone tools. The set-up allows switching between two tool configurations, one with distal and the other one with perpendicular hafting of the scrapers, to allow for ethnographically plausible reconstructions. The data show statistically significant differences between the two gestures: scraping away from the body (PA) generates higher shearing forces, but requires greater hand torque. Moreover, most benchmarks associated with the PA gesture are more highly variable than in the PT gesture

  3. Dynamic Monitoring Reveals Motor Task Characteristics in Prehistoric Technical Gestures.

    PubMed

    Pfleging, Johannes; Stücheli, Marius; Iovita, Radu; Buchli, Jonas

    2015-01-01

    Reconstructing ancient technical gestures associated with simple tool actions is crucial for understanding the co-evolution of the human forelimb and its associated control-related cognitive functions on the one hand, and of the human technological arsenal on the other hand. Although the topic of gesture is an old one in Paleolithic archaeology and in anthropology in general, very few studies have taken advantage of the new technologies from the science of kinematics in order to improve replicative experimental protocols. Recent work in paleoanthropology has shown the potential of monitored replicative experiments to reconstruct tool-use-related motions through the study of fossil bones, but so far comparatively little has been done to examine the dynamics of the tool itself. In this paper, we demonstrate that we can statistically differentiate gestures used in a simple scraping task through dynamic monitoring. Dynamics combines kinematics (position, orientation, and speed) with contact mechanical parameters (force and torque). Taken together, these parameters are important because they play a role in the formation of a visible archaeological signature, use-wear. We present our new affordable, yet precise methodology for measuring the dynamics of a simple hide-scraping task, carried out using a pull-to (PT) and a push-away (PA) gesture. A strain gage force sensor combined with a visual tag tracking system records force, torque, as well as position and orientation of hafted flint stone tools. The set-up allows switching between two tool configurations, one with distal and the other one with perpendicular hafting of the scrapers, to allow for ethnographically plausible reconstructions. The data show statistically significant differences between the two gestures: scraping away from the body (PA) generates higher shearing forces, but requires greater hand torque. Moreover, most benchmarks associated with the PA gesture are more highly variable than in the PT gesture

  4. Simulating system dynamics with arbitrary time step

    NASA Astrophysics Data System (ADS)

    Kantorovich, L.

    2007-02-01

    We suggest a dynamic simulation method that allows efficient and realistic modeling of kinetic processes, such as atomic diffusion, in which time has its actual meaning. Our method is similar in spirit to widely used kinetic Monte Carlo (KMC) techniques; however, in our approach, the time step can be chosen arbitrarily. This has an advantage in some cases, e.g., when the transition rates change with time sufficiently fast over the period of the KMC time step (e.g., due to time dependence of some external factors influencing kinetics such as moving scanning probe microscopy tip or external time-dependent field) or when the clock time is set by some external conditions, and it is convenient to use equal time steps instead of the random choice of the KMC algorithm in order to build up probability distribution functions. We show that an arbitrary choice of the time step can be afforded by building up the complete list of events including the “residence site” and multihop transitions. The idea of the method is illustrated in a simple “toy” model of a finite one-dimensional lattice of potential wells with unequal jump rates to either side, which can be studied analytically. We show that for any choice of the time step, our general kinetics method reproduces exactly the solution of the corresponding master equations for any choice of the time steps. The final kinetics also matches the standard KMC, and this allows better understanding of this algorithm, in which the time step is chosen in a certain way and the system always advances by a single hop.

  5. Conformation switching of AIM2 PYD domain revealed by NMR relaxation and MD simulation.

    PubMed

    Wang, Haobo; Yang, Lijiang; Niu, Xiaogang

    2016-04-29

    Protein absent in melanoma 2 (AIM2) is a double-strand DNA (ds DNA) sensor mainly located in cytoplasm of cell. It includes one N terminal PYD domain and one C terminal HIN domain. When the ds DNA such as DNA viruses and bacteria entered cytoplasm, the HIN domain of AIM2 will recognize and bind to DNA, and the PYD domain will bind to ASC protein which will result in the formation of AIM2 inflammasome. Three AIM2 PYD domain structures have been solved, but every structure yields a unique conformation around the α3 helix region. To understand why different AIM2 PYD structures show different conformations in this region, we use NMR relaxation techniques to study the backbone dynamics of mouse AIM2 PYD domain and perform molecular dynamics (MD) simulations on both mouse and human AIM2 PYD structures. Our results indicate that this region is highly flexible in both mouse and human AIM2 PYD domains, and the PYD domain may exist as a conformation ensemble in solution. Different environment makes the population vary among pre-existing conformational substrates of the ensemble, which may be the reason why different AIM2 PYD structures were observed under different conditions. Further docking analysis reveals that the conformation switching may be important for the autoinhibition of the AIM2 protein. PMID:27037024

  6. A Simulation Program for Dynamic Infrared (IR) Spectra

    ERIC Educational Resources Information Center

    Zoerb, Matthew C.; Harris, Charles B.

    2013-01-01

    A free program for the simulation of dynamic infrared (IR) spectra is presented. The program simulates the spectrum of two exchanging IR peaks based on simple input parameters. Larger systems can be simulated with minor modifications. The program is available as an executable program for PCs or can be run in MATLAB on any operating system. Source…

  7. Animated molecular dynamics simulations of hydrated caesium-smectite interlayers

    PubMed Central

    Sutton, Rebecca; Sposito, Garrison

    2002-01-01

    Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers) provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs+ formed inner sphere complexes with the mineral surface, and could be seen to jump from one attracting location near a layer charge site to the next, while water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. Cs-montmorillonite hydrates featured the largest extent of this sharing interaction, because interlayer ions were able to inhabit positions near surface cavities as well as at their edges, close to oxygen triads. The greater positional freedom of Cs+ within the montmorillonite interlayer, a result of structural hydroxyl orientation and low tetrahedral charge, promoted the optimization of distances between cations and water molecules required for water sharing. Preference of Cs+ for locations near oxygen triads was observed within interlayer beidellite and hectorite. Water molecules also could be seen to interact directly with the mineral surface, entering its surface cavities to approach attracting charge sites and structural hydroxyls. With increasing water content, water molecules exhibited increased frequency and duration of both cavity habitation and water sharing interactions. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output.

  8. Shapiro like steps reveals molecular nanomagnets' spin dynamics

    NASA Astrophysics Data System (ADS)

    Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid

    2015-09-01

    We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet's spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields.

  9. Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells

    NASA Astrophysics Data System (ADS)

    Stingaciu, Laura-Roxana; O'Neill, Hugh; Liberton, Michelle; Urban, Volker S.; Pakrasi, Himadri B.; Ohl, Michael

    2016-01-01

    Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement of the thylakoid membranes in response to environmental conditions have been widely investigated. However, there is limited knowledge about the internal dynamics of these membranes in terms of their flexibility and motion during the photosynthetic process. We present a direct observation of thylakoid membrane undulatory motion in vivo and show a connection between membrane mobility and photosynthetic activity. High-resolution inelastic neutron scattering experiments on the cyanobacterium Synechocystis sp. PCC 6803 assessed the flexibility of cyanobacterial thylakoid membrane sheets and the dependence of the membranes on illumination conditions. We observed softer thylakoid membranes in the dark that have three-to four fold excess mobility compared to membranes under high light conditions. Our analysis indicates that electron transfer between photosynthetic reaction centers and the associated electrochemical proton gradient across the thylakoid membrane result in a significant driving force for excess membrane dynamics. These observations provide a deeper understanding of the relationship between photosynthesis and cellular architecture.

  10. Photon echo spectroscopy reveals structure-dynamics relationships in carotenoids

    NASA Astrophysics Data System (ADS)

    Christensson, N.; Polivka, T.; Yartsev, A.; Pullerits, T.

    2009-06-01

    Based on simultaneous analysis of the frequency-resolved transient grating, peak shift, and echo width signals, we present a model for the third-order optical response of carotenoids including population dynamics and system-bath interactions. Our frequency-resolved photon echo experiments show that the model needs to incorporate the excited-state absorption from both the S2 and the S1 states. We apply our model to analyze the experimental results on astaxanthin and lycopene, aiming to elucidate the relation between structure and system-bath interactions. Our analysis allows us to relate structural motifs to changes in the energy-gap correlation functions. We find that the terminal rings of astaxanthin lead to increased coupling between slow molecular motions and the electronic transition. We also find evidence for stronger coupling to higher frequency overdamped modes in astaxanthin, pointing to the importance of the functional groups in providing coupling to fluctuations influencing the dynamics in the passage through the conical intersection governing the S2-S1 relaxation.

  11. Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells

    DOE PAGESBeta

    Stingaciu, Laura-Roxana; O’Neill, Hugh; Liberton, Michelle; Urban, Volker S.; Pakrasi, Himadri B.; Ohl, Michael

    2016-01-21

    Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement of the thylakoid membranes in response to environmental conditions have been widely investigated. However, there is limited knowledge about the internal dynamics of these membranes in terms of their flexibility and motion during the photosynthetic process. We present a direct observation of thylakoid membrane undulatory motion in vivo and show a connection between membrane mobility and photosynthetic activity. High-resolutionmore » inelastic neutron scattering experiments on the cyanobacterium Synechocystis sp. PCC 6803 assessed the flexibility of cyanobacterial thylakoid membrane sheets and the dependence of the membranes on illumination conditions. We observed softer thylakoid membranes in the dark that have three-to four fold excess mobility compared to membranes under high light conditions. We find our analysis indicates that electron transfer between photosynthetic reaction centers and the associated electrochemical proton gradient across the thylakoid membrane result in a significant driving force for excess membrane dynamics. Lastly, these observations provide a deeper understanding of the relationship between photosynthesis and cellular architecture.« less

  12. Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells

    PubMed Central

    Stingaciu, Laura-Roxana; O’Neill, Hugh; Liberton, Michelle; Urban, Volker S.; Pakrasi, Himadri B.; Ohl, Michael

    2016-01-01

    Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement of the thylakoid membranes in response to environmental conditions have been widely investigated. However, there is limited knowledge about the internal dynamics of these membranes in terms of their flexibility and motion during the photosynthetic process. We present a direct observation of thylakoid membrane undulatory motion in vivo and show a connection between membrane mobility and photosynthetic activity. High-resolution inelastic neutron scattering experiments on the cyanobacterium Synechocystis sp. PCC 6803 assessed the flexibility of cyanobacterial thylakoid membrane sheets and the dependence of the membranes on illumination conditions. We observed softer thylakoid membranes in the dark that have three-to four fold excess mobility compared to membranes under high light conditions. Our analysis indicates that electron transfer between photosynthetic reaction centers and the associated electrochemical proton gradient across the thylakoid membrane result in a significant driving force for excess membrane dynamics. These observations provide a deeper understanding of the relationship between photosynthesis and cellular architecture. PMID:26790980

  13. Invisible Electronic States and Their Dynamics Revealed by Perturbations

    NASA Astrophysics Data System (ADS)

    Merer, Anthony J.

    2011-06-01

    Sooner or later everyone working in the field of spectroscopy encounters perturbations. These can range in size from a small shift of a single rotational level to total destruction of the vibrational and rotational patterns of an electronic state. To some workers perturbations are a source of terror, but to others they are the most fascinating features of molecular spectra, because they give information about molecular dynamics, and about states that would otherwise be invisible as a result of unfavorable selection rules. An example of the latter is the essentially complete characterization of the tilde{b}^3A_2 state of SO_2 from the vibronic perturbations it causes in the tilde{a}^3B_1 state. The S_1-trans state of acetylene is a beautiful example of dynamics in action. The level patterns of the three bending vibrations change dramatically with increasing vibrational excitation as a result of the vibrational angular momentum and the approach to the isomerization barrier. Several vibrational levels of the S_1-cis isomer, previously thought to be unobservable, can now be assigned. They obtain their intensity through interactions with nearby levels of the trans isomer.

  14. Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Shekhar, Adarsh

    Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

  15. Population dynamics of flaviviruses revealed by molecular phylogenies.

    PubMed Central

    Zanotto, P M; Gould, E A; Gao, G F; Harvey, P H; Holmes, E C

    1996-01-01

    The phylogeny of 123 complete envelope gene sequences was reconstructed in order to understand the evolution of tick- and mosquito-borne flaviviruses. An analysis of phylogenetic tree structure reveals a continual and asymmetric branching process in the tick-borne flaviviruses, compared with an explosive radiation in the last 200 years in viruses transmitted by mosquitoes. The distinction between these two viral groups probably reflects differences in modes of dispersal, propagation, and changes in the size of host populations. The most serious implication of this work is that growing human populations are being exposed to an expanding range of increasingly diverse viral strains. PMID:8570593

  16. Shapiro like steps reveals molecular nanomagnets’ spin dynamics

    SciTech Connect

    Abdollahipour, Babak; Abouie, Jahanfar Ebrahimi, Navid

    2015-09-15

    We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields.

  17. Blood Sugar Measurement in Zebrafish Reveals Dynamics of Glucose Homeostasis

    PubMed Central

    Eames, Stefani C.; Philipson, Louis H.; Prince, Victoria E.

    2010-01-01

    Abstract The adult zebrafish has the potential to become an important model for diabetes-related research. To realize this potential, small-scale methods for analyzing pancreas function are required. The measurement of blood glucose level is a commonly used method for assessing β-cell function, but the small size of the zebrafish presents challenges both for collecting blood samples and for measuring glucose. We have developed methods for collecting microsamples of whole blood and plasma for the measurement of hematocrit and blood glucose. We demonstrate that two hand-held glucose meters designed for use by human diabetics return valid results with zebrafish blood. Additionally, we present methods for fasting and for performing postprandial glucose and intraperitoneal glucose tolerance tests. We find that the dynamics of zebrafish blood glucose homeostasis are consistent with patterns reported for other omnivorous teleost fish. PMID:20515318

  18. Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes.

    PubMed

    Buck, Moritz; Nilsson, Louise K J; Brunius, Carl; Dabiré, Roch K; Hopkins, Richard; Terenius, Olle

    2016-01-01

    The intolerable burden of malaria has for too long plagued humanity and the prospect of eradicating malaria is an optimistic, but reachable, target in the 21(st) century. However, extensive knowledge is needed about the spatial structure of mosquito populations in order to develop effective interventions against malaria transmission. We hypothesized that the microbiota associated with a mosquito reflects acquisition of bacteria in different environments. By analyzing the whole-body bacterial flora of An. gambiae mosquitoes from Burkina Faso by 16 S amplicon sequencing, we found that the different environments gave each mosquito a specific bacterial profile. In addition, the bacterial profiles provided precise and predicting information on the spatial dynamics of the mosquito population as a whole and showed that the mosquitoes formed clear local populations within a meta-population network. We believe that using microbiotas as proxies for population structures will greatly aid improving the performance of vector interventions around the world. PMID:26960555

  19. Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes

    PubMed Central

    Buck, Moritz; Nilsson, Louise K. J.; Brunius, Carl; Dabiré, Roch K.; Hopkins, Richard; Terenius, Olle

    2016-01-01

    The intolerable burden of malaria has for too long plagued humanity and the prospect of eradicating malaria is an optimistic, but reachable, target in the 21st century. However, extensive knowledge is needed about the spatial structure of mosquito populations in order to develop effective interventions against malaria transmission. We hypothesized that the microbiota associated with a mosquito reflects acquisition of bacteria in different environments. By analyzing the whole-body bacterial flora of An. gambiae mosquitoes from Burkina Faso by 16 S amplicon sequencing, we found that the different environments gave each mosquito a specific bacterial profile. In addition, the bacterial profiles provided precise and predicting information on the spatial dynamics of the mosquito population as a whole and showed that the mosquitoes formed clear local populations within a meta-population network. We believe that using microbiotas as proxies for population structures will greatly aid improving the performance of vector interventions around the world. PMID:26960555

  20. COMBINED DELAY AND GRAPH EMBEDDING OF EPILEPTIC DISCHARGES IN EEG REVEALS COMPLEX AND RECURRENT NONLINEAR DYNAMICS

    PubMed Central

    Erem, B.; Hyde, D.E.; Peters, J.M.; Duffy, F.H.; Brooks, D.H.; Warfield, S.K.

    2015-01-01

    The dynamical structure of the brain’s electrical signals contains valuable information about its physiology. Here we combine techniques for nonlinear dynamical analysis and manifold identification to reveal complex and recurrent dynamics in interictal epileptiform discharges (IEDs). Our results suggest that recurrent IEDs exhibit some consistent dynamics, which may only last briefly, and so individual IED dynamics may need to be considered in order to understand their genesis. This could potentially serve to constrain the dynamics of the inverse source localization problem. PMID:26366250

  1. Numerical simulation of diffusion-controlled droplet growth Dynamical correlation effects

    NASA Technical Reports Server (NTRS)

    Beenakker, C. W. J.

    1986-01-01

    Diffusion-controlled coarsening (Ostwald ripening) of precipitated solutions is studied by numerical simulation. An algorithm is devised which exploits the screening of solute concentration fields, thereby removing the restriction to small systems of previous work. Simulation of the coarsening of 5000 droplets at 10-percent volume fraction reveals long-ranged dynamical correlations which broaden the droplet size-distribution function and increase the coarsening-rate coefficient.

  2. Single-cell dynamics reveals sustained growth during diauxic shifts.

    PubMed

    Boulineau, Sarah; Tostevin, Filipe; Kiviet, Daniel J; ten Wolde, Pieter Rein; Nghe, Philippe; Tans, Sander J

    2013-01-01

    Stochasticity in gene regulation has been characterized extensively, but how it affects cellular growth and fitness is less clear. We study the growth of E. coli cells as they shift from glucose to lactose metabolism, which is characterized by an obligatory growth arrest in bulk experiments that is termed the lag phase. Here, we follow the growth dynamics of individual cells at minute-resolution using a single-cell assay in a microfluidic device during this shift, while also monitoring lac expression. Mirroring the bulk results, the majority of cells displays a growth arrest upon glucose exhaustion, and resume when triggered by stochastic lac expression events. However, a significant fraction of cells maintains a high rate of elongation and displays no detectable growth lag during the shift. This ability to suppress the growth lag should provide important selective advantages when nutrients are scarce. Trajectories of individual cells display a highly non-linear relation between lac expression and growth, with only a fraction of fully induced levels being sufficient for achieving near maximal growth. A stochastic molecular model together with measured dependencies between nutrient concentration, lac expression level, and growth accurately reproduces the observed switching distributions. The results show that a growth arrest is not obligatory in the classic diauxic shift, and underscore that regulatory stochasticity ought to be considered in terms of its impact on growth and survival. PMID:23637881

  3. Dynamics modeling and simulation of autonomous underwater vehicles with appendages

    NASA Astrophysics Data System (ADS)

    Su, Yumin; Zhao, Jinxin; Cao, Jian; Zhang, Guocheng

    2013-03-01

    To provide a simulation system platform for designing and debugging a small autonomous underwater vehicle's (AUV) motion controller, a six-degree of freedom (6-DOF) dynamic model for AUV controlled by thruster and fins with appendages is examined. Based on the dynamic model, a simulation system for the AUV's motion is established. The different kinds of typical motions are simulated to analyze the motion performance and the maneuverability of the AUV. In order to evaluate the influences of appendages on the motion performance of the AUV, simulations of the AUV with and without appendages are performed and compared. The results demonstrate the AUV has good maneuverability with and without appendages.

  4. Multifractal analysis of Barkhausen noise reveals the dynamic nature of criticality at hysteresis loop

    NASA Astrophysics Data System (ADS)

    Tadić, Bosiljka

    2016-06-01

    The field-driven magnetisation reversal processes in disordered systems exhibit a collective behaviour that is manifested in the scale-invariance of avalanches, closely related to underlying dynamical mechanisms. Using the multifractal time series analysis, we study the structure of fluctuations at different scales in the accompanying Barkhausen noise. The stochastic signal represents the magnetisation discontinuities along the hysteresis loop of a three-dimensional random field Ising model simulated for varied disorder strength and driving rates. The analysis of the spectrum of the generalised Hurst exponents reveals that the dominant segments of the signal with large fluctuations represent two distinct classes of stochastic processes in weak and strong pinning regimes. Furthermore, in the weak pinning regime, the part of the signal originating from the beginning of the hysteresis loop has a different multifractal spectrum than the signal near the coercive field. The enhanced fluctuations (primarily in the central part of the hysteresis loop) for increased driving rate and larger system size, lead to a further broadening of the spectrum. The analysed Barkhausen signals are also shown to exhibit temporal correlations and power-law distributions of the magnetisation discontinuity and avalanche sizes, in agreement with previous studies. The multifractal properties of Barkhausen noise describe the dynamical state of domains and precisely discriminate the weak pinning, permitting the motion of individual walls, from the mechanisms occurring in strongly disordered systems.

  5. Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity

    PubMed Central

    Alexeyenko, Andrey; Wassenberg, Deena M.; Lobenhofer, Edward K.; Yen, Jerry; Linney, Elwood; Sonnhammer, Erik L. L.; Meyer, Joel N.

    2010-01-01

    Background In order to generate hypotheses regarding the mechanisms by which 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin) causes toxicity, we analyzed global gene expression changes in developing zebrafish embryos exposed to this potent toxicant in the context of a dynamic gene network. For this purpose, we also computationally inferred a zebrafish (Danio rerio) interactome based on orthologs and interaction data from other eukaryotes. Methodology/Principal Findings Using novel computational tools to analyze this interactome, we distinguished between dioxin-dependent and dioxin-independent interactions between proteins, and tracked the temporal propagation of dioxin-dependent transcriptional changes from a few genes that were altered initially, to large groups of biologically coherent genes at later times. The most notable processes altered at later developmental stages were calcium and iron metabolism, embryonic morphogenesis including neuronal and retinal development, a variety of mitochondria-related functions, and generalized stress response (not including induction of antioxidant genes). Within the interactome, many of these responses were connected to cytochrome P4501A (cyp1a) as well as other genes that were dioxin-regulated one day after exposure. This suggests that cyp1a may play a key role initiating the toxic dysregulation of those processes, rather than serving simply as a passive marker of dioxin exposure, as suggested by earlier research. Conclusions/Significance Thus, a powerful microarray experiment coupled with a flexible interactome and multi-pronged interactome tools (which are now made publicly available for microarray analysis and related work) suggest the hypothesis that dioxin, best known in fish as a potent cardioteratogen, has many other targets. Many of these types of toxicity have been observed in mammalian species and are potentially caused by alterations to cyp1a. PMID:20463971

  6. Comparisons of Kinematics and Dynamics Simulation Software Tools

    NASA Technical Reports Server (NTRS)

    Shiue, Yeu-Sheng Paul

    2002-01-01

    Kinematic and dynamic analyses for moving bodies are essential to system engineers and designers in the process of design and validations. 3D visualization and motion simulation plus finite element analysis (FEA) give engineers a better way to present ideas and results. Marshall Space Flight Center (MSFC) system engineering researchers are currently using IGRIP from DELMIA Inc. as a kinematic simulation tool for discrete bodies motion simulations. Although IGRIP is an excellent tool for kinematic simulation with some dynamic analysis capabilities in robotic control, explorations of other alternatives with more powerful dynamic analysis and FEA capabilities are necessary. Kinematics analysis will only examine the displacement, velocity, and acceleration of the mechanism without considering effects from masses of components. With dynamic analysis and FEA, effects such as the forces or torques at the joint due to mass and inertia of components can be identified. With keen market competition, ALGOR Mechanical Event Simulation (MES), MSC visualNastran 4D, Unigraphics Motion+, and Pro/MECHANICA were chosen for explorations. In this study, comparisons between software tools were presented in terms of following categories: graphical user interface (GUI), import capability, tutorial availability, ease of use, kinematic simulation capability, dynamic simulation capability, FEA capability, graphical output, technical support, and cost. Propulsion Test Article (PTA) with Fastrac engine model exported from IGRIP and an office chair mechanism were used as examples for simulations.

  7. Energy dynamics in a simulation of LAPD turbulence

    SciTech Connect

    Friedman, B.; Carter, T. A.; Schaffner, D.; Umansky, M. V.; Dudson, B.

    2012-10-15

    Energy dynamics calculations in a 3D fluid simulation of drift wave turbulence in the linear Large Plasma Device [W. Gekelman et al., Rev. Sci. Instrum. 62, 2875 (1991)] illuminate processes that drive and dissipate the turbulence. These calculations reveal that a nonlinear instability dominates the injection of energy into the turbulence by overtaking the linear drift wave instability that dominates when fluctuations about the equilibrium are small. The nonlinear instability drives flute-like (k{sub Parallel-To }=0) density fluctuations using free energy from the background density gradient. Through nonlinear axial wavenumber transfer to k{sub Parallel-To }{ne}0 fluctuations, the nonlinear instability accesses the adiabatic response, which provides the requisite energy transfer channel from density to potential fluctuations as well as the phase shift that causes instability. The turbulence characteristics in the simulations agree remarkably well with experiment. When the nonlinear instability is artificially removed from the system through suppressing k{sub Parallel-To }=0 modes, the turbulence develops a coherent frequency spectrum which is inconsistent with experimental data. This indicates the importance of the nonlinear instability in producing experimentally consistent turbulence.

  8. Molecular dynamics simulation indicating cold denaturation of β-hairpins

    NASA Astrophysics Data System (ADS)

    Shao, Qiang; Shi, Jiye; Zhu, Weiliang

    2013-02-01

    The folding of a series of β-hairpin structured polypeptides, which share high sequence similarity but differ significantly in structure resistance to temperature decrease, was investigated in the present study using integrated-tempering-sampling molecular dynamics simulations on microsecond time scale. MrH3a is a single mutant (I16A) and MrH4a is a double mutant (Y3L/I16A) of the wild-type polypeptide MrH1. MrH3b and MrH4b have an additional mutation in the turn region (INGK → IDPGK) of MrH3a and MrH4a, respectively. It was observed in the present study that the cold denaturation tendency follows the order of MrH1 > MrH4a > MrH3a, while the folded structures of MrH3b and MrH4b have the enhanced stability and are not subject to cold denaturation. These observations are in good agreement with experimental results of Maynard et al. and Dyer et al. Comparative analysis of simulation results for the 5 polypeptides revealed potential mechanism of β-hairpin cold denaturation. The main determinant of cold denaturation tendency is likely the stability decrease of backbone hydrogen bonds at low temperatures, which in turn is affected by the packing manner of the hydrophobic core cluster of β-hairpin structures.

  9. Dynamical simulations of strongly correlated electron materials

    NASA Astrophysics Data System (ADS)

    Kress, Joel; Barros, Kipton; Batista, Cristian; Chern, Gia-Wei; Kotliar, Gabriel

    We present a formulation of quantum molecular dynamics that includes electron correlation effects via the Gutzwiller method. Our new scheme enables the study of the dynamical behavior of atoms and molecules with strong electron interactions. The Gutzwiller approach goes beyond the conventional mean-field treatment of the intra-atomic electron repulsion and captures crucial correlation effects such as band narrowing and electron localization. We use Gutzwiller quantum molecular dynamics to investigate the Mott transition in the liquid phase of a single-band metal and uncover intriguing structural and transport properties of the atoms.

  10. An electro-fluid-dynamic simulator for the cardiovascular system.

    PubMed

    Felipini, Celso Luiz; de Andrade, Aron José Pazin; Lucchi, Júlio César; da Fonseca, Jeison Willian Gomes; Nicolosi, Denys

    2008-04-01

    This work presents the initial studies and the proposal for a cardiovascular system electro-fluid-dynamic simulator to be applied in the development of left ventricular assist devices (LVADs). The simulator, which is being developed at University Sao Judas Tadeu and at Institute Dante Pazzanese of Cardiology, is composed of three modules: (i) an electrical analog model of the cardiovascular system operating in the PSpice electrical simulator environment; (ii) an electronic controller, based on laboratory virtual instrumentation engineering workbench (LabVIEW) acquisition and control tool, which will act over the physical simulator; and (iii) the physical simulator: a fluid-dynamic equipment composed of pneumatic actuators and compliance tubes for the simulation of active cardiac chambers and big vessels. The physical simulator (iii) is based on results obtained from the electrical analog model (i) and physiological parameters. PMID:18370952

  11. Mosquito population dynamics from cellular automata-based simulation

    NASA Astrophysics Data System (ADS)

    Syafarina, Inna; Sadikin, Rifki; Nuraini, Nuning

    2016-02-01

    In this paper we present an innovative model for simulating mosquito-vector population dynamics. The simulation consist of two stages: demography and dispersal dynamics. For demography simulation, we follow the existing model for modeling a mosquito life cycles. Moreover, we use cellular automata-based model for simulating dispersal of the vector. In simulation, each individual vector is able to move to other grid based on a random walk. Our model is also capable to represent immunity factor for each grid. We simulate the model to evaluate its correctness. Based on the simulations, we can conclude that our model is correct. However, our model need to be improved to find a realistic parameters to match real data.

  12. Revealing the dynamics of Class 0 protostellar discs with ALMA

    NASA Astrophysics Data System (ADS)

    Seifried, D.; Sánchez-Monge, Á.; Walch, S.; Banerjee, R.

    2016-06-01

    We present synthetic ALMA observations of Keplerian, protostellar discs in the Class 0 stage studying the emission of molecular tracers like 13CO, C18O, HCO+, H13CO+, N2H+, and H2CO. We model the emission of discs around low- and intermediate-mass protostars. We show that under optimal observing conditions ALMA is able to detect the discs already in the earliest stage of protostellar evolution, although the emission is often concentrated to the innermost 50 au. Therefore, a resolution of a few 0.1 arcsec might be too low to detect Keplerian discs around Class 0 objects. We also demonstrate that under optimal conditions for edge-on discs Keplerian rotation signatures are recognisable, from which protostellar masses can be inferred. For this we here introduce a new approach, which allows us to determine protostellar masses with higher fidelity than before. Furthermore, we show that it is possible to reveal Keplerian rotation even for strongly inclined discs and that ALMA should be able to detect possible signs of fragmentation in face-on discs. In order to give some guidance for future ALMA observations, we investigate the influence of varying observing conditions and source distances. We show that it is possible to probe Keplerian rotation in inclined discs with an observing time of 2 h and a resolution of 0.1 arcsec, even in the case of moderate weather conditions. Furthermore, we demonstrate that under optimal conditions, Keplerian discs around intermediate-mass protostars should be detectable up to kpc distances.

  13. Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors

    NASA Astrophysics Data System (ADS)

    Sala, Adrien; Shoaib, Muhammad; Anufrieva, Olga; Mutharasu, Gnanavel; Jahan Hoque, Rawnak; Yli-Harja, Olli; Kandhavelu, Meenakshisundaram

    2015-05-01

    In E. coli, promoter closed and open complexes are key steps in transcription initiation, where magnesium-dependent RNA polymerase catalyzes RNA synthesis. However, the exact mechanism of initiation remains to be fully elucidated. Here, using single mRNA detection and dual reporter studies, we show that increased intracellular magnesium concentration affects Plac initiation complex formation resulting in a highly dynamic process over the cell growth phases. Mg2+ regulates transcription transition, which modulates bimodality of mRNA distribution in the exponential phase. We reveal that Mg2+ regulates the size and frequency of the mRNA burst by changing the open complex duration. Moreover, increasing magnesium concentration leads to higher intrinsic and extrinsic noise in the exponential phase. RNAP-Mg2+ interaction simulation reveals critical movements creating a shorter contact distance between aspartic acid residues and Nucleotide Triphosphate residues and increasing electrostatic charges in the active site. Our findings provide unique biophysical insights into the balanced mechanism of genetic determinants and magnesium ion in transcription initiation regulation during cell growth.

  14. Dynamics of water confined in lyotropic liquid crystals: Molecular dynamics simulations of the dynamic structure factor

    NASA Astrophysics Data System (ADS)

    Mantha, Sriteja; Yethiraj, Arun

    2016-02-01

    The properties of water under confinement are of practical and fundamental interest. In this work, we study the properties of water in the self-assembled lyotropic phases of Gemini surfactants with a focus on testing the standard analysis of quasi-elastic neutron scattering (QENS) experiments. In QENS experiments, the dynamic structure factor is measured and fit to models to extract the translational diffusion constant, DT, and rotational relaxation time, τR. We test this procedure by using simulation results for the dynamic structure factor, extracting the dynamic parameters from the fit as is typically done in experiments, and comparing the values to those directly measured in the simulations. We find that the de-coupling approximation, where the intermediate scattering function is assumed to be a product of translational and rotational contributions, is quite accurate. The jump-diffusion and isotropic rotation models, however, are not accurate when the degree of confinement is high. In particular, the exponential approximations for the intermediate scattering function fail for highly confined water and the values of DT and τR can differ from the measured value by as much as a factor of two. Other models have more fit parameters, however, and with the range of energies and wave-vectors accessible to QENS, the typical analysis appears to be the best choice. In the most confined lamellar phase, the dynamics are sufficiently slow that QENS does not access a large enough time scale.

  15. Dynamics of adaptive structures: Design through simulations

    NASA Technical Reports Server (NTRS)

    Park, K. C.; Alexander, S.

    1993-01-01

    The use of a helical bi-morph actuator/sensor concept by mimicking the change of helical waveform in bacterial flagella is perhaps the first application of bacterial motions (living species) to longitudinal deployment of space structures. However, no dynamical considerations were analyzed to explain the waveform change mechanisms. The objective is to review various deployment concepts from the dynamics point of view and introduce the dynamical considerations from the outset as part of design considerations. Specifically, the impact of the incorporation of the combined static mechanisms and dynamic design considerations on the deployment performance during the reconfiguration stage is studied in terms of improved controllability, maneuvering duration, and joint singularity index. It is shown that intermediate configurations during articulations play an important role for improved joint mechanisms design and overall structural deployability.

  16. Oman metamorphic sole formation reveals early subduction dynamics

    NASA Astrophysics Data System (ADS)

    Soret, Mathieu; Agard, Philippe; Dubacq, Benoît; Plunder, Alexis; Ildefonse, Benoît; Yamato, Philippe; Prigent, Cécile

    2016-04-01

    Metamorphic soles correspond to m to ~500m thick tectonic slices welded beneath most of the large-scale ophiolites. They typically show a steep inverted metamorphic structure where the pressure and temperature conditions of crystallization increase upward (from 500±100°C at 0.5±0.2 GPa to 800±100°C at 1.0±0.2 GPa), with isograds subparallel to the contact with the overlying ophiolitic peridotite. The proportion of mafic rocks in metamorphic soles also increases from the bottom (meta-sediments rich) to the top (approaching the ophiolite peridotites). These soles are interpreted as the result of heat transfer from the incipient mantle wedge toward the nascent slab (associated with large-scale fluid transfer and possible shear heating) during the first My of intra-oceanic subduction (as indicated by radiometric ages). Metamorphic soles provide therefore major constraints on early subduction dynamics (i.e., thermal structure, fluid migration and rheology along the nascent slab interface). We present a detailed structural and petrological study of the metamorphic sole from 4 major cross-sections along the Oman ophiolite. We show precise pressure-temperature estimates obtained by pseudosection modelling and EBSD measurements performed on both the garnet-bearing and garnet-free high-grade sole. Results allow quantification of the micro-scale deformation and highlight differences in pressure-temperature-deformation conditions between the 4 different locations, showing that the inverted metamorphic gradient through the sole is not continuous in all locations. Based on these new constraints, we suggest a new tectonic-petrological model for the formation of metamorphic soles below ophiolites. This model involves the stacking of several homogeneous slivers of oceanic crust leading to the present-day structure of the sole. In this view, these thrusts are the result of rheological contrasts between the sole and the peridotite as the plate interface progressively cools down

  17. Simulating Hamiltonian Dynamics with a Truncated Taylor Series

    NASA Astrophysics Data System (ADS)

    Somma, Rolando

    2015-03-01

    One of the main motivations for quantum computers is their ability to efficiently simulate the dynamics of quantum systems. Since the mid-1990s, many algorithms have been developed to simulate Hamiltonian dynamics on a quantum computer, with applications to problems such as simulating spin models and quantum chemistry. While it is now well known that quantum computers can efficiently simulate Hamiltonian dynamics, ongoing work has improved the performance and expanded the scope of such simulations. In this talk, I will describe a very simple and efficient algorithm for simulating Hamiltonian dynamics on a quantum computer by approximating the truncated Taylor series of the evolution operator. This algorithm can simulate the time evolution of a wide variety of physical systems. The cost of this algorithm depends only logarithmically on the inverse of the desired precision, and can be shown to be optimal. Such a cost also represents an exponential improvement over known methods for Hamiltonian simulation based on, e.g., Trotter-Suzuki approximations. Roughly speaking, doubling the number of digits of accuracy of the simulation only doubles the complexity. The new algorithm and its analysis are highly simplified due to a technique for implementing linear combinations of unitary operations to directly apply the truncated Taylor series. This is joint work with Dominic Berry, Andrew Childs, Richard Cleve, and Robin Kothari.

  18. HUBBLE IMAGES REVEAL A YOUNG STAR'S DYNAMIC DISK AND JETS

    NASA Technical Reports Server (NTRS)

    2002-01-01

    These images of HH 30 show changes over only a five-year period in the disk and jets of this newborn star, which is about half a million years old. The pictures were taken between 1995 and 2000 with the Wide Field and Planetary Camera 2 aboard NASA's Hubble Space Telescope. Astronomers are interested in the disk because it is probably similar to the one from which the Sun and the planets in our solar system formed. Hubble reveals an edge-on disk (located at the bottom of the images), which appears as a flattened cloud of dust split into two halves by a dark lane. The disk blocks light from the central star. All that is visible is the reflection of the star's light by dust above and below the plane of the disk. The disk's diameter is 450 astronomical units (one astronomical unit equals the Earth-Sun distance). Shadows billions of miles in size can be seen moving across the disk. In 1995 and 2000, the left and right sides of the disk were about the same brightness, but in 1998 the right side was brighter. These patterns may be caused by bright spots on the star or variations in the disk near the star. The dust cloud near the top of these frames is illuminated by the star and reflects changes in its brightness. The star's magnetic field plays a major role in forming the jets (located above and below the disk), which look like streams of water from a fire hose. The powerful magnetic field creates the jets by channeling gas from the disk along the magnetic poles above and below the star. The gaps between the compact knots of gas seen in the jet above the disk indicate that this is a sporadic process. By tracking the motion of these knots over time, astronomers have measured the jet's speed at between 200,000 to 600,000 miles per hour (160,000 and 960,000 kilometers per hour). Oddly, the jet below the disk is moving twice as fast as the one above it. Credits: NASA, Alan Watson (Universidad Nacional Autonoma de Mexico), Karl Stapelfeldt (Jet Propulsion Laboratory), John

  19. Perspective: Computer simulations of long time dynamics.

    PubMed

    Elber, Ron

    2016-02-14

    Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances. PMID:26874473

  20. Perspective: Computer simulations of long time dynamics

    PubMed Central

    Elber, Ron

    2016-01-01

    Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances. PMID:26874473

  1. A fast recursive algorithm for molecular dynamics simulation

    NASA Technical Reports Server (NTRS)

    Jain, A.; Vaidehi, N.; Rodriguez, G.

    1993-01-01

    The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.

  2. Ionospheric simulation compared with Dynamics Explorer observations for November 22, 1981

    SciTech Connect

    Sojka, J.J.; Bowline, M.; Schunk, R.W. ); Craven, J.D.; Frank, L.A. ); Sharber, J.R.; Winningham, J.D. ); Brace, L.H. )

    1992-02-01

    Dynamics Explorer (DE) 2 electric field and particle data have been used to constrain the inputs of a time-dependent ionospheric model (TDIM) for a simulation of the ionosphere on November 22, 1981. The simulated densities have then been critically compared with the DE 2 electron density observations. This comparison uncovers a model-data disagreement in the morning sector trough, generally good agreement of the background density in the polar cap and evening sector trough, and a difficulty in modeling the observed polar F layer patches. From this comparison, the consequences of structure in the electric field and precipitation inputs can be seen. This is further highlighted during a substorm period for which DE 1 auroral images were available. Using these images, a revised dynamic particle precipitation pattern was used in the ionospheric model; the resulting densities were different from the original simulation. With this revised dynamic precipitation model, improved density agreement is obtained in the auroral/polar regions where the plasma convection is not stagnant. However, the dynamic study also reveals a difficulty of matching dynamic plasma convection is not stagnant. However, the dynamic study also reveals a difficulty of matching dynamic auroral patterns with static empirical convection patterns. In this case, the matching of the models produced intense auroral precipitation in a stagnation region, which, in turn, led to exceedingly large TDIM densities.

  3. Colloidal suspension simulates linear dynamic pressure profile

    NASA Technical Reports Server (NTRS)

    Mc Cann, R. J.

    1966-01-01

    Missile nose fairings immersed in colloidal suspension prepared with various specific gravities simulate pressure profiles very similar to those encountered during reentry. Stress and deflection conditions similar to those expected during atmospheric reentry are thus attained in the laboratory.

  4. Simulating food web dynamics along a gradient: quantifying human influence.

    PubMed

    Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M

    2012-01-01

    Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics

  5. Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.

    SciTech Connect

    Lau, E Y; Krishnan, V V

    2007-07-18

    The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.

  6. Studies of climate dynamics with innovative global-model simulations

    NASA Astrophysics Data System (ADS)

    Shi, Xiaoming

    Climate simulations with different degrees of idealization are essential for the development of our understanding of the climate system. Studies in this dissertation employ carefully designed global-model simulations for the goal of gaining theoretical and conceptual insights into some problems of climate dynamics. Firstly, global warming-induced changes in extreme precipitation are investigated using a global climate model with idealized geography. The precipitation changes over an idealized north-south mid-latitude mountain barrier at the western margin of an otherwise flat continent are studied. The intensity of the 40 most intense events on the western slopes increases by about ~4°C of surface warming. In contrast, the intensity of the top 40 events on the eastern mountain slopes increases at about ~6°C. This higher sensitivity is due to enhanced ascent during the eastern-slope events, which can be explained in terms of linear mountain-wave theory relating to global warming-induced changes in the upper-tropospheric static stability and the tropopause level. Dominated by different dynamical factors, changes in the intensity of extreme precipitation events over plains and oceans might differ from changes over mountains. So the response of extreme precipitation over mountains and flat areas are further compared using larger data sets of simulated extreme events over the two types of surfaces. It is found that the sensitivity of extreme precipitation to increases in global mean surface temperature is 3% per °C lower over mountains than over the oceans or the plains. The difference in sensitivity among these regions is not due to thermodynamic effects, but rather to differences between the gravity-wave dynamics governing vertical velocities over the mountains and the cyclone dynamics governing vertical motions over the oceans and plains. The strengthening of latent heating in the storms over oceans and plains leads to stronger ascent in the warming climate

  7. Infrared signatures of the peptide dynamical transition: a molecular dynamics simulation study.

    PubMed

    Kobus, Maja; Nguyen, Phuong H; Stock, Gerhard

    2010-07-21

    Recent two-dimensional infrared (2D-IR) experiments on a short peptide 3(10)-helix in chloroform solvent [E. H. G. Backus et al., J. Phys. Chem. B 113, 13405 (2009)] revealed an intriguing temperature dependence of the homogeneous line width, which was interpreted in terms of a dynamical transition of the peptide. To explain these findings, extensive molecular dynamics simulations at various temperatures were performed in order to construct the free energy landscape of the system. The study recovers the familiar picture of a glass-forming system, which below the glass transition temperature T(g) is trapped in various energy basins, while it diffuses freely between these basins above T(g). In fact, one finds at T(g) approximately 270 K a sharp rise of the fluctuations of the backbone dihedral angles, which reflects conformational transitions of the peptide. The corresponding C=O frequency fluctuations are found to be a sensitive probe of the peptide conformational dynamics from femtosecond to nanosecond time scales and lead to 2D-IR spectra that qualitatively match the experiment. The calculated homogeneous line width, however, does not show the biphasic temperature dependence observed in experiment. PMID:20649342

  8. Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Kobus, Maja; Nguyen, Phuong H.; Stock, Gerhard

    2010-07-01

    Recent two-dimensional infrared (2D-IR) experiments on a short peptide 310-helix in chloroform solvent [E. H. G. Backus et al., J. Phys. Chem. B 113, 13405 (2009)] revealed an intriguing temperature dependence of the homogeneous line width, which was interpreted in terms of a dynamical transition of the peptide. To explain these findings, extensive molecular dynamics simulations at various temperatures were performed in order to construct the free energy landscape of the system. The study recovers the familiar picture of a glass-forming system, which below the glass transition temperature Tg is trapped in various energy basins, while it diffuses freely between these basins above Tg. In fact, one finds at Tg≈270 K a sharp rise of the fluctuations of the backbone dihedral angles, which reflects conformational transitions of the peptide. The corresponding CO frequency fluctuations are found to be a sensitive probe of the peptide conformational dynamics from femtosecond to nanosecond time scales and lead to 2D-IR spectra that qualitatively match the experiment. The calculated homogeneous line width, however, does not show the biphasic temperature dependence observed in experiment.

  9. Simulation of dynamic interface fracture using spectral boundary integral method

    NASA Astrophysics Data System (ADS)

    Harish, Ajay Bangalore

    Simulation of three-dimensional dynamic fracture events constitutes one of the most challenging topics in the field of computational mechanics. Spontaneous dynamic fracture along the interface of two elastic solids is of great importance and interest to a number of disciplines in engineering and science. Applications include dynamic fractures in aircraft structures, earthquakes, thermal shocks in nuclear containment vessels and delamination in layered composite materials.

  10. A Process for Comparing Dynamics of Distributed Space Systems Simulations

    NASA Technical Reports Server (NTRS)

    Cures, Edwin Z.; Jackson, Albert A.; Morris, Jeffery C.

    2009-01-01

    The paper describes a process that was developed for comparing the primary orbital dynamics behavior between space systems distributed simulations. This process is used to characterize and understand the fundamental fidelities and compatibilities of the modeling of orbital dynamics between spacecraft simulations. This is required for high-latency distributed simulations such as NASA s Integrated Mission Simulation and must be understood when reporting results from simulation executions. This paper presents 10 principal comparison tests along with their rationale and examples of the results. The Integrated Mission Simulation (IMSim) (formerly know as the Distributed Space Exploration Simulation (DSES)) is a NASA research and development project focusing on the technologies and processes that are related to the collaborative simulation of complex space systems involved in the exploration of our solar system. Currently, the NASA centers that are actively participating in the IMSim project are the Ames Research Center, the Jet Propulsion Laboratory (JPL), the Johnson Space Center (JSC), the Kennedy Space Center, the Langley Research Center and the Marshall Space Flight Center. In concept, each center participating in IMSim has its own set of simulation models and environment(s). These simulation tools are used to build the various simulation products that are used for scientific investigation, engineering analysis, system design, training, planning, operations and more. Working individually, these production simulations provide important data to various NASA projects.

  11. Dynamics of a compound vesicle: numerical simulations

    NASA Astrophysics Data System (ADS)

    Veerapaneni, Shravan; Young, Yuan-Nan; Vlahovska, Petia; Blawzdziewicz, Jerzy

    2010-11-01

    Vesicles (self-enclosing lipid membranes) in simple linear flows are known to exhibit rich dynamics such as tank-treading, tumbling, trembling (swinging), and vacillating breathing. Recently, vesicles have been used as a multi-functional platform for drug-delivery. In this work, the dynamics of simplified models for such compound vesicles is investigated numerically using a state-of-the-art boundary-integral code that has been validated with high accuracy and efficiency. Results show that for a vesicle enclosing a rigid particle in a simple shear flow, transition from tank-treading to tumbling is possible even in the absence of viscosity mismatch in the interior and exterior fluids. We will discuss the shape transformations, multiple particle interactions and the flow properties. Comparison with results from analytical modeling gives insights to the underlying physics for such novel dynamics.

  12. Dynamics Simulation Model for Space Tethers

    NASA Technical Reports Server (NTRS)

    Levin, E. M.; Pearson, J.; Oldson, J. C.

    2006-01-01

    This document describes the development of an accurate model for the dynamics of the Momentum Exchange Electrodynamic Reboost (MXER) system. The MXER is a rotating tether about 100-km long in elliptical Earth orbit designed to catch payloads in low Earth orbit and throw them to geosynchronous orbit or to Earth escape. To ensure successful rendezvous between the MXER tip catcher and a payload, a high-fidelity model of the system dynamics is required. The model developed here quantifies the major environmental perturbations, and can predict the MXER tip position to within meters over one orbit.

  13. Particle dynamics simulations of Turing patterns

    NASA Astrophysics Data System (ADS)

    Dziekan, P.; Lemarchand, A.; Nowakowski, B.

    2012-08-01

    The direct simulation Monte Carlo method is used to reproduce Turing patterns at the microscopic level in reaction-diffusion systems. In order to satisfy the basic condition for the development of such a spatial structure, we propose a model involving a solvent, which allows for disparate diffusivities of individual reactive species. One-dimensional structures are simulated in systems of various lengths. Simulation results agree with the macroscopic predictions obtained by integration of the reaction-diffusion equations. Additional effects due to internal fluctuations are observed, such as temporal transitions between structures of different wavelengths in a confined system. For a structure developing behind a propagating wave front, the fluctuations suppress the induction period and accelerate the formation of the Turing pattern. These results support the ability of reaction-diffusion models to robustly reproduce axial segmentation including the formation of early vertebrae or somites in noisy biological environments.

  14. Gamma ray observatory dynamics simulator in Ada (GRODY)

    NASA Technical Reports Server (NTRS)

    1990-01-01

    This experiment involved the parallel development of dynamics simulators for the Gamma Ray Observatory in both FORTRAN and Ada for the purpose of evaluating the applicability of Ada to the NASA/Goddard Space Flight Center's flight dynamics environment. The experiment successfully demonstrated that Ada is a viable, valuable technology for use in this environment. In addition to building a simulator, the Ada team evaluated training approaches, developed an Ada methodology appropriate to the flight dynamics environment, and established a baseline for evaluating future Ada projects.

  15. Destination state screening of active spaces in spin dynamics simulations

    NASA Astrophysics Data System (ADS)

    Krzystyniak, M.; Edwards, Luke J.; Kuprov, Ilya

    2011-06-01

    We propose a novel avenue for state space reduction in time domain Liouville space spin dynamics simulations, using detectability as a selection criterion - only those states that evolve into or affect other detectable states are kept in the simulation. This basis reduction procedure (referred to as destination state screening) is formally exact and can be applied on top of the existing state space restriction techniques. As demonstrated below, in many cases this results in further reduction of matrix dimension, leading to considerable acceleration of many spin dynamics simulation types. Destination state screening is implemented in the latest version of the Spinach library (http://spindynamics.org).

  16. Brownian dynamics simulation for modeling ion permeation across bionanotubes.

    PubMed

    Krishnamurthy, Vikram; Chung, Shin-Ho

    2005-03-01

    The principles underlying Brownian dynamics (BD), its statistical consistency, and algorithms for practical implementation are outlined here. The ability to compute current flow across ion channels confers a distinct advantage to BD simulations compared to other simulation techniques. Thus, two obvious applications of BD ion channels are in calculation of the current-voltage and current-concentration curves, which can be directly compared to the physiological measurements to assess the reliability of the model and predictive power of the method. We illustrate how BD simulations are used to unravel the permeation dynamics in two biological ion channels-the KcsA K+ channel and CIC Cl- channel. PMID:15816176

  17. Computer simulation of multigrid body dynamics and control

    NASA Technical Reports Server (NTRS)

    Swaminadham, M.; Moon, Young I.; Venkayya, V. B.

    1990-01-01

    The objective is to set up and analyze benchmark problems on multibody dynamics and to verify the predictions of two multibody computer simulation codes. TREETOPS and DISCOS have been used to run three example problems - one degree-of-freedom spring mass dashpot system, an inverted pendulum system, and a triple pendulum. To study the dynamics and control interaction, an inverted planar pendulum with an external body force and a torsional control spring was modeled as a hinge connected two-rigid body system. TREETOPS and DISCOS affected the time history simulation of this problem. System state space variables and their time derivatives from two simulation codes were compared.

  18. Simulation analysis of dynamic working performance for star trackers.

    PubMed

    Shen, Juan; Zhang, Guangjun; Wei, Xinguo

    2010-12-01

    The elongated imaging track pertaining to a star spot recorded in the image sensor of a star tracker will diffuse over several pixels at a high angular velocity, leading to an inaccurate, even false, attitude value. A computer simulation of the attitude determination from a dynamic star tracker is developed first, based on a dynamic mathematical model of the star-spot imaging and an efficiency validation of the star centroiding algorithm in the dynamic condition. Then major error sources affecting the attitude accuracy in the dynamic condition are analyzed and discussed systematically based on the simulation results. A mathematical model calculating the average star number detected in the field of view is also deduced, using simulation results and signal processing theory, with image trailing ranging from 0 to 20 pixels during exposure. The summarized regularity is helpful in the system design and accuracy evaluation of a star tracker. PMID:21119749

  19. SSME-HAS dynamic load simulators

    NASA Technical Reports Server (NTRS)

    1975-01-01

    The space shuttle main engine propellant valve actuators (SSME) were designed to simulate the loads reflected into the SSME by the chamber coolant valve, the fuel preburner, and the oxidizer. The design, and functional description are included along with a list of the drawings. The load fixture control transform, friction torque, and flow calculations are reported.

  20. Programmable quantum simulation by dynamic Hamiltonian engineering

    NASA Astrophysics Data System (ADS)

    Hayes, David; Flammia, Steven T.; Biercuk, Michael J.

    2014-08-01

    Quantum simulation is a promising near term application for quantum information processors with the potential to solve computationally intractable problems using just a few dozen interacting qubits. A range of experimental platforms have recently demonstrated the basic functionality of quantum simulation applied to quantum magnetism, quantum phase transitions and relativistic quantum mechanics. However, in all cases, the physics of the underlying hardware restricts the achievable inter-particle interactions and forms a serious constraint on the versatility of the simulators. To broaden the scope of these analog devices, we develop a suite of pulse sequences that permit a user to efficiently realize average Hamiltonians that are beyond the native interactions of the system. Specifically, this approach permits the generation of all symmetrically coupled translation-invariant two-body Hamiltonians with homogeneous on-site terms, a class which includes all spin-1/2 XYZ chains, but generalized to include long-range couplings. Our work builds on previous work proving that universal simulation is possible using both entangling gates and single-qubit unitaries. We show that determining the appropriate ‘program’ of unitary pulse sequences which implements an arbitrary Hamiltonian transformation can be formulated as a linear program over functions defined by those pulse sequences, running in polynomial time and scaling efficiently in hardware resources. Our analysis extends from circuit model quantum information to adiabatic quantum evolutions, representing an important and broad-based success in applying functional analysis to the field of quantum information.

  1. SIMULATING FISH ASSEMBLAGE DYNAMICS IN RIVER NETWORKS

    EPA Science Inventory

    My recently retired colleague, Joan Baker, and I have developed a prototype computer simulation model for studying the effects of human and non-human alterations of habitats and species availability on fish assemblage populations. The fish assemblage model, written in R, is a sp...

  2. Dynamic Process Simulation for Analysis and Design.

    ERIC Educational Resources Information Center

    Nuttall, Herbert E., Jr.; Himmelblau, David M.

    A computer program for the simulation of complex continuous process in real-time in an interactive mode is described. The program is user oriented, flexible, and provides both numerical and graphic output. The program has been used in classroom teaching and computer aided design. Typical input and output are illustrated for a sample problem to…

  3. Ab initio molecular dynamics simulation of aqueous solution of nitric oxide in different formal oxidation states

    NASA Astrophysics Data System (ADS)

    Venâncio, Mateus F.; Rocha, Willian R.

    2015-10-01

    Ab initio molecular dynamics simulations were used to investigate the early chemical events involved in the dynamics of nitric oxide (NOrad), nitrosonium cation (NO+) and nitroxide anion (NO-) in aqueous solution. The NO+ ion is very reactive in aqueous solution having a lifetime of ∼4 × 10-13 s, which is shorter than the value of 3 × 10-10 s predicted experimentally. The NO+ reacts generating the nitrous acid as an intermediate and the NO2- ion as the final product. The dynamics of NOrad revealed the reversibly formation of a transient anion radical species HONOrad -.

  4. Simulations of Energetic Particles Interacting with Dynamical Magnetic Turbulence

    NASA Astrophysics Data System (ADS)

    Hussein, M.; Shalchi, A.

    2016-02-01

    We explore the transport of energetic particles in interplanetary space by using test-particle simulations. In previous work such simulations have been performed by using either magnetostatic turbulence or undamped propagating plasma waves. In the current paper we simulate for the first time particle transport in dynamical turbulence. To do so we employ two models, namely the damping model of dynamical turbulence and the random sweeping model. We compute parallel and perpendicular diffusion coefficients and compare our numerical findings with solar wind observations. We show that good agreement can be found between simulations and the Palmer consensus range for both dynamical turbulence models if the ratio of turbulent magnetic field and mean field is δB/B0 = 0.5.

  5. Multi-petaflop/s quantum and reactive molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Nakano, Aiichiro

    We have developed a divide-conquer-recombine algorithmic framework for large quantum molecular dynamics (QMD) and reactive molecular dynamics (RMD) simulations. The algorithms have achieved parallel efficiency over 0.98 on 786,432 IBM Blue Gene/Q processors for 39.8 trillion electronic degrees-of-freedom QMD in the framework of density functional theory and 67.6 billion-atom RMD. We will discuss several applications including (1) 16,616-atom QMD simulation of rapid hydrogen production from water using metallic alloy nanoparticles, (2) 6,400-atom nonadiabatic QMD simulation of exciton dynamics for efficient solar cells, and (3) 112 million-atom RMD simulation of nanocarbon synthesis by high temperature oxidation of SiC nanoparticles.

  6. Dynamic simulation of chemical industry wastewater treatment plants.

    PubMed

    Bury, S J; Groot, C K; Huth, C; Hardt, N

    2002-01-01

    High variability, stringent effluent permits, and often extreme operating conditions define the practice of wastewater treatment in the chemical industry. This paper reviews the benefits and challenges of applying dynamic simulation to chemical-industry wastewater treatment plants by describing case studies at full-scale wastewater treatment plants (WWTP). The applications range from process troubleshooting to optimization and control. The applications have been valuable and useful in developing a deeper understanding of the plants as integrated systems. However there still remains substantial work to implement the dynamic simulations for daily real-time use by plant engineers and operators. This opportunity to improve plant operations is still largely untapped and will remain so until dynamic state estimation and data reconciliation are incorporated into simulation packages for use in developing the on-line simulations. PMID:11936653

  7. Simulating the dynamic response of magnesium alloys

    NASA Astrophysics Data System (ADS)

    Lloyd, Jeffrey; Becker, Richard

    Unlike several conventional metals, the mechanical response of magnesium is severely anisotropic for quasistatic and dynamic loading conditions. In this work we present a crystal-based strength model that is the same order of magnitude in computational cost as rate-dependent isotropic strength models, yet is able to capture essential features exhibited by textured magnesium polycrystals. The model demarcates plastic deformation into contributions from basal slip, extension twinning, and non-basal slip mechanisms. Comparisons are made between model predictions and experiments for two magnesium alloys with differing processing histories. The model is then used to explore and quantify the dependence of metallurgical and processing variations for several dynamic experiments that probe propensity for localization and failure under complex loading conditions.

  8. Event-Scale Morphodynamics and Sediment Sorting in a Dynamic Braided River Revealed by TLS

    NASA Astrophysics Data System (ADS)

    Vericat, D.; Brasington, J.

    2008-12-01

    In the last decade, advances in topographic survey and digital elevation modelling have enabled a revolution in the study of fluvial morphodynamics. Despite this recent progress, our understanding of braided river dynamics remains limited by the time-space scale of studies. Hindered by high labour and flight costs, together with slow ground-based survey methods, studies to date have focused either on event-scale dynamics of morphological units (Ferguson and Ashworth, 1992; Lane et al., 1995; Milan et al., 2007) or seasonal-annual dynamics of larger system-scale reaches (sensu Lane, 2006; e.g., Brasington et al., 2003; Lane et al., 2003). Terrestrial Laser Scanning technology offers the potential to acquire rapidly, reach-scale datasets which record topographic information at the resolution of bed grain-scale upwards. However, as yet, no detailed 3d datasets exist that reveal the system-scale evolution of a braided river through a continuous sequence of floods. Such data are urgently required to address unresolved and fundamental questions concerning the controls and behaviour of braided rivers and are also needed to validate morphodynamic simulation models (Brasington and Richards, 2007). Our recent wok has demonstrated that TLS can be applied to recover centimetre-scale channel morphology, maps of particle size, sorting, packing and floodplain roughness (Brasington et al., 2007, 2008; Antonarakis, 2008a,b; Hodge et al., in review). This potential is illustrated by the results obtained in a field study conducted in January 2008. This used TLS to monitor the evolution of channel morphology and develop methods to derive models of bed roughness and facies in a small 500 x 300 m reach of the actively braided Rees River, New Zealand. Fieldwork comprised repeat surveys before and after 3 competent events, combining laser scans from eight positions with bathymetric data obtained by RTK GPS. The resulting point clouds incorporated between 48-110 million survey points, with

  9. Seeking new mutation clues from Bacillus licheniformis amylase by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lu, Tao

    2009-07-01

    Amylase is one of the most important industrial enzymes in the world. Researchers have been searching for a highly thermal stable mutant for many years, but most focus on point mutations of one or few nitrogenous bases. According to this molecular dynamic simulation of amylase from Bacillus licheniformis (BLA), the deletion of some nitrogenous bases would be more efficacious than point mutations. The simulation reveals strong fluctuation of the BLA structure at optimum temperature. The fluctuation of the outer domains of BLA is stronger than that of the core domain. Molecular simulation provides a clue to design thermal stable amylases through deletion mutations in the outer domain.

  10. Coarse-grain molecular dynamics simulations of diblock copolymer surfactants interacting with a lipid bilayer

    NASA Astrophysics Data System (ADS)

    Srinivas, Goundla; Klein, Michael L.

    2004-01-01

    The interaction of surfactant diblock poly(ethylene oxide)-poly(ethylethylene) copolymers (PEO-PEE) with a lipid bilayer of dimyristoylphosphatidylcholine has been studied by means of coarse-grain molecular dynamics simulations. The effect of the surfactants on the lipid bilayer was studied over a wide range of diblock copolymer concentrations. The simulations show that the hydrophilic PEO chains adopt different structures at low and high concentrations. In particular, the computed density profiles reveal that the PEO chains extend over a longer range from the bilayer surface, with increasing copolymer concentration. The simulated density profiles are in agreement with the scaling law predictions.

  11. Quantum dynamics simulation with classical oscillators

    NASA Astrophysics Data System (ADS)

    Briggs, John S.; Eisfeld, Alexander

    2013-12-01

    In a previous paper [J. S. Briggs and A. Eisfeld, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.85.052111 85, 052111 (2012)] we showed that the time development of the complex amplitudes of N coupled quantum states can be mapped by the time development of positions and velocities of N coupled classical oscillators. Here we examine to what extent this mapping can be realized to simulate the “quantum,” properties of entanglement and qubit manipulation. By working through specific examples, e.g., of quantum gate operation, we seek to illuminate quantum and classical differences which hitherto have been treated more mathematically. In addition, we show that important quantum coupled phenomena, such as the Landau-Zener transition and the occurrence of Fano resonances can be simulated by classical oscillators.

  12. Molecular dynamics simulation of propagating cracks

    NASA Technical Reports Server (NTRS)

    Mullins, M.

    1982-01-01

    Steady state crack propagation is investigated numerically using a model consisting of 236 free atoms in two (010) planes of bcc alpha iron. The continuum region is modeled using the finite element method with 175 nodes and 288 elements. The model shows clear (010) plane fracture to the edge of the discrete region at moderate loads. Analysis of the results obtained indicates that models of this type can provide realistic simulation of steady state crack propagation.

  13. Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene

    SciTech Connect

    Cawkwell, M. J. Niklasson, Anders M. N.; Dattelbaum, Dana M.

    2015-02-14

    The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

  14. Simulation in a dynamic prototyping environment: Petri nets or rules?

    NASA Technical Reports Server (NTRS)

    Moore, Loretta A.; Price, Shannon; Hale, Joseph P.

    1994-01-01

    An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.

  15. Simulation in a dynamic prototyping environment: Petri nets or rules?

    NASA Technical Reports Server (NTRS)

    Moore, Loretta A.; Price, Shannon W.; Hale, Joseph P.

    1994-01-01

    An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are normally delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.

  16. Simulating Dynamics Of The Gamma-Ray Observatory Satellite

    NASA Technical Reports Server (NTRS)

    Stark, M.

    1991-01-01

    GRODY developed alongside GROSS computer program (GSC-13147), a FORTRAN dynamics-simulator program performing same functions. GRODY conceived for use in case study to assess feasibility and effectiveness of Ada programming language for development of flight-dynamics software. Designed for those familiar with analysis of attitudes of spacecraft. Supports planning of maneuvers as well as analytical testing and evaluation of attitude-determination and -control system used on board Gamma-Ray Observatory (GRO) satellite. Simulates computer and control processor electronics aboard GRO satellite. Enables analyst to check and update commands sent from ground and values of parameters, obtain displays of status of simulation, interrupt simulation, analyze previous runs, and obtain printed output of simulation runs. Written mainly in Ada (99 percent) with remainder in FORTRAN.

  17. Slow dynamics of nanocomposite polymer aerogels as revealed by X-ray photocorrelation spectroscopy (XPCS)

    SciTech Connect

    Hernández, Rebeca E-mail: aurora.nogales@csic.es; Mijangos, Carmen; Nogales, Aurora E-mail: aurora.nogales@csic.es; Ezquerra, Tiberio A.; Sprung, Michael

    2014-01-14

    We report on a novel slow dynamics of polymer xerogels, aerogels, and nanocomposite aerogels with iron oxide nanoparticles, as revealed by X-ray photon correlation spectroscopy. The polymer aerogel and its nanocomposite aerogels, which are porous in nature, exhibit hyper-diffusive dynamics at room temperature. In contrast, non-porous polymer xerogels exhibit an absence of this peculiar dynamics. This slow dynamical process has been assigned to a relaxation of the characteristic porous structure of these materials and not to the presence of nanoparticles.

  18. A reduced basis method for molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Vincent-Finley, Rachel Elisabeth

    In this dissertation, we develop a method for molecular simulation based on principal component analysis (PCA) of a molecular dynamics trajectory and least squares approximation of a potential energy function. Molecular dynamics (MD) simulation is a computational tool used to study molecular systems as they evolve through time. With respect to protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds. To capture motion at all levels, time steps on the order of a femtosecond are employed when solving the equations of motion and simulations must continue long enough to capture the desired large-scale motion. To date, simulations of solvated proteins on the order of nanoseconds have been reported. It is typically the case that simulations of a few nanoseconds do not provide adequate information for the study of large-scale motions. Thus, the development of techniques that allow longer simulation times can advance the study of protein function and dynamics. In this dissertation we use principal component analysis (PCA) to identify the dominant characteristics of an MD trajectory and to represent the coordinates with respect to these characteristics. We augment PCA with an updating scheme based on a reduced representation of a molecule and consider equations of motion with respect to the reduced representation. We apply our method to butane and BPTI and compare the results to standard MD simulations of these molecules. Our results indicate that the molecular activity with respect to our simulation method is analogous to that observed in the standard MD simulation with simulations on the order of picoseconds.

  19. Simulated livestock dynamics--effects of pastoral offtake practices and drift on cattle wealth.

    PubMed

    Baptist, R

    1990-05-01

    Pastoral cattle herds were simulated to demonstrate a species-independent package (DADAS) for the analysis and simulation of livestock dynamics. A cow culling age of 11 years was expected to maximise offtake rate and to stabilise the cattle population. This threshold was derived by the deterministic module of the package used. A closer look at six offtake patterns using the stochastic module of the simulation program revealed that those who cull cows at an age limit would fare less well than those who cull cows only when sterile. Within each offtake pattern the cumulative effects of chance fluctuations in sex-ratio of calves, mortality, sterility, age at first calving and calving interval resulted in cattle wealth indicators varying widely between replicate herds. The example shows that livestock dynamics simulation on personal computers is feasible for planning, teaching and research purposes. PMID:2371755

  20. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    SciTech Connect

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D. Kühn, Oliver

    2015-06-28

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.

  1. Executive Summary: Special Section on Credible Computational Fluid Dynamics Simulations

    NASA Technical Reports Server (NTRS)

    Mehta, Unmeel B.

    1998-01-01

    This summary presents the motivation for the Special Section on the credibility of computational fluid dynamics (CFD) simulations, its objective, its background and context, its content, and its major conclusions. Verification and validation (V&V) are the processes for establishing the credibility of CFD simulations. Validation assesses whether correct things are performed and verification assesses whether they are performed correctly. Various aspects of V&V are discussed. Progress is made in verification of simulation models. Considerable effort is still needed for developing a systematic validation method that can assess the credibility of simulated reality.

  2. GRODY - GAMMA RAY OBSERVATORY DYNAMICS SIMULATOR IN ADA

    NASA Technical Reports Server (NTRS)

    Stark, M.

    1994-01-01

    Analysts use a dynamics simulator to test the attitude control system algorithms used by a satellite. The simulator must simulate the hardware, dynamics, and environment of the particular spacecraft and provide user services which enable the analyst to conduct experiments. Researchers at Goddard's Flight Dynamics Division developed GRODY alongside GROSS (GSC-13147), a FORTRAN simulator which performs the same functions, in a case study to assess the feasibility and effectiveness of the Ada programming language for flight dynamics software development. They used popular object-oriented design techniques to link the simulator's design with its function. GRODY is designed for analysts familiar with spacecraft attitude analysis. The program supports maneuver planning as well as analytical testing and evaluation of the attitude determination and control system used on board the Gamma Ray Observatory (GRO) satellite. GRODY simulates the GRO on-board computer and Control Processor Electronics. The analyst/user sets up and controls the simulation. GRODY allows the analyst to check and update parameter values and ground commands, obtain simulation status displays, interrupt the simulation, analyze previous runs, and obtain printed output of simulation runs. The video terminal screen display allows visibility of command sequences, full-screen display and modification of parameters using input fields, and verification of all input data. Data input available for modification includes alignment and performance parameters for all attitude hardware, simulation control parameters which determine simulation scheduling and simulator output, initial conditions, and on-board computer commands. GRODY generates eight types of output: simulation results data set, analysis report, parameter report, simulation report, status display, plots, diagnostic output (which helps the user trace any problems that have occurred during a simulation), and a permanent log of all runs and errors. The

  3. A molecular dynamics simulation study of dynamic process and mesoscopic structure in liquid mixture systems

    NASA Astrophysics Data System (ADS)

    Yang, Peng

    The focus of this dissertation is the Molecular Dynamics (MD) simulation study of two different systems. In thefirst system, we study the dynamic process of graphene exfoliation, particularly graphene dispersion using ionic surfactants (Chapter 2). In the second system, we investigate the mesoscopic structure of binary solute/ionic liquid (IL) mixtures through the comparison between simulations and corresponding experiments (Chapter 3 and 4). In the graphene exfoliation study, we consider two separation mechanisms: changing the interlayer distance and sliding away the relative distance of two single-layer graphene sheets. By calculating the energy barrier as a function of separation (interlayer or sliding-away) distance and performing sodium dodecyl sulfate (SDS) structure analysis around graphene surface in SDS surfactant/water + bilayer graphene mixture systems, we find that the sliding-away mechanism is the dominant, feasible separation process. In this process, the SDS-graphene interaction gradually replaces the graphene-graphene Van der Waals (VdW) interaction, and decreases the energy barrier until almost zero at critical SDS concentration. In solute/IL study, we investigate nonpolar (CS2) and dipolar (CH 3CN) solute/IL mixture systems. MD simulation shows that at low concentrations, IL is nanosegregated into an ionic network and nonpolar domain. It is also found that CS2 molecules tend to be localized into the nonpolar domain, while CH3CN interacts with nonpolar domain as well as with the charged head groups in the ionic network because of its amphiphilicity. At high concentrations, CH3CN molecules eventually disrupt the nanostructural organization. This dissertation is organized in four chapters: (1) introduction to graphene, ionic liquids and the methodology of MD; (2) MD simulation of graphene exfoliation; (3) Nanostructural organization in acetonitrile/IL mixtures; (4) Nanostructural organization in carbon disulfide/IL mixtures; (5) Conclusions. Results

  4. Molecular-dynamics simulation of hydrogen diffusion in palladium

    NASA Astrophysics Data System (ADS)

    Li, Yinggang; Wahnström, Göran

    1992-12-01

    Molecular-dynamics simulations for hydrogen diffusion in Pd are performed for a system consisting of 256 Pd atoms and 8 H atoms at the temperature T=623 K. Under these conditions detailed quasielastic-neutron-scattering (QNS) data are available. For the interatomic interactions we use the embedded-atom method (EAM), which incorporates some essential many-body effects in metals. Based on the EAM approach, the wave-vector dependence of the width of the QNS peak is investigated in detail. It is found that a single electronically adiabatic potential-energy surface cannot reproduce the observed wave-vector dependence. After incorporating the coupling of hydrogen atoms to the low-lying electron-hole pair excitations among the conduction electrons, close agreement with the experimental data is obtained. This is a strong indication that one has to go beyond the Born-Oppenheimer approximation in order to characterize correctly the diffusive motion of hydrogen in metals. To reveal the diffusive behavior in more detail, the residence time distribution and the correlation character in diffusion direction are investigated. We found that including the nonadiabatic corrections reduces the probability for the H atoms to move over several lattice sites without getting trapped in between. As a result, the motion of the H atoms becomes more similar to that assumed in the Chudley-Elliott model, which describes well the QNS data for the wave-vector dependence of the width.

  5. Excipient-assisted vinpocetine nanoparticles: experiments and molecular dynamic simulations.

    PubMed

    Li, Cai-Xia; Wang, Hao-Bo; Oppong, Daniel; Wang, Jie-Xin; Chen, Jian-Feng; Le, Yuan

    2014-11-01

    Hydrophilic excipients can be used to increase the solubility and bioavailability of poorly soluble drugs. In this work, the conventional water-soluble pharmaceutical excipients hydroxypropylmethylcellulose (HPMC), polyvinylpyrrolidone (PVP), and lactose (LAC) were used as solid supports to prevent drug nanoparticles from aggregation and enhance drug dissolution. Excipient-assisted vinpocetine (VIN) nanoparticles were prepared by reactive precipitation. The analysis results indicated that HPMC was a suitable excipient to prepare VIN nanoparticles. VIN/HPMC nanoparticles had a mean size of 130 nm within a narrow distribution. The dissolution rate of VIN nanoparticles was significantly faster than those of a physical mixture of VIN/HPMC and raw VIN. VIN/HPMC nanoparticles had a higher dissolution profile than VIN/PVP and VIN/LAC nanoparticles. Besides, molecular dynamics (MD) simulation was applied to investigate the molecular interactions between VIN and excipients. The calculated results revealed that VIN interacted with excipients by Coulomb and Lennard-Jones (LJ) interactions. Few hydrogen bonds were formed between VIN and excipients. The HPMC affording smaller particle size may be a result of the stronger interactions between VIN and HPMC (mainly LJ interaction) and the property of HPMC. These characteristics may greatly influence the adsorption behavior and may be the crucial parameter for the better performance of HPMC. PMID:25244002

  6. Simulating Timescale Dynamics of Network Traffic Using Homogeneous Modeling

    PubMed Central

    Yuan, Jian; Mills, Kevin L.

    2006-01-01

    Simulating and understanding traffic dynamics in large networks are difficult and challenging due to the complexity of such networks and the limitations inherent in simulation modeling. Typically, simulation models used to study traffic dynamics include substantial detail representing protocol mechanisms across several layers of functionality. Such models must be restricted in space and time in order to be computationally tractable. We propose an alternative simulation approach that uses homogeneous modeling with an increased level of abstraction, in order to explore networks at larger space-time scales than otherwise feasible and to develop intuition and insight about the space-time dynamics of large networks. To illustrate the utility of our approach, we examine some current understandings of the timescale dynamics of network traffic, and we discuss some speculative results obtained with homogeneous modeling. Using a wavelet-based technique, we show correlation structures, and changes in correlation structures, of network traffic under variations in traffic sources, transport mechanisms, and network structure. Our simulation results justify further investigation of our approach, which might benefit from cross-verifications against more detailed simulation models. PMID:27274931

  7. Solar simulator for solar dynamic space power system testing

    NASA Technical Reports Server (NTRS)

    Jefferies, Kent S.

    1993-01-01

    Planned vacuum tank testing of a solar dynamic space power system requires a solar simulator. Several solar simulators were previously built and used for vacuum tank testing of various space systems. However, the apparent solar subtense angle, i.e., the angular size of the apparent sun as viewed from the experiment, of these solar simulators is too large to enable testing of solar dynamic systems. A new design was developed to satisfy the requirements of the solar dynamic testing. This design provides 1.8 kW/m(sup 2) onto a 4.5M diameter test area from a source that subtends only 1 deg, full cone angle. Key features that enable this improved performance are (1) elimination of the collimating mirror commonly used in solar simulators to transform the diverging beam into a parallel beam; (2) a redesigned lamp module that has increased efficiency; and (3) the use of a segmented reflective surface to combine beams from several individual lamp modules at the pseudosun. Each segment of this reflective surface has complex curvature to control the distribution of light. By developing a new solar simulator design for testing of the solar dynamic system instead of modifying current designs, the initial cost was cut in half, the efficiency was increased by 50 percent reducing the operating costs by one-third, and the volume occupied by the solar simulator was reduced by a factor of 10.

  8. Multiscale Simulation of Microbe Structure and Dynamics

    PubMed Central

    Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V.; Cheluvaraja, Srinath C.; Ortoleva, Peter J.

    2012-01-01

    A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin. PMID:21802438

  9. Dynamic stall simulation including turbulence modeling

    SciTech Connect

    Allet, A.; Halle, S.; Paraschivoiu, I.

    1995-09-01

    The objective of this study is to investigate the two-dimensional unsteady flow around an airfoil undergoing a Darrieus motion in dynamic stall conditions. For this purpose, a numerical solver based on the solution of the Reynolds-averaged Navier-Stokes equations expressed in a streamfunction-vorticity formulation in a non-inertial frame of reference was developed. The governing equations are solved by the streamline upwind Petrov-Galerkin finite element method (FEM). Temporal discretization is achieved by second-order-accurate finite differences. The resulting global matrix system is linearized by the Newton method and solved by the generalized minimum residual method (GMRES) with an incomplete triangular factorization preconditioning (ILU). Turbulence effects are introduced in the solver by an eddy viscosity model. The investigation centers on an evaluation of the possibilities of several turbulence models, including the algebraic Cebeci-Smith model (CSM) and the nonequilibrium Johnson-King model (JKM). In an effort to predict dynamic stall features on rotating airfoils, first the authors present some testing results concerning the performance of both turbulence models for the flat plate case. Then, computed flow structure together with aerodynamic coefficients for a NACA 0015 airfoil in Darrieus motion under stall conditions are presented.

  10. Structure-dynamics relationships in bursting neuronal networks revealed using a prediction framework.

    PubMed

    Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Ruohonen, Keijo; Linne, Marja-Leena

    2013-01-01

    The question of how the structure of a neuronal network affects its functionality has gained a lot of attention in neuroscience. However, the vast majority of the studies on structure-dynamics relationships consider few types of network structures and assess limited numbers of structural measures. In this in silico study, we employ a wide diversity of network topologies and search among many possibilities the aspects of structure that have the greatest effect on the network excitability. The network activity is simulated using two point-neuron models, where the neurons are activated by noisy fluctuation of the membrane potential and their connections are described by chemical synapse models, and statistics on the number and quality of the emergent network bursts are collected for each network type. We apply a prediction framework to the obtained data in order to find out the most relevant aspects of network structure. In this framework, predictors that use different sets of graph-theoretic measures are trained to estimate the activity properties, such as burst count or burst length, of the networks. The performances of these predictors are compared with each other. We show that the best performance in prediction of activity properties for networks with sharp in-degree distribution is obtained when the prediction is based on clustering coefficient. By contrast, for networks with broad in-degree distribution, the maximum eigenvalue of the connectivity graph gives the most accurate prediction. The results shown for small ([Formula: see text]) networks hold with few exceptions when different neuron models, different choices of neuron population and different average degrees are applied. We confirm our conclusions using larger ([Formula: see text]) networks as well. Our findings reveal the relevance of different aspects of network structure from the viewpoint of network excitability, and our integrative method could serve as a general framework for structure-dynamics

  11. Particle Motion Analysis Reveals Nanoscale Bond Characteristics and Enhances Dynamic Range for Biosensing.

    PubMed

    Visser, Emiel W A; van IJzendoorn, Leo J; Prins, Menno W J

    2016-03-22

    Biofunctionalized colloidal particles are widely used as labels in bioanalytical assays, lab-on-chip devices, biophysical research, and in studies on live biological systems. With detection resolution going down to the level of single particles and single molecules, understanding the nature of the interaction of the particles with surfaces and substrates becomes of paramount importance. Here, we present a comprehensive study of motion patterns of colloidal particles maintained in close proximity to a substrate by short molecular tethers (40 nm). The motion of the particles (500-1000 nm) was optically tracked with a very high localization accuracy (below 3 nm). A surprisingly large variation in motion patterns was observed, which can be attributed to properties of the particle-molecule-substrate system, namely the bond number, the nature of the bond, particle protrusions, and substrate nonuniformities. Experimentally observed motion patterns were compared to numerical Monte Carlo simulations, revealing a close correspondence between the observed motion patterns and properties of the molecular system. Particles bound via single tethers show distinct disc-, ring-, and bell-shaped motion patterns, where the ring- and bell-shaped patterns are caused by protrusions on the particle in the direct vicinity of the molecular attachment point. Double and triple tethered particles exhibit stripe-shaped and triangular-shaped motion patterns, respectively. The developed motion pattern analysis allows for discrimination between particles bound by different bond types, which opens the possibility to improve the limit of detection and the dynamic range of bioanalytical assays, with a projected increase of dynamic range by nearly 2 orders of magnitude. PMID:26913834

  12. Structure-Dynamics Relationships in Bursting Neuronal Networks Revealed Using a Prediction Framework

    PubMed Central

    Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Ruohonen, Keijo; Linne, Marja-Leena

    2013-01-01

    The question of how the structure of a neuronal network affects its functionality has gained a lot of attention in neuroscience. However, the vast majority of the studies on structure-dynamics relationships consider few types of network structures and assess limited numbers of structural measures. In this in silico study, we employ a wide diversity of network topologies and search among many possibilities the aspects of structure that have the greatest effect on the network excitability. The network activity is simulated using two point-neuron models, where the neurons are activated by noisy fluctuation of the membrane potential and their connections are described by chemical synapse models, and statistics on the number and quality of the emergent network bursts are collected for each network type. We apply a prediction framework to the obtained data in order to find out the most relevant aspects of network structure. In this framework, predictors that use different sets of graph-theoretic measures are trained to estimate the activity properties, such as burst count or burst length, of the networks. The performances of these predictors are compared with each other. We show that the best performance in prediction of activity properties for networks with sharp in-degree distribution is obtained when the prediction is based on clustering coefficient. By contrast, for networks with broad in-degree distribution, the maximum eigenvalue of the connectivity graph gives the most accurate prediction. The results shown for small () networks hold with few exceptions when different neuron models, different choices of neuron population and different average degrees are applied. We confirm our conclusions using larger () networks as well. Our findings reveal the relevance of different aspects of network structure from the viewpoint of network excitability, and our integrative method could serve as a general framework for structure-dynamics studies in biosciences. PMID:23935998

  13. Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces

    PubMed Central

    Louet, Maxime; Seifert, Christian; Hensen, Ulf; Gräter, Frauke

    2015-01-01

    The Catabolite Activator Protein (CAP) is a showcase example for entropic allostery. For full activation and DNA binding, the homodimeric protein requires the binding of two cyclic AMP (cAMP) molecules in an anti-cooperative manner, the source of which appears to be largely of entropic nature according to previous experimental studies. We here study at atomic detail the allosteric regulation of CAP with Molecular dynamics (MD) simulations. We recover the experimentally observed entropic penalty for the second cAMP binding event with our recently developed force covariance entropy estimator and reveal allosteric communication pathways with Force Distribution Analyses (FDA). Our observations show that CAP binding results in characteristic changes in the interaction pathways connecting the two cAMP allosteric binding sites with each other, as well as with the DNA binding domains. We identified crucial relays in the mostly symmetric allosteric activation network, and suggest point mutants to test this mechanism. Our study suggests inter-residue forces, as opposed to coordinates, as a highly sensitive measure for structural adaptations that, even though minute, can very effectively propagate allosteric signals. PMID:26244893

  14. Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces.

    PubMed

    Louet, Maxime; Seifert, Christian; Hensen, Ulf; Gräter, Frauke

    2015-08-01

    The Catabolite Activator Protein (CAP) is a showcase example for entropic allostery. For full activation and DNA binding, the homodimeric protein requires the binding of two cyclic AMP (cAMP) molecules in an anti-cooperative manner, the source of which appears to be largely of entropic nature according to previous experimental studies. We here study at atomic detail the allosteric regulation of CAP with Molecular dynamics (MD) simulations. We recover the experimentally observed entropic penalty for the second cAMP binding event with our recently developed force covariance entropy estimator and reveal allosteric communication pathways with Force Distribution Analyses (FDA). Our observations show that CAP binding results in characteristic changes in the interaction pathways connecting the two cAMP allosteric binding sites with each other, as well as with the DNA binding domains. We identified crucial relays in the mostly symmetric allosteric activation network, and suggest point mutants to test this mechanism. Our study suggests inter-residue forces, as opposed to coordinates, as a highly sensitive measure for structural adaptations that, even though minute, can very effectively propagate allosteric signals. PMID:26244893

  15. Gas dynamic simulations of galaxy formation

    NASA Technical Reports Server (NTRS)

    Evrard, August E.

    1993-01-01

    Results are presented from a simulation modeling the formation of a group of galaxies in a 'standard' cold, dark matter universe with delta = 1, h sub 0 = 50 km/(s(Mpc)), baryon fraction omega sub b = 0.1 and spectrum normalization sigma sub 8 = 0.6 (bias parameter b = 1.7). Initial conditions are generated within a periodic box with comoving length 16 Mpc in a manner constrained to produce a small cluster of total mass approximately 10 exp 14 solar mass. Two sets of 643 particles are used to model the dark matter and baryon fluids. Each gas particle represents 1.08 x 10 exp -8 solar mass, implying an L* galaxy is resolved by approximately 1000 particles. The system is evolved self-consistently in three dimensions using the combined N-body/hydrodynamic scheme P3MSPH up to a final redshift z = 1. Evolving to the present is prohibited by the fact that the mean density in the simulated volume is above critical and the entire volume would be going nonlinear beyond this point, We are currently analyzing another run with somewhat poorer mass resolution which was evolved to the present.

  16. Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding.

    PubMed

    Park, Jiho; Czapla, Luke; Amaro, Rommie E

    2013-08-26

    CYP19A1, also known as aromatase or estrogen synthetase, is the rate-limiting enzyme in the biosynthesis of estrogens from their corresponding androgens. Several clinically used breast cancer therapies target aromatase. In this work, explicitly solvated all-atom molecular dynamics simulations of aromatase with a model of the lipid bilayer and the transmembrane helix are performed. The dynamics of aromatase and the role of titration of an important amino acid residue involved in aromatization of androgens are investigated via two 250-ns long simulations. One simulation treats the protonated form of the catalytic aspartate 309, which appears more consistent with crystallographic data for the active site, while the simulation of the deprotonated form shows some notable conformational shifts. Ensemble-based computational solvent mapping experiments indicate possible novel druggable binding sites that could be utilized by next-generation inhibitors. In addition, the effects of protonation on the ligand positioning and channel dynamics are investigated using geometrical models that estimate the opening width of critical channels. Significant differences in channel dynamics between the protonated and deprotonated trajectories are exhibited, suggesting that the mechanism for substrate and product entry and the aromatization process may be coupled to a "locking" mechanism and channel opening. Our results may be particularly relevant in the design of novel drugs, which may be useful therapeutic treatments of cancers such as those of the breast and prostate. PMID:23927370

  17. Development of semiclassical molecular dynamics simulation method.

    PubMed

    Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi

    2016-04-28

    Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383

  18. Simulation of plume dynamics using particle graphics

    NASA Astrophysics Data System (ADS)

    Tourtellott, John; Coker, Charles F.; Crow, Dennis R.

    2000-07-01

    To enhance the fidelity of numerical flow field (plume) imagery in hardware-in-the-loop (HIL) systems, new methods using particle system graphics have been developed. To render infrared (IR) images that are consistent with the underlying physical phenomenology, techniques for particle placement, pixel rasterization and drawing were developed and implemented in computer software. The software was integrated into an existing HIL scene generator and used to demonstrate several new capabilities. Moving particle systems were used to depict the internal flow and turbulence common to plumes. Persistent particle systems were used to depict the trail of hot gas and particulates left behind typical plumes. The addition of plume dynamic behaviors such as these can potentially improve HIL systems and, as a result, improve the testing of seekers and other weapon systems.

  19. Dynamic Discharge Arc Driver. [computerized simulation

    NASA Technical Reports Server (NTRS)

    Dannenberg, R. E.; Slapnicar, P. I.

    1975-01-01

    A computer program using nonlinear RLC circuit analysis was developed to accurately model the electrical discharge performance of the Ames 1-MJ energy storage and arc-driver system. Solutions of circuit parameters are compared with experimental circuit data and related to shock speed measurements. Computer analysis led to the concept of a Dynamic Discharge Arc Driver (DDAD) capable of increasing the range of operation of shock-driven facilities. Utilization of mass addition of the driver gas offers a unique means of improving driver performance. Mass addition acts to increase the arc resistance, which results in better electrical circuit damping with more efficient Joule heating, producing stronger shock waves. Preliminary tests resulted in an increase in shock Mach number from 34 to 39 in air at an initial pressure of 2.5 torr.

  20. Expansion techniques for collisionless stellar dynamical simulations

    NASA Astrophysics Data System (ADS)

    Meiron, Yohai

    2016-02-01

    We present ETICS, a collisionless N-body code based on two kinds of series expansions of the Poisson equation, implemented for graphics processing units (GPUs). The code is publicly available and can be used as a standalone program or as a library (an AMUSE plugin is included). One of the two expansion methods available is the self-consistent field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other is the multipole expansion (MEX) method, which is a Taylor-like expansion of the Green's function. MEX, which has been advocated in the past, has not gained as much popularity as SCF. Both are particle-field methods and optimized for collisionless galactic dynamics, but while SCF is a ``pure'' expansion, MEX is an expansion in just the angular part; thus, MEX is capable of capturing radial structure easily, while SCF needs a large number of radial terms.

  1. Modeling and simulation of consumer response to dynamic pricing.

    SciTech Connect

    Valenzuela, J.; Thimmapuram, P.; Kim, J

    2012-08-01

    Assessing the impacts of dynamic-pricing under the smart grid concept is becoming extremely important for deciding its full deployment. In this paper, we develop a model that represents the response of consumers to dynamic pricing. In the model, consumers use forecasted day-ahead prices to shift daily energy consumption from hours when the price is expected to be high to hours when the price is expected to be low while maintaining the total energy consumption as unchanged. We integrate the consumer response model into the Electricity Market Complex Adaptive System (EMCAS). EMCAS is an agent-based model that simulates restructured electricity markets. We explore the impacts of dynamic-pricing on price spikes, peak demand, consumer energy bills, power supplier profits, and congestion costs. A simulation of an 11-node test network that includes eight generation companies and five aggregated consumers is performed for a period of 1 month. In addition, we simulate the Korean power system.

  2. Simulation of ceramics fracture due to high rate dynamic impact

    NASA Astrophysics Data System (ADS)

    Kazarinov, N. A.; Bratov, V. A.; Petrov, Y. V.

    2015-11-01

    In this paper dynamic fracture process due to high-speed impact of steel plunger into ceramic sample is simulated. The developed numerical model is based on finite element method and a concept of incubation time criterion, which is proven applicable in order to predict brittle fracture under high-rate deformation. Simulations were performed for ZrO2(Y2O3) ceramic plates. To characterize fracture process quantitatively fracture surface area parameter is introduced and controlled. This parameter gives the area of new surface created during dynamic fracture of a sample and is essentially connected to energetic peculiarities of fracture process. Multiple simulations with various parameters made it possible to explore dependencies of fracture area on plunger velocity and material properties. Energy required to create unit of fracture area at fracture initiation (dynamic analogue of Griffith surface energy) was evaluated and was found to be an order of magnitude higher as comparing to its static value.

  3. Molecular dynamics simulation of interfacial adhesion

    SciTech Connect

    Yarovsky, I.; Chaffee, A.L.

    1996-12-31

    Chromium salts are often used in the pretreatment stages of steel painting processes in order to improve adhesion at the metal oxide/primer interface. Although well established empirically, the chemical basis for the improved adhesion conferred by chromia is not well understood. A molecular level understanding of this behaviour should provide a foundation for the design of materials offering improved adhesion control. Molecular modelling of adhesion involves simulation and analysis of molecular behaviour at the interface between two interacting phases. The present study concerns behaviour at the boundary between the metal coated steel surface (with or without chromium pretreatment) and an organic primer based on a solid epoxide resin produced from bisphenol A and epichlorohydrin. An epoxy resin oligomer of molecular weight 3750 was used as the model for the primer.

  4. Analytical Dynamics and Nonrigid Spacecraft Simulation

    NASA Technical Reports Server (NTRS)

    Likins, P. W.

    1974-01-01

    Application to the simulation of idealized spacecraft are considered both for multiple-rigid-body models and for models consisting of combination of rigid bodies and elastic bodies, with the elastic bodies being defined either as continua, as finite-element systems, or as a collection of given modal data. Several specific examples are developed in detail by alternative methods of analytical mechanics, and results are compared to a Newton-Euler formulation. The following methods are developed from d'Alembert's principle in vector form: (1) Lagrange's form of d'Alembert's principle for independent generalized coordinates; (2) Lagrange's form of d'Alembert's principle for simply constrained systems; (3) Kane's quasi-coordinate formulation of D'Alembert's principle; (4) Lagrange's equations for independent generalized coordinates; (5) Lagrange's equations for simply constrained systems; (6) Lagrangian quasi-coordinate equations (or the Boltzmann-Hamel equations); (7) Hamilton's equations for simply constrained systems; and (8) Hamilton's equations for independent generalized coordinates.

  5. Molecular dynamics simulations of heme reorientational motions in myoglobin.

    PubMed Central

    Henry, E R

    1993-01-01

    Molecular dynamics simulations of 2-ns duration were performed on carbonmonoxymyoglobin and deoxymyoglobin in vacuo to study the reorientational dynamics of the heme group. The heme in both simulations undergoes reorientations of approximately 5 degrees amplitude on a subpicosecond time scale, which produce a rapid initial decay in the reorientational correlation function to about 0.99. The heme also experiences infrequent changes in average orientation of approximately 10 degrees amplitude, which lead to a larger slow decay of the reorientational correlation function over a period of hundreds of picoseconds. The simulations have not converged with respect to these infrequent transitions. However, an estimate of the order parameter for rapid internal motions of the heme from those orientations which are sampled by the simulations suggests that the subnanosecond orientational dynamics of the heme accounts for at least 30% of the unresolved initial anisotropy decay observed in the nanosecond time-resolved optical absorption experiments on myoglobin reported by Ansari et al. in a companion paper (Ansari, A., C.M. Jones, E.R. Henry, J. Hofrichter, and W.A. Eaton. 1992. Biophys. J. 64:852-868.). A more complete sampling of the accessible heme orientations would most likely increase this fraction further. The simulation of the liganded molecule also suggests that the conformational dynamics of the CO ligand may contribute significantly to discrepancies between the ligand conformation as probed by x-ray diffraction and by infrared-optical photoselection experiments. The protein back-bone explores multiple conformations during the simulations, with the largest structural changes appearing in the E and F helices, which are in contact with the heme. The variations in the heme orientation correlate with the conformational dynamics of the protein on a time scale of hundreds of picoseconds, suggesting that the heme orientation may provide a useful probe of dynamical processes

  6. Robotic Simulation of Flexible-Body Spacecraft Dynamics

    NASA Technical Reports Server (NTRS)

    Brannan, Justin C.; Carignan, Craig R.

    2016-01-01

    A robotic testbed has been developed to conduct hardware-in-the-loop simulations of a robotic servicer interacting with a client satellite on-orbit. By creating an analytical model of a satellite with flexible appendages, it is possible to simulate the system response to external force and torque inputs and compare the predicted system motion to a robot mass simulator outfitted with physical appendages. This validation effort includes multiple test cases that encompass the types of interaction forces a satellite might experience during a nominal on-orbit servicing mission and aims to show the simulation's ability to capture the physical system response. After incorporating the flexible-body dynamics into the robotic mass simulator at NASA Goddard Space Flight Center (GSFC), a hardware-in-the-loop simulation can be used to characterize the potential impact of structural flexibility on an end-to-end satellite servicing mission.

  7. Combined molecular dynamics-spin dynamics simulations of bcc iron

    SciTech Connect

    Perera, Meewanage Dilina N; Yin, Junqi; Landau, David P; Nicholson, Don M; Stocks, George Malcolm; Eisenbach, Markus; Brown, Greg

    2014-01-01

    Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.

  8. Dynamic Multiscale Quantum Mechanics/Electromagnetics Simulation Method.

    PubMed

    Meng, Lingyi; Yam, ChiYung; Koo, SiuKong; Chen, Quan; Wong, Ngai; Chen, GuanHua

    2012-04-10

    A newly developed hybrid quantum mechanics and electromagnetics (QM/EM) method [Yam et al. Phys. Chem. Chem. Phys.2011, 13, 14365] is generalized to simulate the real time dynamics. Instead of the electric and magnetic fields, the scalar and vector potentials are used to integrate Maxwell's equations in the time domain. The TDDFT-NEGF-EOM method [Zheng et al. Phys. Rev. B2007, 75, 195127] is employed to simulate the electronic dynamics in the quantum mechanical region. By allowing the penetration of a classical electromagnetic wave into the quantum mechanical region, the electromagnetic wave for the entire simulating region can be determined consistently by solving Maxwell's equations. The transient potential distributions and current density at the interface between quantum mechanical and classical regions are employed as the boundary conditions for the quantum mechanical and electromagnetic simulations, respectively. Charge distribution, current density, and potentials at different temporal steps and spatial scales are integrated seamlessly within a unified computational framework. PMID:26596737

  9. Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers

    SciTech Connect

    Vashishta, Priya; Kalia, Rajiv

    2005-02-24

    Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report.

  10. Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems

    PubMed Central

    Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus

    2014-01-01

    Background Molecular Dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. Scope of review In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Major Conclusions Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. General Significance Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. PMID:25450171

  11. Study of simulating dynamic polarization laser echo signal

    NASA Astrophysics Data System (ADS)

    Yang, Di; Liu, Qing; Zhan, Yong-hong; Zeng, Chang-e.

    2014-12-01

    In the test for the laser seeker in the hardware-in-loop simulation, acquiring the effect of polarization laser echo wave to optical stress polarization of the seeker and to the polarization guidance performance was not considered. A new method to generating the dynamic polarization laser echo signal was provided based on the scene model; furthermore, the method to adding the polarization characters to the energy scene was introduced. At last, the insufficient of the method to generating and simulating the dynamic polarization signal was analyzed.

  12. Simulation: A tool for steam plant dynamic analysis

    NASA Astrophysics Data System (ADS)

    Anneveld, H.

    Stringent requirements of combined cycles makes design and operation of process plants increasingly complex. The behavior of the complete controlled process is studied by way of simulation. By utilizing this method, process conditions can be optimized with reduced risk. This will lead to greater financial benefits. There is a large range of simulation programs which make it possible to study realistically the dynamic behavior of a wide range of complex process conditions and problematic interactions. The steam generation and distribution, the pressure limitation controls, and the dynamic behavior of a steam plant are discussed.

  13. Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.

  14. LINAC BEAM DYNAMICS SIMULATIONS WITH PY-ORBIT

    SciTech Connect

    Shishlo, Andrei P

    2012-01-01

    Linac dynamics simulation capabilities of the PyORBIT code are discussed. PyORBIT is an open source code and a further development of the original ORBIT code that was created and used for design, studies, and commissioning of the SNS ring. The PyORBIT code, like the original one, has a two-layer structure. C++ is used to perform time-consuming computations, and the program flow is controlled from a Python language shell. The flexible structure makes it possible to use PyORBIT also for linac dynamics simulations. A benchmark of PyORBIT with Parmila and the XAL Online model is presented.

  15. Turbulent Simulation of the Dynamics of the Magnetotail

    NASA Technical Reports Server (NTRS)

    Wu, Cheng-Chin

    2003-01-01

    In situ observations indicate that the dynamical processes in the geoplasma environment generally entail localized intermittent processes and anomalous global transports. It was suggested by T. Chang that instead of considering the turbulence as a mixture of interacting waves, such type of patchy intermittency could be more easily understood in terms of the development, interaction, merging, preferential acceleration and evolution of coherent magnetic structures. In this three-year project, we have used direct numerical MHD simulations to study some aspects of the MHD dynamics in Chang's model. Our large-scale numerical calculations and simulations have been supplemented by and coordinated with theoretical studies conducted by Chang and his colleagues.

  16. Numerical simulation of dynamic fracture and failure in solids

    SciTech Connect

    Chen, E.P.

    1994-05-01

    Numerical simulation of dynamic fracture and failure processes in solid continua using Lagrangian finite element techniques is the subject of discussion in this investigation. The specific configurations in this study include penetration of steel projectiles into aluminum blocks and concrete slabs. The failure mode in the aluminum block is excessive deformation while the concrete slab fails by hole growth, spallation, and scabbing. The transient dynamic finite element code LS-DYNA2D was used for the numerical analysis. The erosion capability in LS-DYNA2D was exercised to carry out the fracture and failure simulations. Calculated results were compared to the experimental data. Good correlations were obtained.

  17. Distributed Modeling Reveals the Ecohydrological Dynamics Linked with Woody Plant Encroachment in the Sonoran Desert

    NASA Astrophysics Data System (ADS)

    Pierini, N. A.; Vivoni, E. R.; Anderson, C.; Saripalli, S.; Robles-Morua, A.

    2012-12-01

    moisture and temperature distributions through comparisons of canopy and intercanopy sites. The field and remote sensing observations are then used in simulations using the TIN-based Real-time Integrated Basin Simulator (tRIBS) at high spatiotemporal resolutions over the two study years (2011-2012). Numerical experiments are designed to reveal the influence of the mesquite encroachment patterns on the watershed dynamics. Through the spatiotemporal analysis of model outputs, we identify how and when mesquite trees affect the spatial patterns of energy and water fluxes and their linkage to runoff production. As a result, the distributed model application provides a more complete understanding of the impact of woody encroachment on watershed-scale hydrologic patterns.

  18. Mars 520-d mission simulation reveals protracted crew hypokinesis and alterations of sleep duration and timing

    PubMed Central

    Basner, Mathias; Dinges, David F.; Mollicone, Daniel; Ecker, Adrian; Jones, Christopher W.; Hyder, Eric C.; Di Antonio, Adrian; Savelev, Igor; Kan, Kevin; Goel, Namni; Morukov, Boris V.; Sutton, Jeffrey P.

    2013-01-01

    The success of interplanetary human spaceflight will depend on many factors, including the behavioral activity levels, sleep, and circadian timing of crews exposed to prolonged microgravity and confinement. To address the effects of the latter, we used a high-fidelity ground simulation of a Mars mission to objectively track sleep–wake dynamics in a multinational crew of six during 520 d of confined isolation. Measurements included continuous recordings of wrist actigraphy and light exposure (4.396 million min) and weekly computer-based neurobehavioral assessments (n = 888) to identify changes in the crew's activity levels, sleep quantity and quality, sleep–wake periodicity, vigilance performance, and workload throughout the record-long 17 mo of mission confinement. Actigraphy revealed that crew sedentariness increased across the mission as evident in decreased waking movement (i.e., hypokinesis) and increased sleep and rest times. Light exposure decreased during the mission. The majority of crewmembers also experienced one or more disturbances of sleep quality, vigilance deficits, or altered sleep–wake periodicity and timing, suggesting inadequate circadian entrainment. The results point to the need to identify markers of differential vulnerability to hypokinesis and sleep–wake changes during the prolonged isolation of exploration spaceflight and the need to ensure maintenance of circadian entrainment, sleep quantity and quality, and optimal activity levels during exploration missions. Therefore, successful adaptation to such missions will require crew to transit in spacecraft and live in surface habitats that instantiate aspects of Earth's geophysical signals (appropriately timed light exposure, food intake, exercise) required for temporal organization and maintenance of human behavior. PMID:23297197

  19. Mars 520-d mission simulation reveals protracted crew hypokinesis and alterations of sleep duration and timing.

    PubMed

    Basner, Mathias; Dinges, David F; Mollicone, Daniel; Ecker, Adrian; Jones, Christopher W; Hyder, Eric C; Di Antonio, Adrian; Savelev, Igor; Kan, Kevin; Goel, Namni; Morukov, Boris V; Sutton, Jeffrey P

    2013-02-12

    The success of interplanetary human spaceflight will depend on many factors, including the behavioral activity levels, sleep, and circadian timing of crews exposed to prolonged microgravity and confinement. To address the effects of the latter, we used a high-fidelity ground simulation of a Mars mission to objectively track sleep-wake dynamics in a multinational crew of six during 520 d of confined isolation. Measurements included continuous recordings of wrist actigraphy and light exposure (4.396 million min) and weekly computer-based neurobehavioral assessments (n = 888) to identify changes in the crew's activity levels, sleep quantity and quality, sleep-wake periodicity, vigilance performance, and workload throughout the record-long 17 mo of mission confinement. Actigraphy revealed that crew sedentariness increased across the mission as evident in decreased waking movement (i.e., hypokinesis) and increased sleep and rest times. Light exposure decreased during the mission. The majority of crewmembers also experienced one or more disturbances of sleep quality, vigilance deficits, or altered sleep-wake periodicity and timing, suggesting inadequate circadian entrainment. The results point to the need to identify markers of differential vulnerability to hypokinesis and sleep-wake changes during the prolonged isolation of exploration spaceflight and the need to ensure maintenance of circadian entrainment, sleep quantity and quality, and optimal activity levels during exploration missions. Therefore, successful adaptation to such missions will require crew to transit in spacecraft and live in surface habitats that instantiate aspects of Earth's geophysical signals (appropriately timed light exposure, food intake, exercise) required for temporal organization and maintenance of human behavior. PMID:23297197

  20. Simulating aggregate dynamics in ocean biogeochemical models

    NASA Astrophysics Data System (ADS)

    Jackson, George A.; Burd, Adrian B.

    2015-04-01

    The dynamics of elements in the water column is complex, depending on multiple biological and physical processes operating at very different physical scales. Coagulation of particulate material is important for transforming particles and moving them in the water column. Mechanistic models of coagulation processes provide a means to predict these processes, help interpret observations, and provide insight into the processes occurring. However, most model applications have focused on describing simple marine systems and mechanisms. We argue that further model development, in close collaboration with field and experimental scientists, is required in order to extend the models to describe the large-scale elemental distributions and interactions being studied as part of GEOTRACES. Models that provide a fundamental description of trace element-particle interactions are required as are experimental tests of the mechanisms involved and the predictions arising from models. However, a comparison between simple and complicated models of aggregation and trace metal provides a means for understanding the implications of simplifying assumptions and providing guidance as to which simplifications are needed.

  1. Improving the performance of molecular dynamics simulations on parallel clusters.

    PubMed

    Borstnik, Urban; Hodoscek, Milan; Janezic, Dusanka

    2004-01-01

    In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to configure existing programs for MD simulations to efficiently handle collective communication on parallel clusters with processor interconnections of different speeds. PMID:15032512

  2. Dynamic simulation of coronal mass ejections

    NASA Technical Reports Server (NTRS)

    Steinolfson, R. S.; Wu, S. T.

    1980-01-01

    A model is developed for the formation and propagation through the lower corona of the loop-like coronal transients in which mass is ejected from near the solar surface to the outer corona. It is assumed that the initial state for the transient is a coronal streamer. The initial state for the streamer is a polytropic, hydrodynamic solution to the steady-state radial equation of motion coupled with a force-free dipole magnetic field. The numerical solution of the complete time-dependent equations then gradually approaches a stationary coronal streamer configuration. The streamer configuration becomes the initial state for the coronal transient. The streamer and transient simulations are performed completely independent of each other. The transient is created by a sudden increase in the pressure at the base of the closed-field region in the streamer configuration. Both coronal streamers and coronal transients are calculated for values of the plasma beta (the ratio of thermal to magnetic pressure) varying from 0.1 to 100.

  3. Error and efficiency of replica exchange molecular dynamics simulations

    PubMed Central

    Rosta, Edina; Hummer, Gerhard

    2009-01-01

    We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977

  4. Error and efficiency of replica exchange molecular dynamics simulations.

    PubMed

    Rosta, Edina; Hummer, Gerhard

    2009-10-28

    We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977

  5. Simulating spin dynamics in organic solids under heteronuclear decoupling.

    PubMed

    Frantsuzov, Ilya; Ernst, Matthias; Brown, Steven P; Hodgkinson, Paul

    2015-09-01

    Although considerable progress has been made in simulating the dynamics of multiple coupled nuclear spins, predicting the evolution of nuclear magnetisation in the presence of radio-frequency decoupling remains challenging. We use exact numerical simulations of the spin dynamics under simultaneous magic-angle spinning and RF decoupling to determine the extent to which numerical simulations can be used to predict the experimental performance of heteronuclear decoupling for the CW, TPPM and XiX sequences, using the methylene group of glycine as a model system. The signal decay times are shown to be strongly dependent on the largest spin order simulated. Unexpectedly large differences are observed between the dynamics with and without spin echoes. Qualitative trends are well reproduced by modestly sized spin system simulations, and the effects of finite spin-system size can, in favourable cases, be mitigated by extrapolation. Quantitative prediction of the behaviour in complex parameter spaces is found, however, to be very challenging, suggesting that there are significant limits to the role of numerical simulations in RF decoupling problems, even when specialist techniques, such as state-space restriction, are used. PMID:26073419

  6. Molecular dynamics simulations: Parameter evaluation, application and development

    NASA Astrophysics Data System (ADS)

    Zhou, Jin

    Molecular dynamics (MD) simulation is a theoretical technique for investigating the physical properties of a wide variety of molecules. This dissertation contains my studies on three important parts of the MD simulation: evaluation of parameters in empirical energy functions widely used in MD simulations, application of MD simulation on experimentally interested biological molecules and development of new methods for constraint dynamics simulations. All the work in this thesis made use of CHARMM as an MD simulation tool. The MD simulation uses empirical energy functions parameterized by a set of parameters. These parameters play an important role in the quality of the simulations. I evaluated nine parameter sets from Harvard University and Molecular Simulations, Inc. for protein simulations by the MD simulations of hydrated form of carboxy- myoglobin and interleukin-1/beta, which are rich in two typical protein structure motifs, helix and β sheet structures respectively. It is found that some sets are good at representing helical structure proteins while others are good at β sheet proteins. But all of them need improvement on representing motions at low temperature. Experimental evidence indicates that the 1A coiled-coil domains of the Intermediate Filament (IF) proteins consisting of coiled human keratins 1 and 10 (K1 and K10) are 'hot spots' for substitutional mutations. Some of these mutations are correlated to the human skin diseases-epidermolytic hyperkeratiosis (EH) and epidermolysis bullosa simplex (EBS). The MD simulation technique is used here for the first time to model and simulate these proteins to elucidate the molecular-level effects of these mutations. Lacking the experimental crystal structures, the initial structure of 1A domain of the wild type Intermediate Filament protein and its mutants were modeled from scratch to reproduce the well- known properties of the proteins of this kind followed by identical MD simulations. The important result is

  7. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity

    PubMed Central

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations. PMID:26075210

  8. Efficient dynamic simulation for multiple chain robotic mechanisms

    NASA Technical Reports Server (NTRS)

    Lilly, Kathryn W.; Orin, David E.

    1989-01-01

    An efficient O(mN) algorithm for dynamic simulation of simple closed-chain robotic mechanisms is presented, where m is the number of chains, and N is the number of degrees of freedom for each chain. It is based on computation of the operational space inertia matrix (6 x 6) for each chain as seen by the body, load, or object. Also, computation of the chain dynamics, when opened at one end, is required, and the most efficient algorithm is used for this purpose. Parallel implementation of the dynamics for each chain results in an O(N) + O(log sub 2 m+1) algorithm.

  9. Low-Velocity Aggregate Collisions Simulating Planetary Ring Dynamics

    NASA Astrophysics Data System (ADS)

    Dove, A.; Colwell, J. E.; Bradley, E. T.; Vamos, C.

    2012-12-01

    Proto-planetary and planetary ring system evolution is driven by collisions between small particles and aggregates that may be composed of dust, water ice, or a combination of materials. In these collisional systems, impacts between objects can occur at very low velocities, much less than 1 m/s. Low-velocity impacts can have competing effects: at the lowest velocities, collisions may play a critical role in growth into larger aggregates; at slightly higher velocities, collisions can cause break-up and release of material. In the Saturnian ring system, for instance, particles are excited to such "higher" velocities (10's of cm/s) in regions where density waves enhance particle concentrations. These conditions are present in the A ring, and it has been hypothesized that collisions have an additional effect of modifying the spectral properties of the ring particles, which are composed of a mix of ice and dust (Nicholson et al., 2008). This modification may occur when collisions cause ejection of material with different spectral characteristics, or by breaking particles apart to reveal more pristine interiors. We have designed and built an apparatus to simulate low-velocity collisions between aggregates in a laboratory vacuum environment. In our experiment, two aggregates are launched towards each other; the resulting impact velocities are controlled by the initial spring launch velocity, the masses of the aggregates, and timing of the collisions. Initially, we use lunar regolith simulant to create the aggregates; the simulant can be packed to different densities to control the mass and porosity of the impactors. We also create aggregates that are mixtures of materials, including icy components. A high-speed digital video camera is used to record the impacts to observe the behavior of both impactors and the resulting ejecta material. We observe over a range of velocities to identify the conditions under which aggregates shed only some material from the surface, or

  10. Molecular dynamics simulations of temperature-dependent structures and dynamics of ethylammonium nitrate protic ionic liquid: The role of hydrogen bond

    NASA Astrophysics Data System (ADS)

    Huang, Yiping; Zhou, Guobing; Li, Yunzhi; Yang, Zhen; Shi, Man; Wang, Xueping; Chen, Xiangshu; Zhang, Fei; Li, Wei

    2016-06-01

    Molecular dynamics simulations have been employed to systematically investigate the structure and dynamics properties, hydrogen bond (HB) dynamics of protic ionic liquid (IL) ethylammonium nitrate (EAN) in the temperature range between 300 K and 400 K. The simulation results demonstrate clearly that the temperature almost has little influence on the structures of EAN IL, whereas the translational and the rotational motions of both cations and anions become much faster at higher temperatures. Furthermore, both anions and cations are found to display an obvious sub-diffusive behavior. These changes can be attributed to the temperature-dependent HB strength between the cations and the anions, where the strength of HBs decreases significantly with increasing temperature. Accordingly, the ion-pair association/dissociation dynamics decreases considerably with increasing temperature. Therefore, our simulations reveal at a molecular level that the HBs interactions play an essential role in determining the dynamics properties of protic ILs.

  11. Dynamic risk simulation to assess risk along roads

    NASA Astrophysics Data System (ADS)

    Voumard, Jérémie; Caspar, Olivier; Derron, Marc-Henri; Jaboyedoff, Michel

    2013-04-01

    Risk generated through natural hazards on roads is usually calculated with an equation which integrates various parameters of hazard and traffic. These are static variables as hazard frequency and number of vehicles crossing the dangerous section. This traditional methodology cannot take into account the dynamic variations of traffic and interactions between vehicles such as speeds modifications due to the section sinuosity, slowdowns resulting saturated traffic or creation of vehicles columns in front of traffic lights. The influence of traffic dynamics on the risk estimation is not addressed with the standard methodologies. Here we show, with the help of a dynamic traffic simulator specially developed for this project, that the variations of traffic greatly influence the risk results. Several sections of an alpine road in Switzerland were analyzed with the method of dynamic risk and compared with the results of the conventional method of risk calculation. It was possible to demonstrate that risk significantly increases on sinuous sections with the decreasing of vehicles speed. It has been highlighted that well positioned traffic lights, outside the risk area, can prevent a risk increase during a construction site, while a column of vehicles located within the danger zone greatly increases the risk. These results demonstrate the importance to consider the traffic in a dynamic way to assess risk to the closest field reality. Thus, recommendations to reduce risk on the roads can be given using a dynamic traffic simulator, modeling interactions between vehicles. Eventually, dynamic risk assessment can also be integrated into existing methodologies that consider only static parameters.

  12. Validating clustering of molecular dynamics simulations using polymer models

    PubMed Central

    2011-01-01

    Background Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the

  13. Selection of Solar Simulator for Solar Dynamic Ground Test

    NASA Technical Reports Server (NTRS)

    Tolbert, Carol M.

    1994-01-01

    The 2 kWe Solar Dynamic (SD) Ground Test Demonstration (GTD) experiment will be conducted in 1995 at NASA Lewis Research Center (LeRC). This solar dynamic power system test will be conducted in a simulated space environment and will require an artificial sun. To address the solar simulator requirements for the GTD, Arnold Engineering Development Center (AEDC) was hired under contract to review and visit four existing solar simulator facilities. The four facilities included, AEDC's Mark 1 Chamber, NASA-JSC Chamber A, AEDC's 12V Chamber, and NASA-JPL Space Simulator Chamber. Two design concepts were considered following several months of evaluating existing solar simulator facilities throughout the United States. To satisfy system requirements for the SD GTD experiment the solar simulator needs to provide a uniform light flux to the SD concentrator, provide the light within a subtense angle of one degree, and provide an intensity of one solar constant (1.37 kW/sq m) at airmass zero. Most solar simulators are designed for supplying heat loads to spacecraft where a cone angle as large as 3 degrees is acceptable. It was also concluded that a solar simulator, such like these considered in the AEDC study, would require major facility modifications for NASA LeRC and result in significant impacts to the program. The advanced solar simulator concept developed by NASA LeRC will meet the system requirements for the SD GTD experiment Since SD GTD solar simulator requirements could not be addressed by existing simulator, an advanced concept was considered.

  14. A framework for stochastic simulations and visualization of biological electron-transfer dynamics

    NASA Astrophysics Data System (ADS)

    Nakano, C. Masato; Byun, Hye Suk; Ma, Heng; Wei, Tao; El-Naggar, Mohamed Y.

    2015-08-01

    Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr-Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr-Omc complex due to electron-electron interactions.

  15. Simulation of Pedestrian Dynamic Using a Vector Floor Field Model

    NASA Astrophysics Data System (ADS)

    Yang, Jun; Hou, Zhongsheng; Zhan, Minghui

    2013-04-01

    Simulation of complex scenarios and multi-direction pedestrian flow is a main challenge to microscopic model of pedestrian movement. It is an issue to simulate real pedestrian traffic with great fidelity while keeping its computational cost at an acceptable level. This paper reports on an improved floor field model called vector floor field model to simulate pedestrian flows in some basic scenarios. In this model, vectorization of static floor field and dynamic floor field are used to indicate preference directions and the pedestrian flow tendency, respectively. Pedestrian transition depends on both their preference directions and tendency. The simulations in some basic scenarios are conducted, quantitative comparison to the record of practical experiments and standard floor field model is given as well, and the results indicate the effectivity of this model. An adjusted static vector floor field is also proposed to simulate pedestrian flow in turning scenario. The vector floor field model is also sufficient to simulate some essential features in pedestrian dynamic, such as lane formation. This model can be widely used in the simulation of multi-direction pedestrian at turning, crossing and other junctions.

  16. Structural dynamics of supercooled water from quasielastic neutron scattering and molecular simulations.

    PubMed

    Qvist, Johan; Schober, Helmut; Halle, Bertil

    2011-04-14

    One of the outstanding challenges presented by liquid water is to understand how molecules can move on a picosecond time scale despite being incorporated in a three-dimensional network of relatively strong H-bonds. This challenge is exacerbated in the supercooled state, where the dramatic slowing down of structural dynamics is reminiscent of the, equally poorly understood, generic behavior of liquids near the glass transition temperature. By probing single-molecule dynamics on a wide range of time and length scales, quasielastic neutron scattering (QENS) can potentially reveal the mechanistic details of water's structural dynamics, but because of interpretational ambiguities this potential has not been fully realized. To resolve these issues, we present here an extensive set of high-quality QENS data from water in the range 253-293 K and a corresponding set of molecular dynamics (MD) simulations to facilitate and validate the interpretation. Using a model-free approach, we analyze the QENS data in terms of two motional components. Based on the dynamical clustering observed in MD trajectories, we identify these components with two distinct types of structural dynamics: picosecond local (L) structural fluctuations within dynamical basins and slower interbasin jumps (J). The Q-dependence of the dominant QENS component, associated with J dynamics, can be quantitatively rationalized with a continuous-time random walk (CTRW) model with an apparent jump length that depends on low-order moments of the jump length and waiting time distributions. Using a simple coarse-graining algorithm to quantitatively identify dynamical basins, we map the newtonian MD trajectory on a CTRW trajectory, from which the jump length and waiting time distributions are computed. The jump length distribution is gaussian and the rms jump length increases from 1.5 to 1.9 Å as the temperature increases from 253 to 293 K. The rms basin radius increases from 0.71 to 0.75 Å over the same range. The

  17. Dynamic materials response at multiscales: Experiments and simulations

    NASA Astrophysics Data System (ADS)

    Luo, Sheng-Nian

    One of the grand challenges in materials physics is dynamic responses to impulsive loading, including shock waves, radiation, and pulsed fields, due to their highly transient nature and extremely complex microstructure effects. Dynamic responses, such as plasticity, damage, cavitation, phase changes, and chemical reactions, are inherently multiscale and heavily dependent on microstructure. One has to resort to a suite of tools, including experiments, modeling and simulations, and theory. However, the gaps in spatial or temporal scales between experiments and simulations are still wide, while cross-scale theories are still in early development. To this end, we exploit large-scale molecular dynamics simulations, electron microscopy, and ultrafast synchrotron X-ray imaging and scattering, to probe materials response at length scales ranging from lattice to micron, and time scales, from picosecond to second. For examples, simultaneous, high-speed, X-ray imaging (mesoscale strain-field mapping) and diffraction measurements along with macroscopic measurements have been achieved. Based on classical nucleation theory and large-scale molecular dynamics simulations, we demonstrate the equivalence between length and time scales for nucleation events, which provides a framework to bridge different scales. Certainly, advancing multiscale science requires sustained, concerted, experimental, modeling and theoretical efforts. We have benefited from the colleagues at the Advanced Photon Source, and the Peac Institute of Multiscales Sciences.

  18. Simulating field-scale soil organic carbon dynamics using EPIC

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Simulation models integrate our understanding of soil organic C (SOC) dynamics and are useful tools for evaluating impacts of crop management on soil C sequestration, yet, they require local calibration. Our objectives were to calibrate the Environmental Policy Integrated Climate (EPIC) model, and e...

  19. The 3-axis Dynamic Motion Simulator (DMS) system

    NASA Technical Reports Server (NTRS)

    1975-01-01

    A three-axis dynamic motion simulator (DMS) consisting of a test table with three degrees of freedom and an electronics control system was designed, constructed, delivered, and tested. Documentation, as required in the Data Requirements List (DRL), was also provided.

  20. Diffusion of Particle in Hyaluronan Solution, a Brownian Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Takasu, Masako; Tomita, Jungo

    2004-04-01

    Diffusion of a particle in hyaluronan solution is investigated using Brownian dynamics simulation. The slowing down of diffusion is observed, in accordance with the experimental results. The temperature dependence of the diffusion is calculated, and a turnover is obtained when the temperature is increased.

  1. Simulating Poverty and Inequality Dynamics in Developing Countries

    ERIC Educational Resources Information Center

    Ansoms, An; Geenen, Sara

    2012-01-01

    This article considers how the simulation game of DEVELOPMENT MONOPOLY provides insight into poverty and inequality dynamics in a development context. It first discusses how the game is rooted in theoretical and conceptual frameworks on poverty and inequality. Subsequently, it reflects on selected playing experiences, with special focus on the…

  2. Generating dynamic simulations of movement using computed muscle control.

    PubMed

    Thelen, Darryl G; Anderson, Frank C; Delp, Scott L

    2003-03-01

    Computation of muscle excitation patterns that produce coordinated movements of muscle-actuated dynamic models is an important and challenging problem. Using dynamic optimization to compute excitation patterns comes at a large computational cost, which has limited the use of muscle-actuated simulations. This paper introduces a new algorithm, which we call computed muscle control, that uses static optimization along with feedforward and feedback controls to drive the kinematic trajectory of a musculoskeletal model toward a set of desired kinematics. We illustrate the algorithm by computing a set of muscle excitations that drive a 30-muscle, 3-degree-of-freedom model of pedaling to track measured pedaling kinematics and forces. Only 10 min of computer time were required to compute muscle excitations that reproduced the measured pedaling dynamics, which is over two orders of magnitude faster than conventional dynamic optimization techniques. Simulated kinematics were within 1 degrees of experimental values, simulated pedal forces were within one standard deviation of measured pedal forces for nearly all of the crank cycle, and computed muscle excitations were similar in timing to measured electromyographic patterns. The speed and accuracy of this new algorithm improves the feasibility of using detailed musculoskeletal models to simulate and analyze movement. PMID:12594980

  3. Modeling and Dynamic Simulation of a Large Scale Helium Refrigerator

    NASA Astrophysics Data System (ADS)

    Lv, C.; Qiu, T. N.; Wu, J. H.; Xie, X. J.; Li, Q.

    In order to simulate the transient behaviors of a newly developed 2 kW helium refrigerator, a numerical model of the critical equipment including a screw compressor with variable-frequency drive, plate-fin heat exchangers, a turbine expander, and pneumatic valves wasdeveloped. In the simulation,the calculation of the helium thermodynamic properties arebased on 32-parameter modified Benedict-Webb-Rubin (MBWR) state equation.The start-up process of the warm compressor station with gas management subsystem, and the cool-down process of cold box in an actual operation, were dynamically simulated. The developed model was verified by comparing the simulated results with the experimental data.Besides, system responses of increasing heat load were simulated. This model can also be used to design and optimize other large scale helium refrigerators.

  4. Evaluating the Accuracy of Hessian Approximations for Direct Dynamics Simulations.

    PubMed

    Zhuang, Yu; Siebert, Matthew R; Hase, William L; Kay, Kenneth G; Ceotto, Michele

    2013-01-01

    Direct dynamics simulations are a very useful and general approach for studying the atomistic properties of complex chemical systems, since an electronic structure theory representation of a system's potential energy surface is possible without the need for fitting an analytic potential energy function. In this paper, recently introduced compact finite difference (CFD) schemes for approximating the Hessian [J. Chem. Phys.2010, 133, 074101] are tested by employing the monodromy matrix equations of motion. Several systems, including carbon dioxide and benzene, are simulated, using both analytic potential energy surfaces and on-the-fly direct dynamics. The results show, depending on the molecular system, that electronic structure theory Hessian direct dynamics can be accelerated up to 2 orders of magnitude. The CFD approximation is found to be robust enough to deal with chaotic motion, concomitant with floppy and stiff mode dynamics, Fermi resonances, and other kinds of molecular couplings. Finally, the CFD approximations allow parametrical tuning of different CFD parameters to attain the best possible accuracy for different molecular systems. Thus, a direct dynamics simulation requiring the Hessian at every integration step may be replaced with an approximate Hessian updating by tuning the appropriate accuracy. PMID:26589009

  5. Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

    SciTech Connect

    Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter

    2015-12-07

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

  6. Large Dynamic Range Simulations of Galaxies Hosting Supermassive Black Holes

    NASA Astrophysics Data System (ADS)

    Levine, Robyn

    2011-08-01

    The co-evolution of supermassive black holes (SMBHs) and their host galaxies is a rich problem, spanning a large-dynamic range and depending on many physical processes. Simulating the transport of gas and angular momentum from super-galactic scales all the way down to the outer edge of the black hole's accretion disk requires sophisticated numerical techniques with extensive treatment of baryonic physics. We use a hydrodynamic adaptive mesh refinement simulation to follow the growth and evolution of a typical disk galaxy hosting an SMBH, in a cosmological context (covering a dynamical range of 10 million!). We have adopted a piecemeal approach, focusing our attention on the gas dynamics in the central few hundred parsecs of the simulated galaxy (with boundary conditions provided by the larger cosmological simulation), and beginning with a simplified picture (no mergers or feedback). In this scenario, we find that the circumnuclear disk remains marginally stable against catastrophic fragmentation, allowing stochastic fueling of gas into the vicinity of the SMBH. I will discuss the successes and the limitations of these simulations, and their future direction.

  7. Dynamics simulation and controller interfacing for legged robots

    SciTech Connect

    Reichler, J.A.; Delcomyn, F.

    2000-01-01

    Dynamics simulation can play a critical role in the engineering of robotic control code, and there exist a variety of strategies both for building physical models and for interacting with these models. This paper presents an approach to dynamics simulation and controller interfacing for legged robots, and contrasts it to existing approaches. The authors describe dynamics algorithms and contact-resolution strategies for multibody articulated mobile robots based on the decoupled tree-structure approach, and present a novel scripting language that provides a unified framework for control-code interfacing, user-interface design, and data analysis. Special emphasis is placed on facilitating the rapid integration of control algorithms written in a standard object-oriented language (C++), the production of modular, distributed, reusable controllers, and the use of parameterized signal-transmission properties such as delay, sampling rate, and noise.

  8. Quantum Dynamics Simulations for Modeling Experimental Pump-Probe Measurements

    NASA Astrophysics Data System (ADS)

    Pearson, Brett; Nayyar, Sahil; Liss, Kyle; Weinacht, Thomas

    2016-05-01

    Time-resolved studies of quantum dynamics have benefited greatly from developments in ultrafast table-top and free electron lasers. Advances in computer software and hardware have lowered the barrier for performing calculations such that relatively simple simulations allow for direct comparison with experimental results. We describe here a set of quantum dynamics calculations in low-dimensional molecular systems. The calculations incorporate coupled electronic-nuclear dynamics, including two interactions with an applied field and nuclear wave packet propagation. The simulations were written and carried out by undergraduates as part of a senior research project, with the specific goal of allowing for detailed interpretation of experimental pump-probe data (in additional to the pedagogical value).

  9. Nonadiabatic dynamics of photoinduced proton-coupled electron transfer: comparison of explicit and implicit solvent simulations.

    PubMed

    Auer, Benjamin; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2012-07-01

    Theoretical approaches for simulating the ultrafast dynamics of photoinduced proton-coupled electron transfer (PCET) reactions in solution are developed and applied to a series of model systems. These processes are simulated by propagating nonadiabatic surface hopping trajectories on electron-proton vibronic surfaces that depend on the solute and solvent nuclear coordinates. The PCET system is represented by a four-state empirical valence bond model, and the solvent is treated either as explicit solvent molecules or as a dielectric continuum, in which case the solvent dynamics is described in terms of two collective solvent coordinates corresponding to the energy gaps associated with electron and proton transfer. The explicit solvent simulations reveal two distinct solvent relaxation time scales, where the faster time scale relaxation corresponds to librational motions of solvent molecules in the first solvation shell, and the slower time scale relaxation corresponds to the bulk solvent dielectric response. The charge transfer dynamics is strongly coupled to both the fast and slow time scale solvent dynamics. The dynamical multistate continuum theory is extended to include the effects of two solvent relaxation time scales, and the resulting coupled generalized Langevin equations depend on parameters that can be extracted from equilibrium molecular dynamics simulations. The implicit and explicit solvent approaches lead to qualitatively similar charge transfer and solvent dynamics for model PCET systems, suggesting that the implicit solvent treatment captures the essential elements of the nonequilibrium solvent dynamics for many systems. A combination of implicit and explicit solvent approaches will enable the investigation of photoinduced PCET processes in a variety of condensed phase systems. PMID:22651684

  10. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    SciTech Connect

    Wei Gu; Garcia, A.E.; Schoenborn, B.P.

    1994-12-31

    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

  11. Ultrascale simulations of non-smooth granular dynamics

    NASA Astrophysics Data System (ADS)

    Preclik, Tobias; Rüde, Ulrich

    2015-06-01

    This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their micro-dynamics and thus to extend the time and length scales that can be simulated. The global multi-contact problem is solved using a non-linear block Gauss-Seidel method that is conforming to the subdomain structure. The parallel algorithms employ a sophisticated protocol between processors that delegate algorithmic tasks such as contact treatment and position integration uniquely and robustly to the processors. Communication overhead is minimized through aggressive message aggregation, leading to excellent strong and weak scaling. The robustness and scalability is assessed on three clusters including two peta-scale supercomputers with up to 458,752 processor cores. The simulations can reach unprecedented resolution of up to ten billion () non-spherical particles and contacts.

  12. Simulation of the dynamic inefficiency of the CMS pixel detector

    NASA Astrophysics Data System (ADS)

    Bartók, M.

    2015-05-01

    The Pixel Detector is the innermost part of the CMS Tracker. It therefore has to prevail in the harshest environment in terms of particle fluence and radiation. There are several mechanisms that may decrease the efficiency of the detector. These are mainly caused by data acquisition (DAQ) problems and/or Single Event Upsets (SEU). Any remaining efficiency loss is referred to as the dynamic inefficiency. It is caused by various mechanisms inside the Readout Chip (ROC) and depends strongly on the data occupancy. In the 2012 data, at high values of instantaneous luminosity the inefficiency reached 2% (in the region closest to the interaction point) which is not negligible. In the 2015 run higher instantaneous luminosity is expected, which will result in lower efficiencies; therefore this effect needs to be understood and simulated. A data-driven method has been developed to simulate dynamic inefficiency, which has been shown to successfully simulate the effects.

  13. ParaDiS-FEM dislocation dynamics simulation code primer

    SciTech Connect

    Tang, M; Hommes, G; Aubry, S; Arsenlis, A

    2011-09-27

    The ParaDiS code is developed to study bulk systems with periodic boundary conditions. When we try to perform discrete dislocation dynamics simulations for finite systems such as thin films or cylinders, the ParaDiS code must be extended. First, dislocations need to be contained inside the finite simulation box; Second, dislocations inside the finite box experience image stresses due to the free surfaces. We have developed in-house FEM subroutines to couple with the ParaDiS code to deal with free surface related issues in the dislocation dynamics simulations. This primer explains how the coupled code was developed, the main changes from the ParaDiS code, and the functions of the new FEM subroutines.

  14. Molecular dynamics simulations of a lithium/sodium carbonate mixture.

    PubMed

    Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo

    2016-03-01

    The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates. PMID:26897519

  15. Molecular dynamics simulations of detonation on the roadrunner supercomputer

    NASA Astrophysics Data System (ADS)

    Mniszewski, Susan; Cawkwell, Marc; Germann, Timothy C.

    2012-03-01

    The temporal and spatial scales intrinsic to a real detonating explosive are extremely difficult to capture using molecular dynamics (MD) simulations. Nevertheless, MD remains very attractive since it allows for the resolution of dynamic phenomena at the atomic scale. Large-scale reactive MD simulations in three dimensions require immense computational resources even when simple reactive force fields are employed. We focus on the REBO force field for 'AB' since it has been shown to support a detonation while being simple, analytic, and short-ranged. The transition from two-to three- dimensional simulations is being facilitated by the port of the REBO force field in the parallel MD code SPaSM to LANL's petaflop supercomputer 'Roadrunner'. We provide a detailed discussion of the challenges associated with computing interatomic forces on a hybrid Opteron/Cell BE computational architecture.

  16. Software life cycle dynamic simulation model: The organizational performance submodel

    NASA Technical Reports Server (NTRS)

    Tausworthe, Robert C.

    1985-01-01

    The submodel structure of a software life cycle dynamic simulation model is described. The software process is divided into seven phases, each with product, staff, and funding flows. The model is subdivided into an organizational response submodel, a management submodel, a management influence interface, and a model analyst interface. The concentration here is on the organizational response model, which simulates the performance characteristics of a software development subject to external and internal influences. These influences emanate from two sources: the model analyst interface, which configures the model to simulate the response of an implementing organization subject to its own internal influences, and the management submodel that exerts external dynamic control over the production process. A complete characterization is given of the organizational response submodel in the form of parameterized differential equations governing product, staffing, and funding levels. The parameter values and functions are allocated to the two interfaces.

  17. Quantum simulation of the dynamical Casimir effect with trapped ions

    NASA Astrophysics Data System (ADS)

    Trautmann, N.; Hauke, P.

    2016-04-01

    Quantum vacuum fluctuations are a direct manifestation of Heisenberg’s uncertainty principle. The dynamical Casimir effect (DCE) allows for the observation of these vacuum fluctuations by turning them into real, observable photons. However, the observation of this effect in a cavity QED experiment would require the rapid variation of the length of a cavity with relativistic velocities, a daunting challenge. Here, we propose a quantum simulation of the DCE using an ion chain confined in a segmented ion trap. We derive a discrete model that enables us to map the dynamics of the multimode radiation field inside a variable-length cavity to radial phonons of the ion crystal. We perform a numerical study comparing the ion-chain quantum simulation under realistic experimental parameters to an ideal Fabry–Perot cavity, demonstrating the viability of the mapping. The proposed quantum simulator, therefore, allows for probing the photon (respectively phonon) production caused by the DCE on the single photon level.

  18. Molecular Dynamics Simulation of Electrophoresis of a Telehelic Polymer Chain

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Aniket

    2002-08-01

    We report the conformational and the dynamical properties of an end-labeled polymer chain embedded in a porous medium made of randomly distributed immobile spherical obstacles using a stochastic Molecular Dynamic(MD) simulation method for several obstacle densities and for various bias strenghts applied only to one end of the chain. First, various properties of the chain are studied when the external bias is set to zero. We then extend the stochastic MD simulation to study the electrophresis of a polymer chain driven by (i) a steady and (ii) a time dependent electric field. These studies are relevant for various time dependent gel electrophoresis methods widely used to separate DNA molecules. The qualitative features are compared with experiments, analytic theories, and recent Monte Carlo Simulation results.

  19. Computer simulations of cyclic and acyclic cholinergic agonists: conformational search and molecular dynamics simulations.

    PubMed Central

    McGroddy, K A; Brady, J W; Oswald, R E

    1994-01-01

    Molecular dynamics simulations have been performed on aqueous solutions of two chemically similar nicotinic cholinergic agonists in order to compare their structural and dynamical differences. The cyclic 1,1-dimethyl-4-acetylpiperazinium iodide (HPIP) molecule was previously shown to be a strong agonist for nicotinic acetylcholine receptors (McGroddy et al., 1993), while the acyclic N,N,N,N'-tetramethyl-N'-acetylethylenediamine iodide (HTED) derivative is much less potent. These differences were expected to arise from differences in the solution structures and internal dynamics of the two molecules. HPIP was originally thought to be relatively rigid; however, molecular dynamics simulations suggest that the acetyl portion of the molecule undergoes significant ring dynamics on a psec timescale. The less constrained HTED molecule is relatively rigid, with only one transition observed about any of the major dihedrals in four 100 psec simulations, each started from a different conformation. The average structures obtained from the simulations are very similar to the starting minimized structure in each case, except for the HTED simulation where a single rotation about the N-C-C-N(+) backbone occurred. In each case, HTED had three to five more water molecules in its primary solvation shell than HPIP, indicating that differences in the energetics of desolvation before binding may partially explain the increased potency of HPIP as compared to HTED. Images FIGURE 1 FIGURE 2 PMID:8161685

  20. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

    PubMed

    Janowski, Pawel A; Liu, Chunmei; Deckman, Jason; Case, David A

    2016-01-01

    Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics. PMID:26013419

  1. A novel dynamics combination model reveals the hidden information of community structure

    NASA Astrophysics Data System (ADS)

    Li, Hui-Jia; Li, Huiying; Jia, Chuanliang

    2015-09-01

    The analysis of the dynamic details of community structure is an important question for scientists from many fields. In this paper, we propose a novel Markov-Potts framework to uncover the optimal community structures and their stabilities across multiple timescales. Specifically, we model the Potts dynamics to detect community structure by a Markov process, which has a clear mathematical explanation. Then the local uniform behavior of spin values revealed by our model is shown that can naturally reveal the stability of hierarchical community structure across multiple timescales. To prove the validity, phase transition of stochastic dynamic system is used to indicate that the stability of community structure we proposed is able to describe the significance of community structure based on eigengap theory. Finally, we test our framework on some example networks and find it does not have resolute limitation problem at all. Results have shown the model we proposed is able to uncover hierarchical structure in different scales effectively and efficiently.

  2. Dynamic simulations for the Terrestrial Planet Finder interferometer

    NASA Astrophysics Data System (ADS)

    Li, Ying-Yong; Hamlin, Louise A.; Wirz, Richie; Adams, Douglas; Moore, Greg; Coppolino, Robert; Peng, Chia-Yen; Levine, Marie

    2005-08-01

    The Terrestrial Planet Finder Interferometer (TPF-I) mission requires a set of formation-flying collector telescopes that direct the incoming light to a beam combiner where the beams are combined and detected to identify habitable planets. A baseline TPF collector design, using a primary mirror of 4.2 meters in diameter, is used here to conduct a dynamic study. The objective is to investigate the effects of dynamic response of the spacecraft on the system optical performance at the presence of disturbances that arise from the reaction wheel assembly and thruster loading, respectively. Frequency responses where the frequency is associated with the flywheel speed are presented in the paper. The results focus on the surface oscillation of the primary mirror and the point at which the secondary mirror is located. Transient response simulations under the baseline four thruster-assembly configuration were conducted using various duty cycles and thrust levels determined by the TPF formation rotation requirements. This paper will also describe an investigation conducted using new IMOS (Integrated Modeling of Optical Systems), which is an open, multi-disciplinary, and Matlab-based dynamic/optical system simulation code. A pre-processor that is able to generate the sub-structure modal models required by ISYSD (Integrated System Dynamics) was developed in new IMOS. ISYSD is used to develop a high-fidelity system dynamic model by integrating the sub-structure modal models. Finally, the paper will summarize current and future work in order to meet the TPF dynamic requirements.

  3. Dynamic risk simulation to assess risk along roads

    NASA Astrophysics Data System (ADS)

    Voumard, J.; Caspar, O.; Derron, M.-H.; Jaboyedoff, M.

    2013-04-01

    Risk generated by natural hazards on roads is usually calculated with equations integrating various parameters related to hazard and traffic. These are static variables, like a rockfall hazard estimation for a road section or the average number of vehicles crossing this section every day. This methodology cannot take into account dynamic variations of traffic and interactions between vehicles such as speed modifications due to the sinuosity, slowdowns resulting of saturated traffic or vehicles columns forming in front of traffic lights. The influence of traffic dynamics on the risk estimation is not assessed with standard methodologies. Here we show, by mean of a dynamic traffic simulator, that the traffic variations may greatly influence the risk estimation over time. The risk is analysed on several alpine road sections in Switzerland using a dynamic vehicles approach and compared with the results of the static methodology. It demonstrates that risk significantly increases on sinuous sections because of the decreasing of vehicles speed. A more realistic risk can be obtained from a dynamic approach especially on mountain roads. A dynamic traffic simulator, modelling interactions between vehicles is a helpful tool to support decision making to reduce risk on roads.

  4. Simulation of screw dislocation motion in iron by molecular dynamics simulations.

    PubMed

    Domain, Christophe; Monnet, Ghiath

    2005-11-18

    Molecular dynamics (MD) simulations are used to investigate the response of a/2<111> screw dislocation in iron submitted to pure shear strain. The dislocation glides and remains in a (110) plane; the motion occurs exclusively through the nucleation and propagation of double kinks. The critical stress is calculated as a function of the temperature. A new method is developed and used to determine the activation energy of the double kink mechanism from MD simulations. It is shown that the differences between experimental and simulation conditions lead to a significant difference in activation energy. These differences are explained, and the method developed provides the link between MD and mesoscopic simulations. PMID:16384158

  5. Slow-Onset Inhibition of Mycobacterium tuberculosis InhA: Revealing Molecular Determinants of Residence Time by MD Simulations

    PubMed Central

    Merget, Benjamin; Sotriffer, Christoph A.

    2015-01-01

    An important kinetic parameter for drug efficacy is the residence time of a compound at a drug target, which is related to the dissociation rate constant koff. For the essential antimycobacterial target InhA, this parameter is most likely governed by the ordering of the flexible substrate binding loop (SBL). Whereas the diphenyl ether inhibitors 6PP and triclosan (TCL) do not show loop ordering and thus, no slow-binding inhibition and high koff values, the slightly modified PT70 leads to an ordered loop and a residence time of 24 minutes. To assess the structural differences of the complexes from a dynamic point of view, molecular dynamics (MD) simulations with a total sampling time of 3.0 µs were performed for three ligand-bound and two ligand-free (perturbed) InhA systems. The individual simulations show comparable conformational features with respect to both the binding pocket and the SBL, allowing to define five recurring conformational families. Based on their different occurrence frequencies in the simulated systems, the conformational preferences could be linked to structural differences of the respective ligands to reveal important determinants of residence time. The most abundant conformation besides the stable EI* state is characterized by a shift of Ile202 and Val203 toward the hydrophobic pocket of InhA. The analyses revealed potential directions for avoiding this conformational change and, thus, hindering rapid dissociation: (1) an anchor group in 2'-position of the B-ring for scaffold stabilization, (2) proper occupation of the hydrophobic pocket, and (3) the introduction of a barricade substituent in 5'-position of the diphenyl ether B-ring. PMID:25996598

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

    SciTech Connect

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

    2011-12-31

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

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

    SciTech Connect

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

    2010-11-01

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

  8. Simulating Field-Scale Soil Organic Carbon Dynamics Using EPIC

    SciTech Connect

    Causarano, Hector J.; Shaw, Joey N.; Franzluebbers, A. J.; reeves, D. W.; Raper, Randy L.; Balkcom, Kipling S.; Norfleet, M. L.; Izaurralde, R Cesar

    2007-07-01

    Simulation models integrate our knowledge of soil organic C (SOC) dynamics and are useful tools for evaluating impacts of crop management on soil C sequestration; yet, they require local calibration. Our objectives were to calibrate the Environmental Policy Integrated Climate (EPIC) model, and evaluate its performance for simulating SOC fractions as affected by soil landscape and management. An automated parameter optimization procedure was used to calibrate the model for a site-specific experiment in the Coastal Plain of central Alabama. The ability of EPIC to predict corn (Zea mays L.) and cotton (Gossypium hirsutum L.) yields and SOC dynamics on different soil landscape positions (summit, sideslope and drainageway) during the initial period of conservation tillage adoption (5 years) was evaluated using regression and mean squared deviations. Simulated yield explained 88% of measured yield variation, with greatest disagreement on the sideslope position and highest agreement in the drainageway. Simulations explained approximately 1, 34 and 40% of the total variation in microbial biomass C (MBC), particulate organic C (POC) and total organic C (TOC), respectively. Lowest errors on TOC simulations (0-20 cm) were found on the sideslope and summit. We conclude that the automated parameterization was generally successful, although further work is needed to refine the MBC and POC fractions, and to improve EPIC predictions of SOC dynamics with depth. Overall, EPIC was sensitive to spatial differences in C fractions that resulted from differing soil landscape positions. The model needs additional refinement for accurate simulations of field-scale SOC dynamics affected by short-term management decisions.

  9. Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

    PubMed Central

    Doshi, Urmi; Holliday, Michael J.; Eisenmesser, Elan Z.; Hamelberg, Donald

    2016-01-01

    Detailed understanding of how conformational dynamics orchestrates function in allosteric regulation of recognition and catalysis remains ambiguous. Here, we simulate CypA using multiple-microsecond-long atomistic molecular dynamics in explicit solvent and carry out NMR experiments. We analyze a large amount of time-dependent multidimensional data with a coarse-grained approach and map key dynamical features within individual macrostates by defining dynamics in terms of residue–residue contacts. The effects of substrate binding are observed to be largely sensed at a location over 15 Å from the active site, implying its importance in allostery. Using NMR experiments, we confirm that a dynamic cluster of residues in this distal region is directly coupled to the active site. Furthermore, the dynamical network of interresidue contacts is found to be coupled and temporally dispersed, ranging over 4 to 5 orders of magnitude. Finally, using network centrality measures we demonstrate the changes in the communication network, connectivity, and influence of CypA residues upon substrate binding, mutation, and during catalysis. We identify key residues that potentially act as a bottleneck in the communication flow through the distinct regions in CypA and, therefore, as targets for future mutational studies. Mapping these dynamical features and the coupling of dynamics to function has crucial ramifications in understanding allosteric regulation in enzymes and proteins, in general. PMID:27071107

  10. Deformation behavior of bulk and nanostructured metallic glasses studied via molecular dynamics simulations

    SciTech Connect

    Sopu, D.; Ritter, Y.; Albe, K.; Gleiter, H.

    2011-03-01

    In this study, we characterize the mechanical properties of Cu{sub 64}Zr{sub 36} nanoglasses under tensile load by means of large-scale molecular dynamics simulations and compare the deformation behavior to the case of a homogeneous bulk glass. The simulations reveal that interfaces act as precursors for the formation of multiple shear bands. In contrast, a bulk metallic glass under uniaxial tension shows inhomogeneous plastic flow confined in one dominant shear band. The results suggest that controlling the microstructure of a nanoglass can pave the way for tuning the mechanical properties of glassy materials.

  11. Effects of Antimicrobial Peptide Revealed by Simulations: Translocation, Pore Formation, Membrane Corrugation and Euler Buckling

    PubMed Central

    Chen, Licui; Jia, Nana; Gao, Lianghui; Fang, Weihai; Golubovic, Leonardo

    2013-01-01

    We explore the effects of the peripheral and transmembrane antimicrobial peptides on the lipid bilayer membrane by using the coarse grained Dissipative Particle Dynamics simulations. We study peptide/lipid membrane complexes by considering peptides with various structure, hydrophobicity and peptide/lipid interaction strength. The role of lipid/water interaction is also discussed. We discuss a rich variety of membrane morphological changes induced by peptides, such as pore formation, membrane corrugation and Euler buckling. PMID:23579956

  12. The molecular dynamics simulation of ion-induced ripple growth

    SciTech Connect

    Suele, P.; Heinig, K.-H.

    2009-11-28

    The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength ({lambda}) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths ({lambda}<35 nm) the adatom yield drops hence no surface diffusion takes place which is sufficient for ripple growth. The MD simulations predict that the growth of ripples with {lambda}>35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in {lambda} long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for {lambda}>35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.

  13. Dynamic Simulation of a Wave Rotor Topped Turboshaft Engine

    NASA Technical Reports Server (NTRS)

    Greendyke, R. B.; Paxson, D. E.; Schobeiri, M. T.

    1997-01-01

    The dynamic behavior of a wave rotor topped turboshaft engine is examined using a numerical simulation. The simulation utilizes an explicit, one-dimensional, multi-passage, CFD based wave rotor code in combination with an implicit, one-dimensional, component level dynamic engine simulation code. Transient responses to rapid fuel flow rate changes and compressor inlet pressure changes are simulated and compared with those of a similarly sized, untopped, turboshaft engine. Results indicate that the wave rotor topped engine responds in a stable, and rapid manner. Furthermore, during certain transient operations, the wave rotor actually tends to enhance engine stability. In particular, there is no tendency toward surge in the compressor of the wave rotor topped engine during rapid acceleration. In fact, the compressor actually moves slightly away from the surge line during this transient. This behavior is precisely the opposite to that of an untopped engine. The simulation is described. Issues associated with integrating CFD and component level codes are discussed. Results from several transient simulations are presented and discussed.

  14. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    PubMed Central

    2016-01-01

    Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl−) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. PMID:27118886

  15. Synthesis of recurrent neural networks for dynamical system simulation.

    PubMed

    Trischler, Adam P; D'Eleuterio, Gabriele M T

    2016-08-01

    We review several of the most widely used techniques for training recurrent neural networks to approximate dynamical systems, then describe a novel algorithm for this task. The algorithm is based on an earlier theoretical result that guarantees the quality of the network approximation. We show that a feedforward neural network can be trained on the vector-field representation of a given dynamical system using backpropagation, then recast it as a recurrent network that replicates the original system's dynamics. After detailing this algorithm and its relation to earlier approaches, we present numerical examples that demonstrate its capabilities. One of the distinguishing features of our approach is that both the original dynamical systems and the recurrent networks that simulate them operate in continuous time. PMID:27182811

  16. Simulation and Experimental Investigation of Structural Dynamic Frequency Characteristics Control

    PubMed Central

    Zhang, Xingwu; Chen, Xuefeng; You, Shangqin; He, Zhengjia; Li, Bing

    2012-01-01

    In general, mechanical equipment such as cars, airplanes, and machine tools all operate with constant frequency characteristics. These constant working characteristics should be controlled if the dynamic performance of the equipment demands improvement or the dynamic characteristics is intended to change with different working conditions. Active control is a stable and beneficial method for this, but current active control methods mainly focus on vibration control for reducing the vibration amplitudes in the time domain or frequency domain. In this paper, a new method of dynamic frequency characteristics active control (DFCAC) is presented for a flat plate, which can not only accomplish vibration control but also arbitrarily change the dynamic characteristics of the equipment. The proposed DFCAC algorithm is based on a neural network including two parts of the identification implement and the controller. The effectiveness of the DFCAC method is verified by several simulation and experiments, which provide desirable results. PMID:22666072

  17. Generic solar photovoltaic system dynamic simulation model specification.

    SciTech Connect

    Ellis, Abraham; Behnke, Michael Robert; Elliott, Ryan Thomas

    2013-10-01

    This document is intended to serve as a specification for generic solar photovoltaic (PV) system positive-sequence dynamic models to be implemented by software developers and approved by the WECC MVWG for use in bulk system dynamic simulations in accordance with NERC MOD standards. Two specific dynamic models are included in the scope of this document. The first, a Central Station PV System model, is intended to capture the most important dynamic characteristics of large scale (> 10 MW) PV systems with a central Point of Interconnection (POI) at the transmission level. The second, a Distributed PV System model, is intended to represent an aggregation of smaller, distribution-connected systems that comprise a portion of a composite load that might be modeled at a transmission load bus.

  18. Horizontal Structure of Dynamical Instability at Marine Stratocumulus Cloud Top Revealed in Polarized Light

    NASA Astrophysics Data System (ADS)

    Davis, A. B.; Diner, D. J.; Matheou, G.; Teixeira, J.; Qu, Z.; Emde, C.

    2014-12-01

    Marine stratocumulus (Sc) layers cover vast regions and, due to their high opacities, they play a major role in the Earth's solar radiation budget. They also have remarkably flat upper boundaries due to strong gradients in relative humidity at the top of the boundary layer (BL). However, those very gradients are unstable at scales as small as meters depending on fluctuations of temperature and liquid water content, hence radiative cooling in the thermal IR. The ensuing turbulent mixing of moist and dry air at cloud top due to such small-scale dynamical processes is not benign. It controls the structure of the entire marine BL, hence the Sc life-cycle, hence large-scale subsidence, hence global circulation and, ultimately, climate. This physical connection across many orders of magnitude in scale makes the prognosis and microphysical parameterization of marine Sc particularly challenging for climate modelers. It also makes these clouds high-value targets for remote sensing, both space-based and airborne. Airborne sensors can easily achieve the resolution required to image cloud-top instabilities but natural sunlight is so highly scattered that the finest spatial features are all but erased by the "radiative smoothing" process. However, we will show that JPL's Airborne Multi-angle Spectro-Polarimetric Imager (AirMSPI), which flies on NASA's ER-2 aircraft at 20 km altitude, reveals in near-backscattered polarized light the previously unseen horizontal structure of the marine Sc cloud top physics and dynamics at 10 m resolution across a 10 km swath. It appears as a complex network of meandering filaments. Large-Eddy Simulation modeling of these oceanic clouds with bin microphysics and state-of-the-art polarized 3D radiative transfer have been harnessed to model AirMSPI observations of the first three Stokes vector components in the relevant observational geometry for a 2.5x2.5 km^2 region. Synthetic imagery obtained at JPL's High-Performance Computing facility shows

  19. Experimental characterization of energetic material dynamics for multiphase blast simulation.

    SciTech Connect

    Beresh, Steven Jay; Wagner, Justin L.; Kearney, Sean Patrick; Wright, Elton K.; Baer, Melvin R.; Pruett, Brian Owen Matthew

    2011-09-01

    Currently there is a substantial lack of data for interactions of shock waves with particle fields having volume fractions residing between the dilute and granular regimes, which creates one of the largest sources of uncertainty in the simulation of energetic material detonation. To close this gap, a novel Multiphase Shock Tube has been constructed to drive a planar shock wave into a dense gas-solid field of particles. A nearly spatially isotropic field of particles is generated in the test section by a gravity-fed method that results in a spanwise curtain of spherical 100-micron particles having a volume fraction of about 19%. Interactions with incident shock Mach numbers of 1.66, 1.92, and 2.02 were achieved. High-speed schlieren imaging simultaneous with high-frequency wall pressure measurements are used to reveal the complex wave structure associated with the interaction. Following incident shock impingement, transmitted and reflected shocks are observed, which lead to differences in particle drag across the streamwise dimension of the curtain. Shortly thereafter, the particle field begins to propagate downstream and spread. For all three Mach numbers tested, the energy and momentum fluxes in the induced flow far downstream are reduced about 30-40% by the presence of the particle field. X-Ray diagnostics have been developed to penetrate the opacity of the flow, revealing the concentrations throughout the particle field as it expands and spreads downstream with time. Furthermore, an X-Ray particle tracking velocimetry diagnostic has been demonstrated to be feasible for this flow, which can be used to follow the trajectory of tracer particles seeded into the curtain. Additional experiments on single spherical particles accelerated behind an incident shock wave have shown that elevated particle drag coefficients can be attributed to increased compressibility rather than flow unsteadiness, clarifying confusing results from the historical database of shock tube

  20. Dynamical phase transitions reveal amyloid-like states on protein folding landscapes.

    PubMed

    Weber, Jeffrey K; Jack, Robert L; Schwantes, Christian R; Pande, Vijay S

    2014-08-19

    Developing an understanding of protein misfolding processes presents a crucial challenge for unlocking the mysteries of human disease. In this article, we present our observations of β-sheet-rich misfolded states on a number of protein dynamical landscapes investigated through molecular dynamics simulation and Markov state models. We employ a nonequilibrium statistical mechanical theory to identify the glassy states in a protein's dynamics, and we discuss the nonnative, β-sheet-rich states that play a distinct role in the slowest dynamics within seven protein folding systems. We highlight the fundamental similarity between these states and the amyloid structures responsible for many neurodegenerative diseases, and we discuss potential consequences for mechanisms of protein aggregation and intermolecular amyloid formation. PMID:25140433

  1. Noise Response Data Reveal Novel Controllability Gramian for Nonlinear Network Dynamics.

    PubMed

    Kashima, Kenji

    2016-01-01

    Control of nonlinear large-scale dynamical networks, e.g., collective behavior of agents interacting via a scale-free connection topology, is a central problem in many scientific and engineering fields. For the linear version of this problem, the so-called controllability Gramian has played an important role to quantify how effectively the dynamical states are reachable by a suitable driving input. In this paper, we first extend the notion of the controllability Gramian to nonlinear dynamics in terms of the Gibbs distribution. Next, we show that, when the networks are open to environmental noise, the newly defined Gramian is equal to the covariance matrix associated with randomly excited, but uncontrolled, dynamical state trajectories. This fact theoretically justifies a simple Monte Carlo simulation that can extract effectively controllable subdynamics in nonlinear complex networks. In addition, the result provides a novel insight into the relationship between controllability and statistical mechanics. PMID:27264780

  2. Noise Response Data Reveal Novel Controllability Gramian for Nonlinear Network Dynamics

    NASA Astrophysics Data System (ADS)

    Kashima, Kenji

    2016-06-01

    Control of nonlinear large-scale dynamical networks, e.g., collective behavior of agents interacting via a scale-free connection topology, is a central problem in many scientific and engineering fields. For the linear version of this problem, the so-called controllability Gramian has played an important role to quantify how effectively the dynamical states are reachable by a suitable driving input. In this paper, we first extend the notion of the controllability Gramian to nonlinear dynamics in terms of the Gibbs distribution. Next, we show that, when the networks are open to environmental noise, the newly defined Gramian is equal to the covariance matrix associated with randomly excited, but uncontrolled, dynamical state trajectories. This fact theoretically justifies a simple Monte Carlo simulation that can extract effectively controllable subdynamics in nonlinear complex networks. In addition, the result provides a novel insight into the relationship between controllability and statistical mechanics.

  3. Noise Response Data Reveal Novel Controllability Gramian for Nonlinear Network Dynamics

    PubMed Central

    Kashima, Kenji

    2016-01-01

    Control of nonlinear large-scale dynamical networks, e.g., collective behavior of agents interacting via a scale-free connection topology, is a central problem in many scientific and engineering fields. For the linear version of this problem, the so-called controllability Gramian has played an important role to quantify how effectively the dynamical states are reachable by a suitable driving input. In this paper, we first extend the notion of the controllability Gramian to nonlinear dynamics in terms of the Gibbs distribution. Next, we show that, when the networks are open to environmental noise, the newly defined Gramian is equal to the covariance matrix associated with randomly excited, but uncontrolled, dynamical state trajectories. This fact theoretically justifies a simple Monte Carlo simulation that can extract effectively controllable subdynamics in nonlinear complex networks. In addition, the result provides a novel insight into the relationship between controllability and statistical mechanics. PMID:27264780

  4. Structural dynamics of potassium channel gating revealed by single molecule FRET

    PubMed Central

    Borschel, William F.; Ha, Taekjip; Nichols, Colin G.

    2016-01-01

    Crystallography has provided invaluable insights to ion channel selectivity and gating, but to advance understanding to a new level, dynamic views of channel structures within membranes are essential. We labeled tetrameric KirBac1.1 potassium channels with single donor and acceptor fluorophores at different sites, and examined structural dynamics within lipid membranes by single molecule FRET. We found that the extracellular region is structurally rigid in both closed and open states, whereas the N-terminal slide helix undergoes marked conformational fluctuations. The cytoplasmic C-terminal domain fluctuates between two major structural states both of which become less dynamic and move away from the pore axis and away from the membrane in closed channels. Our results reveal mobile and rigid conformations of functionally relevant KirBac1.1 channel motifs, implying similar dynamics for similar motifs in eukaryotic Kir channels and for cation channels in general. PMID:26641713

  5. Dynamical Effects and Product Distributions in Simulated CN + Methane Reactions.

    PubMed

    Preston, Thomas J; Hornung, Balázs; Pandit, Shubhrangshu; Harvey, Jeremy N; Orr-Ewing, Andrew J

    2016-07-14

    Dynamics of collisions between structured molecular species quickly become complex as molecules become large. Reactions of methane with halogen and oxygen atoms serve as model systems for polyatomic molecule chemical dynamics, and replacing the atomic reagent with a diatomic radical affords further insights. A new, full-dimensional potential energy surface for collisions between CN + CH4 to form HCN + CH3 is developed and then used to perform quasi-classical simulations of the reaction. Coupled-cluster energies serve as input to an empirical valence bonding (EVB) model, which provides an analytical function for the surface. Efficient sampling permits simulation of velocity-map ion images and exploration of dynamics over a range of collision energies. Reaction populates HCN vibration, and energy partitioning changes with collision energy. The reaction cross-section depends on the orientation of the diatomic CN radical. A two-dimensional extension of the cone of acceptance for an atom in the line-of-centers model appropriately describes its reactivity. The simulation results foster future experiments and diatomic extensions to existing atomic models of chemical collisions and reaction dynamics. PMID:26812395

  6. Dynamic molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts.

    PubMed

    Frank, Martin; Gutbrod, Peter; Hassayoun, Chokri; von Der Lieth, Claus-W

    2003-10-01

    Molecular dynamics is a rapidly developing field of science and has become an established tool for studying the dynamic behavior of biomolecules. Although several high quality programs for performing molecular dynamic simulations are freely available, only well-trained scientists are currently able to make use of the broad scientific potential that molecular dynamic simulations offer to gain insight into structural questions at an atomic level. The "Dynamic Molecules" approach is the first internet portal that provides an interactive access to set up, perform and analyze molecular dynamic simulations. It is completely based on standard web technologies and uses only publicly available software. The aim is to open molecular dynamics techniques to a broader range of users including undergraduate students, teachers and scientists outside the bioinformatics field. The time-limiting factors are the availability of free capacity on the computing server to run the simulations and the time required to transport the history file through the internet for the animation mode. The interactive access mode of the portal is acceptable for animations of molecules having up to about 500 atoms. PMID:12908101

  7. Climate Simulations with an Isentropic Finite Volume Dynamical Core

    SciTech Connect

    Chen, Chih-Chieh; Rasch, Philip J.

    2012-04-15

    This paper discusses the impact of changing the vertical coordinate from a hybrid pressure to a hybrid-isentropic coordinate within the finite volume dynamical core of the Community Atmosphere Model (CAM). Results from a 20-year climate simulation using the new model coordinate configuration are compared to control simulations produced by the Eulerian spectral and FV dynamical cores of CAM which both use a pressure-based ({sigma}-p) coordinate. The same physical parameterization package is employed in all three dynamical cores. The isentropic modeling framework significantly alters the simulated climatology and has several desirable features. The revised model produces a better representation of heat transport processes in the atmosphere leading to much improved atmospheric temperatures. We show that the isentropic model is very effective in reducing the long standing cold temperature bias in the upper troposphere and lower stratosphere, a deficiency shared among most climate models. The warmer upper troposphere and stratosphere seen in the isentropic model reduces the global coverage of high clouds which is in better agreement with observations. The isentropic model also shows improvements in the simulated wintertime mean sea-level pressure field in the northern hemisphere.

  8. Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo

    SciTech Connect

    Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.

    2000-10-10

    Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.

  9. A dynamic traffic simulator for roads affected by natural hasards

    NASA Astrophysics Data System (ADS)

    Voumard, J.; Jaboyedoff, M.; Derron, M.-H.

    2012-04-01

    This work focuses on the issue of natural hazards threatening roads. Nowadays, risk estimations of rock falls or landslides affecting whole sections of road are generally quite accurate and under relatively good control. Mitigation measures provide intervention means to reduce the hazards along roads. However, as classical models of risk calculation on communication routes do not take into account the dynamic traffic parameters, little is known on the way of reducing the risk at road level. It is not known precisely what really happens on the road when an event occurs and how vehicles interact. A dynamic traffic simulator in development provides information on factors having an impact on the risk level related to the road. Variables such as visibility, curvature radius of turns or vehicle type were included in the model. Varying these variables within dynamic traffic simulations can suggest solutions to minimize the risks for road users. These simulations can provide answers to various questions, such as: does speed have a significant impact on the risk incurred by drivers? Is it possible to significantly reduce the risk with appropriate speeds? The simulation is performed with the MATLAB © software. The model is yet to be calibrated and validated through in situ tests.

  10. NETIMIS: Dynamic Simulation of Health Economics Outcomes Using Big Data.

    PubMed

    Johnson, Owen A; Hall, Peter S; Hulme, Claire

    2016-02-01

    Many healthcare organizations are now making good use of electronic health record (EHR) systems to record clinical information about their patients and the details of their healthcare. Electronic data in EHRs is generated by people engaged in complex processes within complex environments, and their human input, albeit shaped by computer systems, is compromised by many human factors. These data are potentially valuable to health economists and outcomes researchers but are sufficiently large and complex enough to be considered part of the new frontier of 'big data'. This paper describes emerging methods that draw together data mining, process modelling, activity-based costing and dynamic simulation models. Our research infrastructure includes safe links to Leeds hospital's EHRs with 3 million secondary and tertiary care patients. We created a multidisciplinary team of health economists, clinical specialists, and data and computer scientists, and developed a dynamic simulation tool called NETIMIS (Network Tools for Intervention Modelling with Intelligent Simulation; http://www.netimis.com ) suitable for visualization of both human-designed and data-mined processes which can then be used for 'what-if' analysis by stakeholders interested in costing, designing and evaluating healthcare interventions. We present two examples of model development to illustrate how dynamic simulation can be informed by big data from an EHR. We found the tool provided a focal point for multidisciplinary team work to help them iteratively and collaboratively 'deep dive' into big data. PMID:26879667

  11. Molecular-dynamics simulation of a ceramide bilayer

    NASA Astrophysics Data System (ADS)

    Pandit, Sagar A.; Scott, H. Larry

    2006-01-01

    Ceramide is the simplest lipid in the biologically important class of glycosphingolipids. Ceramide is an important signaling molecule and a major component of the strateum corneum layer in the skin. In order to begin to understand the biophysical properties of ceramide, we have carried out a molecular-dynamics simulation of a hydrated 16:0 ceramide lipid bilayer at 368K (5° above the main phase transition). In this paper we describe the simulation and present the resulting properties of the bilayer. We compare the properties of the simulated ceramide bilayer to an earlier simulation of 18:0 sphingomyelin, and we discuss the results as they relate to experimental data for ceramide and other sphingolipids. The most significant differences arise at the lipid/water interface, where the lack of a large ceramide polar group leads to a different electron density and a different electrostatic potential but, surprisingly, not a different overall "dipole potential," when ceramide is compared to sphingomyelin.

  12. A dynamic simulation tool for hydrogen fuel cell vehicles

    NASA Astrophysics Data System (ADS)

    Moore, R. M.; Hauer, K. H.; Friedman, D.; Cunningham, J.; Badrinarayanan, P.; Ramaswamy, S.; Eggert, A.

    This paper describes a dynamic fuel cell vehicle simulation (FCVSim) tool for the load-following direct-hydrogen (DH) fuel cell vehicle. The emphasis is on simulation of the direct-hydrogen fuel cell system (FC System) within the vehicle simulation tool. This paper is focused on the subsystems that are specific to the load-following direct-hydrogen model. The four major subsystems discussed are the fuel cell stack, the air supply, the water and thermal management (WTM), and the hydrogen supply. The discussion provides the details of these subsystem simulations. The basic vehicle configuration has been previously outlined by Hauer [An Analysis Tool For Fuel Cell Vehicle Hardware and Software (Controls) with an Application to Fuel Economy Comparisons of Alternative System Designs, Dissertation, UC California, Davis, USA, 2001] and Hauer and Moore [Fuel Cells for Automotive Applications, Professional Engineering Publishing, 2003, pp. 157-177, ISBN 1860584233] and is only briefly reviewed in this paper.

  13. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    NASA Technical Reports Server (NTRS)

    Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

    2000-01-01

    We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

  14. Advanced beam-dynamics simulation tools for RIA.

    SciTech Connect

    Garnett, R. W.; Wangler, T. P.; Billen, J. H.; Qiang, J.; Ryne, R.; Crandall, K. R.; Ostroumov, P.; York, R.; Zhao, Q.; Physics; LANL; LBNL; Tech Source; Michigan State Univ.

    2005-01-01

    We are developing multi-particle beam-dynamics simulation codes for RIA driver-linac simulations extending from the low-energy beam transport (LEBT) line to the end of the linac. These codes run on the NERSC parallel supercomputing platforms at LBNL, which allow us to run simulations with large numbers of macroparticles. The codes have the physics capabilities needed for RIA, including transport and acceleration of multiple-charge-state beams, beam-line elements such as high-voltage platforms within the linac, interdigital accelerating structures, charge-stripper foils, and capabilities for handling the effects of machine errors and other off-normal conditions. This year will mark the end of our project. In this paper we present the status of the work, describe some recent additions to the codes, and show some preliminary simulation results.

  15. Novel procedure for thermal equilibration in molecular dynamics simulation.

    PubMed

    Gallo, Marco T; Grant, Barry J; Teodoro, Miguel L; Melton, Julia; Cieplak, Piotr; Phillips, George N; Stec, Boguslaw

    2009-04-01

    We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence. PMID:25125797

  16. Novel procedure for thermal equilibration in molecular dynamics simulation

    PubMed Central

    Gallo, Marco T.; Grant, Barry J.; Teodoro, Miguel L.; Melton, Julia; Cieplak, Piotr; Phillips, George N.; Stec, Boguslaw

    2014-01-01

    We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence. PMID:25125797

  17. Spotting the difference in molecular dynamics simulations of biomolecules.

    PubMed

    Sakuraba, Shun; Kono, Hidetoshi

    2016-08-21

    Comparing two trajectories from molecular simulations conducted under different conditions is not a trivial task. In this study, we apply a method called Linear Discriminant Analysis with ITERative procedure (LDA-ITER) to compare two molecular simulation results by finding the appropriate projection vectors. Because LDA-ITER attempts to determine a projection such that the projections of the two trajectories do not overlap, the comparison does not suffer from a strong anisotropy, which is an issue in protein dynamics. LDA-ITER is applied to two test cases: the T4 lysozyme protein simulation with or without a point mutation and the allosteric protein PDZ2 domain of hPTP1E with or without a ligand. The projection determined by the method agrees with the experimental data and previous simulations. The proposed procedure, which complements existing methods, is a versatile analytical method that is specialized to find the "difference" between two trajectories. PMID:27544096

  18. Insights into Buforin II Membrane Translocation from Molecular Dynamics Simulations

    PubMed Central

    Elmore, Donald E.

    2012-01-01

    Buforin II is a histone-derived antimicrobial peptide that readily translocates across lipid membranes without causing significant membrane permeabilization. Previous studies showed that mutating the sole proline of buforin II dramatically decreases its translocation. As well, researchers have proposed that the peptide crosses membranes in a cooperative manner through forming transient toroidal pores. This paper reports molecular dynamics simulations designed to investigate the structure of buforin II upon membrane entry and evaluate whether the peptide is able to form toroidal pore structures. These simulations showed a relationship between protein-lipid interactions and increased structural deformations of the buforin N-terminal region promoted by proline. Moreover, simulations with multiple peptides show how buforin II can embed deeply into membranes and potentially form toroidal pores. Together, these simulations provide structural insight into the translocation process for buforin II in addition to providing more general insight into the role proline can play in antimicrobial peptides. PMID:23022591

  19. Survey of Dynamic Simulation Programs for Nuclear Fuel Reprocessing

    SciTech Connect

    Troy J. Tranter; Daryl R. Haefner

    2008-06-01

    The absence of any industrial scale nuclear fuel reprocessing in the U.S. has precluded the necessary driver for developing the advanced simulation capability now prevalent in so many other industries. Modeling programs to simulate the dynamic behavior of nuclear fuel separations and processing were originally developed to support the US government’s mission of weapons production and defense fuel recovery. Consequently there has been little effort is the US devoted towards improving this specific process simulation capability during the last two or three decades. More recent work has been focused on elucidating chemical thermodynamics and developing better models of predicting equilibrium in actinide solvent extraction systems. These equilibrium models have been used to augment flowsheet development and testing primarily at laboratory scales. The development of more robust and complete process models has not kept pace with the vast improvements in computational power and user interface and is significantly behind simulation capability in other chemical processing and separation fields.

  20. Computational Fluid Dynamics (CFD) simulation of the Madison Dynamo Experiment.

    NASA Astrophysics Data System (ADS)

    Haehn, N. S.; Forest, C. B.; Weber, C. R.; Kendrick, R. D.; Taylor, N. Z.; Oakley, J. G.; Bonazza, R.; Spence, Erik

    2007-11-01

    The Madison Dynamo Experiment is designed to study a self-generated magnetic field called a dynamo. The flow characteristics of a water experiment that is dimensionally similar to the liquid sodium experiment has been modeled using the Computational Fluid Dynamics (CFD) software Fluent. Results from the CFD simulations are used to confirm flow characteristics measured experimentally by both Laser Doppler Velocimetry (LDV) and Particle Imaging Velocimetry (PIV). Simulations can also give insight into the flow characteristics in regions of the experiment which are not accessible via the LDV and PIV systems. The results from the simulations are also used as input for a MHD code to predict the threshold for Dynamo onset. The CFD simulations -- in conjunction with the MHD dynamo prediction code -- can be used to design modifications to the experiment to minimize costly changes. The CFD code has shown that the addition of an equatorial baffle along with several poloidal baffles can lower the threshold for Dynamo onset.