Science.gov

Sample records for dynamics simulations reveal

  1. Reveal protein dynamics by combining computer simulation and neutron scattering

    NASA Astrophysics Data System (ADS)

    Hong, Liang; Smith, Jeremy; CenterMolecular Biophysics Team

    2014-03-01

    Protein carries out most functions in living things on the earth through characteristic modulation of its three-dimensional structure over time. Understanding the microscopic nature of the protein internal motion and its connection to the function and structure of the biomolecule is a central topic in biophysics, and of great practical importance for drug design, study of diseases, and the development of renewable energy, etc. Under physiological conditions, protein exhibits a complex dynamics landscape, i.e., a variety of diffusive and conformational motions occur on similar time and length scales. This variety renders difficult the derivation of a simplified description of protein internal motions in terms of a small number of distinct, additive components. This difficulty is overcome by our work using a combined approach of Molecular Dynamics (MD) simulations and the Neutron Scattering experiments. Our approach enables distinct protein motions to be characterized separately, furnishing an in-depth understanding of the connection between protein structure, dynamics and function.

  2. 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.

  3. 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

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

    PubMed

    Hertig, Samuel; Latorraca, Naomi R; Dror, Ron O

    2016-06-01

    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

  5. Molecular dynamics simulations reveal proton transfer pathways in cytochrome C-dependent nitric oxide reductase.

    PubMed

    Pisliakov, Andrei V; Hino, Tomoya; Shiro, Yoshitsugu; Sugita, Yuji

    2012-01-01

    Nitric oxide reductases (NORs) are membrane proteins that catalyze the reduction of nitric oxide (NO) to nitrous oxide (N(2)O), which is a critical step of the nitrate respiration process in denitrifying bacteria. Using the recently determined first crystal structure of the cytochrome c-dependent NOR (cNOR) [Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, et al. (2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330: 1666-70.], we performed extensive all-atom molecular dynamics (MD) simulations of cNOR within an explicit membrane/solvent environment to fully characterize water distribution and dynamics as well as hydrogen-bonded networks inside the protein, yielding the atomic details of functionally important proton channels. Simulations reveal two possible proton transfer pathways leading from the periplasm to the active site, while no pathways from the cytoplasmic side were found, consistently with the experimental observations that cNOR is not a proton pump. One of the pathways, which was newly identified in the MD simulation, is blocked in the crystal structure and requires small structural rearrangements to allow for water channel formation. That pathway is equivalent to the functional periplasmic cavity postulated in cbb(3) oxidase, which illustrates that the two enzymes share some elements of the proton transfer mechanisms and confirms a close evolutionary relation between NORs and C-type oxidases. Several mechanisms of the critical proton transfer steps near the catalytic center are proposed. PMID:22956904

  6. 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.

  7. Quantum Dynamics Simulations Reveal Vibronic Effects on the Optical Properties of [n]Cycloparaphenylenes.

    PubMed

    Reddy, V Sivaranjana; Camacho, Cristopher; Xia, Jianlong; Jasti, Ramesh; Irle, Stephan

    2014-09-01

    The size-dependent ultraviolet/visible photophysical property trends of [n]cycloparaphenylenes ([n]CPPs, n = 6, 8, and 10) are theoretically investigated using quantum dynamics simulations. For geometry optimizations on the ground- and excited-state Born-Oppenheimer potential energy surfaces (PESs), we employ density functional theory (DFT) and time-dependent DFT calculations. Harmonic normal-mode analyses are carried out for the electronic ground state at Franck-Condon geometries. A diabatic Hamiltonian, comprising four low-lying singlet excited electronic states and 26 vibrational degrees of freedom of CPP, is constructed within the linear vibronic coupling (VC) model to elucidate the absorption spectral features in the range of 300-500 nm. Quantum nuclear dynamics is simulated within the multiconfiguration time-dependent Hartree approach to calculate the vibronic structure of the excited electronic states. The symmetry-forbidden S0 → S1 transition appears in the longer wavelength region of the spectrum with weak intensity due to VC. It is found that the Jahn-Teller and pseudo-Jahn-Teller effects in the doubly degenerate S2 and S3 electronic states are essential in the quantitative interpretation of the experimental observation of a broad absorption peak around 340 nm. The vibronic mixing of the S1 state with higher electronic states is responsible for the efficient photoluminescence from the S1 state. The fluorescence properties are characterized on the basis of the stationary points of the excited-state PESs. The findings reveal that vibronic effects become important in determining the photophysical properties of CPPs with increased ring size. PMID:26588546

  8. 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

  9. 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.

  10. 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

  11. 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

  12. Hydrated Electron Transfer to Nucleobases in Aqueous Solutions Revealed by Ab Initio Molecular Dynamics Simulations.

    PubMed

    Zhao, Jing; Wang, Mei; Fu, Aiyun; Yang, Hongfang; Bu, Yuxiang

    2015-08-01

    We present an ab initio molecular dynamics (AIMD) simulation study into the transfer dynamics of an excess electron from its cavity-shaped hydrated electron state to a hydrated nucleobase (NB)-bound state. In contrast to the traditional view that electron localization at NBs (G/A/C/T), which is the first step for electron-induced DNA damage, is related only to dry or prehydrated electrons, and a fully hydrated electron no longer transfers to NBs, our AIMD simulations indicate that a fully hydrated electron can still transfer to NBs. We monitored the transfer dynamics of fully hydrated electrons towards hydrated NBs in aqueous solutions by using AIMD simulations and found that due to solution-structure fluctuation and attraction of NBs, a fully hydrated electron can transfer to a NB gradually over time. Concurrently, the hydrated electron cavity gradually reorganizes, distorts, and even breaks. The transfer could be completed in about 120-200 fs in four aqueous NB solutions, depending on the electron-binding ability of hydrated NBs and the structural fluctuation of the solution. The transferring electron resides in the π*-type lowest unoccupied molecular orbital of the NB, which leads to a hydrated NB anion. Clearly, the observed transfer of hydrated electrons can be attributed to the strong electron-binding ability of hydrated NBs over the hydrated electron cavity, which is the driving force, and the transfer dynamics is structure-fluctuation controlled. This work provides new insights into the evolution dynamics of hydrated electrons and provides some helpful information for understanding the DNA-damage mechanism in solution.

  13. 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

  14. 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.

  15. Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Oroguchi, Tomotaka; Ikeguchi, Mitsunori

    2011-01-01

    The combination of small-angle X-ray solution scattering (SAXS) experiments and molecular dynamics (MD) simulations is now becoming a powerful tool to study protein conformations in solution at an atomic resolution. In this study, we investigated effects of ionic strength on SAXS data theoretically by using MD simulations of hen egg white lysozyme at various NaCl concentrations from 0 to 1 M. The calculated SAXS excess intensities showed a significant dependence on ion concentration, which originates from the different solvent density distributions in the presence and absence of ions. The addition of ions induced a slow convergence of the SAXS data, and a ˜20 ns simulation is required to obtain convergence of the SAXS data with the presence of ions whereas only a 0.2 ns simulation is sufficient in the absence of ions. To circumvent the problem of the slow convergence in the presence of ions, we developed a novel method that reproduces the SAXS excess intensities with the presence of ions from short MD trajectories in pure water. By applying this method to SAXS data for the open and closed forms of transferrin at 1 M ion concentration, the correct form could be identified by simply using short MD simulations of the protein in pure water for 0.2 ns.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

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

    PubMed

    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 C(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.

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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

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

    PubMed

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

    2016-07-08

    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.

  10. 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

  11. 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.

  12. 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

  13. Unbinding pathways of GW4064 from human farnesoid X receptor as revealed by molecular dynamics simulations.

    PubMed

    Li, Weihua; Fu, Jing; Cheng, Feixiong; Zheng, Mingyue; Zhang, Jian; Liu, Guixia; Tang, Yun

    2012-11-26

    Farnesoid X receptor (FXR, NR1H4) is a member of a nuclear receptor superfamily, which plays important roles in bile acid homeostasis, lipoprotein and glucose metabolism, and hepatic regeneration. GW4064 is a potent and selective FXR agonist and has become a tool compound to probe the physiological functions of FXR. Until now, the mechanism of GW4064 entering and leaving the FXR pocket is still poorly understood. Here, we report a computational study of GW4064 unbinding pathways from FXR by using several molecular dynamics (MD) simulation techniques. Based on the crystal structure of FXR in complex with GW4064, conventional MD was first used to refine the binding and check the stability of GW4064 in the FXR pocket. Random acceleration MD simulations were then performed to explore the possible unbinding pathways of GW4064 from FXR. Four main pathway clusters were found, among which three subpathways, namely Paths 2A, 2B, and 1B, were observed most frequently. Multiple steered MD simulations were further employed to estimate the maximum rupture force and the sum of the forces and to characterize the intermediate states of the ligand unbinding process. By comparing the average force profiles and structural changes, Paths 2A and 2B were identified to be the most favorable unbinding pathways. The former is located between the H1-H2 loop and the H5-H6 loop, and the latter is located in the cleft formed by the H5-H6 loop, H6, and H7. Moreover, the residues lining the pathways were analyzed for their roles in ligand unbinding. Based on our results, the possible structural modification strategies on GW4064 were also proposed.

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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

  3. Molecular dynamics simulations reveal the assembly mechanism of polysaccharides in marine aerosols.

    PubMed

    Sun, Lu; Li, Xin; Hede, Thomas; Tu, Yaoquan; Leck, Caroline; Ågren, Hans

    2014-12-21

    The high Arctic marine environment has recently detected polymer gels in atmospheric aerosol particles and cloud water originating from the surface microlayer of the open leads within the pack ice area. These polysaccharide molecules are water insoluble but water solvated, highly surface-active and highly hydrated (99% water). In order to add to the understanding and to complement missing laboratory characterization of marine polymer gels we have in this work performed an atomistic study of the assembly process and interfacial properties of polysaccharides. Our study reveals a number of salient features of the microscopic process behind polysaccharide assembly into nanogels. With three- and four-repeating units the polysaccharides assemble into a cluster in 50 ns. The aggregates grow quicker by absorbing one or two polymers each time, depending on the unit length and the type of inter-bridging cation. Although both the hydrophobic and hydrophilic domains are contracted, the latter dominates distinctly upon the contraction of solvent accessible surface areas. The establishment of inter-chain hydrogen-bonds is the key to the assembly while ionic bridges can further promote aggregation. During the assembly of the more bent four-unit polymers, intra-chain hydrogen bonds are significantly diminished by Ca(2+). Meanwhile, the percentage of Ca(2+) acting as an ionic bridge is more eminent, highlighting the significance of Ca(2+) ions for longer-chain polysaccharides. The aggregates are able to enhance surface tension more in the presence of Ca(2+) than in the presence of Na(+) owing to their more compact structure. These conclusions all demonstrate that studies of the present kind provide insight into the self-assembly process and interfacial properties of marine gels. We hope this understanding will keep up the interest in the complex and the fascinating relationship between marine microbiology, atmospheric aerosols, clouds and climate.

  4. 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.

  5. 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.

  6. Energetic Changes Caused by Antigenic Module Insertion in a Virus-Like Particle Revealed by Experiment and Molecular Dynamics Simulations

    PubMed Central

    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

  7. 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

  8. ``Cooperativity blockage'' in the mixed alkali effect as revealed by molecular-dynamics simulations of alkali metasilicate glass

    NASA Astrophysics Data System (ADS)

    Habasaki, Junko; Ngai, K. L.; Hiwatari, Yasuaki

    2004-07-01

    The relaxation dynamics of a complex interacting system can be drastically changed when mixing with another component having different dynamics. In this work, we elucidate the effect of the less mobile guest ions on the dynamics of the more mobile host ions in mixed alkali glasses by molecular-dynamics (MD) simulations. One MD simulation was carried out on lithium metasilicate glass with the guest ions created by freezing some randomly chosen lithium ions at their initial locations at 700 K. A remarkable slowing down of the dynamics of the majority mobile Li ions was observed both in the self-part of the density-density correlation function, Fs(k,t), and in the mean-squared displacements. On the other hand, there is no significant change in the structure. The motion of the Li ions in the unadulterated Li metasilicate glass is dynamically heterogeneous. In the present work, the fast and slow ions were divided into two groups. The number of fast ions, which shows faster dynamics (Lévy flight) facilitated by cooperative jumps, decreases considerably when small amount of Li ions are frozen. Consequently there is a large overall reduction of the mobility of the Li ions. The result is also in accordance with the experimental finding in mixed alkali silicate glasses that the most dramatic reduction of ionic conductivity occurs in the dilute foreign alkali limit. Similar suppression of the cooperative jumps is observed in the MD simulation data of mixed alkali system, LiKSiO3. Naturally, the effect found here is appropriately described as "cooperativity blockage." Slowing down of the motion of Li ions also was observed when a small number of oxygen atoms chosen at random were frozen. The effect is smaller than the case of freezing some the Li ions, but it is not negligible. The cooperativity blockage is also implemented by confining the Li metasilicate glass inside two parallel walls formed by freezing Li ions in the same metasilicate glass. Molecular-dynamics simulations

  9. 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.

  10. Ab initio simulations reveal that reaction dynamics strongly affect product selectivity for the cracking of alkanes over H-MFI.

    PubMed

    Zimmerman, Paul M; Tranca, Diana C; Gomes, Joseph; Lambrecht, Daniel S; Head-Gordon, Martin; Bell, Alexis T

    2012-11-28

    Product selectivity of alkane cracking catalysis in the H-MFI zeolite is investigated using both static and dynamic first-principles quantum mechanics/molecular mechanics simulations. These simulations account for the electrostatic- and shape-selective interactions in the zeolite and provide enthalpic barriers that are closely comparable to experiment. Cracking transition states for n-pentane lead to a metastable intermediate (a local minimum with relatively small barriers to escape to deeper minima) where the proton is shared between two hydrocarbon fragments. The zeolite strongly stabilizes these carbocations compared to the gas phase, and the conversion of this intermediate to more stable species determines the product selectivity. Static reaction pathways on the potential energy surface starting from the metastable intermediate include a variety of possible conversions into more stable products. One-picosecond quasiclassical trajectory simulations performed at 773 K indicate that dynamic paths are substantially more diverse than the potential energy paths. Vibrational motion that is dynamically sampled after the cracking transition state causes spilling of the metastable intermediate into a variety of different products. A nearly 10-fold change in the branching ratio between C2/C3 cracking channels is found upon inclusion of post-transition-state dynamics, relative to static electronic structure calculations. Agreement with experiment is improved by the same factor. Because dynamical effects occur soon after passing through the rate-limiting transition state, it is the dynamics, and not only the potential energy barriers, that determine the catalytic selectivity. This study suggests that selectivity in zeolite catalysis is determined by high temperature pathways that differ significantly from 0 K potential surfaces.

  11. Molecular dynamics simulations reveal a dielectric-responsive coronal structure in protein-polymer surfactant hybrid nanoconstructs.

    PubMed

    Brogan, Alex P S; Sessions, Richard B; Perriman, Adam W; Mann, Stephen

    2014-12-01

    Solvent-free liquid proteins are a new class of thermally stable hybrid bionanomaterials that are produced by extensive lyophilization of aqueous solutions of protein-polymer surfactant nanoconjugates followed by thermal annealing. The hybrid constructs, which consist of a globular protein core surrounded by a monolayer of electrostatically coupled polymer surfactant molecules, exhibit nativelike structure, function, and backbone dynamics over a large temperature range. Despite the key importance of the polymer surfactant shell, very little is known about the atomistic structure of the corona and how it influences the phase behavior and properties of these novel nanoscale objects. Here we present molecular dynamics simulations of protein-polymer surfactant nanoconjugates consisting of globular cores of myoglobin or lysozyme and demonstrate that the derived structural parameters are highly consistent with experimental values. We show that the coronal layer structure is responsive to the dielectric constant of the medium and that the mobility of the polymer surfactant molecules is significantly hindered in the solvent-free state, providing a basis for the origins of retained protein dynamics in these novel biofluids. Taken together, our results suggest that the extension of molecular dynamics simulations to hybrid nanoscale objects could be of generic value in diverse areas of soft matter chemistry, bioinspired engineering, and biomolecular nanotechnology.

  12. Unique Aspects of the Structure and Dynamics of Elementary Iβ Cellulose Microfibrils Revealed by Computational Simulations1[OPEN

    PubMed Central

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

    2015-01-01

    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

  13. 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

  14. Interactions of benzotriazole UV stabilizers with human serum albumin: Atomic insights revealed by biosensors, spectroscopies and molecular dynamics simulations.

    PubMed

    Zhuang, Shulin; Wang, Haifei; Ding, Keke; Wang, Jiaying; Pan, Liumeng; Lu, Yanli; Liu, Qingjun; Zhang, Chunlong

    2016-02-01

    Benzotriazole UV stabilizers (BZTs) belong to one prominent group of ultraviolet (UV) stabilizers and are widely used in various plastics materials. Their large production volumes, frequent detections in the environment and potential toxicities have raised increasing public concern. BZTs can be transported in vivo by transport proteins in plasma and the binding association to transport proteins may serve as a significant parameter to evaluate the bioaccumulative potential. We utilized a novel HSA biosensor, circular dichroism spectroscopy, fluorescence spectroscopy to detect the dynamic interactions of six BZTs (UV-326, UV-327, UV-328, UV-329, UV-P, and BZT) with human serum albumin (HSA), and characterized the corresponding structure-activity relationships (SAR) by molecular dynamics simulations. All test BZTs potently bind at Sudlow site I of HSA with a binding constant of 10(4) L/mol at 298 K. Minor changes in the moieties of BZTs affect their interactions with HSA and differently induce conformations of HSA. Their binding reduced electrochemical impedance spectra and α-helix content of HSA, caused slight red-shifted emission, and changed fluorescence lifetime components of HSA in a concentration-dependent mode. UV-327 and UV-329 form hydrogen bonds with HSA, while UV-329, UV-P and BZT bind HSA with more favorable electrostatic interactions. Our in vitro and in silico study offered a significant framework toward the understanding of risk assessment of BZTs and provides guide for future design of environmental benign BZTs-related materials.

  15. Interactions of benzotriazole UV stabilizers with human serum albumin: Atomic insights revealed by biosensors, spectroscopies and molecular dynamics simulations.

    PubMed

    Zhuang, Shulin; Wang, Haifei; Ding, Keke; Wang, Jiaying; Pan, Liumeng; Lu, Yanli; Liu, Qingjun; Zhang, Chunlong

    2016-02-01

    Benzotriazole UV stabilizers (BZTs) belong to one prominent group of ultraviolet (UV) stabilizers and are widely used in various plastics materials. Their large production volumes, frequent detections in the environment and potential toxicities have raised increasing public concern. BZTs can be transported in vivo by transport proteins in plasma and the binding association to transport proteins may serve as a significant parameter to evaluate the bioaccumulative potential. We utilized a novel HSA biosensor, circular dichroism spectroscopy, fluorescence spectroscopy to detect the dynamic interactions of six BZTs (UV-326, UV-327, UV-328, UV-329, UV-P, and BZT) with human serum albumin (HSA), and characterized the corresponding structure-activity relationships (SAR) by molecular dynamics simulations. All test BZTs potently bind at Sudlow site I of HSA with a binding constant of 10(4) L/mol at 298 K. Minor changes in the moieties of BZTs affect their interactions with HSA and differently induce conformations of HSA. Their binding reduced electrochemical impedance spectra and α-helix content of HSA, caused slight red-shifted emission, and changed fluorescence lifetime components of HSA in a concentration-dependent mode. UV-327 and UV-329 form hydrogen bonds with HSA, while UV-329, UV-P and BZT bind HSA with more favorable electrostatic interactions. Our in vitro and in silico study offered a significant framework toward the understanding of risk assessment of BZTs and provides guide for future design of environmental benign BZTs-related materials. PMID:26454115

  16. 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.

  17. NMR spectroscopy and molecular dynamics simulation of r(CCGCUGCGG)₂ reveal a dynamic UU internal loop found in myotonic dystrophy type 1.

    PubMed

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

    2011-02-01

    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 bond structure; however, the UU protons undergo exchange indicating structural dynamics. Molecular dynamics simulations show that the single hydrogen bond structure is the most populated one but the UU pair interconverts among zero, one, and two hydrogen bond pairs. These studies have implications for the recognition of the DM1 RNA by small molecules and proteins.

  18. 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

  19. 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

  20. 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.

  1. 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.

  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. Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations.

    PubMed

    Re, Suyong; Nishima, Wataru; Tahara, Tahei; Sugita, Yuji

    2014-12-18

    Ordering of water structures near the surface of biological membranes has been recently extensively studied using interface-selective techniques like vibrational sum frequency generation (VSFG) spectroscopy. The detailed structures of interface water have emerged for charged lipids, but those for neutral zwitterionic lipids remain obscure. We analyze an all-atom molecular dynamics (MD) trajectory of a hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer to characterize the orientation of interface waters in different chemical environments. The structure and dynamics of interfacial waters strongly depend on both their vertical position along the bilayer normal as well as vicinal lipid charged groups. Water orientation in the vicinity of phosphate groups is opposite to that around choline groups. The results are consistent with observed VSFG spectra and demonstrate that a mosaic of water orientation structures exists on the surface of a neutral zwitterionic phospholipid bilayer, reflecting rapid water exchange and the influence of local chemical environments. PMID:26273985

  4. Dynamical Mechanisms of Ozone Anomalies Formation as Revealed by Global-Scale and Regional Simulations with PlanetWRF and CAM modelling systems

    NASA Astrophysics Data System (ADS)

    Barodka, Siarhei; Krasouski, Alexander; Svetashev, Alexander; Turishev, Leonid; Zhuchkevich, Veronika

    2013-04-01

    parameterization scheme should allow for the possible radiative feedback on ozone dynamics. We perform global simulations with the PlanetWRF - WRFChem system and compare results with those obtained with the CAM system. Furthermore, to perform regional simulations on finer grids resolving mesoscale processes we use nested domains following spatial region of local ozone anomalies of interest. We perform studies of several cases of both negative (miniholes) and positive local ozone anomalies over the territory of Europe. Furthermore, we investigate the connection between ozone anomalies dynamics in the stratosphere and tropospheric weather phenomena. For that purpose we introduce perturbations to the initial conditions. First, we modify the variable fields on stratospheric model levels to see its possible impact on tropospheric phenomena. Independently, in a subsequent numerical experiment we introduce disturbances in surface and tropospheric variable fields in order to trace its influence on the stratospheric ozone dynamics. Intercomparison of modelling results is given, revealing interactions of the synoptic pressure formations with features of the stratospheric circulation. Apart from that, we analyze the role of vertical motions and ozone radiative heating on local anomalies formation. [1] Mangold A. et al - A model study of the January 2006 low total ozone episode over Western Europe and comparison with ozone sonde data // Atmospheric Chemistry and Physics, 9. - 2009. - pp. 6429-6451. [2] Semane N. et al - A very deep ozone minihole in the Northern Hemisphere stratosphere at mid-latitudes during the winter of 2000 // Tellus, 54A. - 2002. - pp. 382-389. [3] Liu C. et al - Dynamic formation of extreme ozone minimum events over the Tibetan Plateau during northern winters 1987-2001 // Journal of Geophysical Research, Vol. 115, D18311. - 2010.

  5. Molecular dynamics simulations on pars intercerebralis major peptide-C (PMP-C) reveal the role of glycosylation and disulfide bonds in its enhanced structural stability and function.

    PubMed

    Kaushik, Sandeep; Mohanty, Debasisa; Surolia, Avadhesha

    2012-01-01

    Fucosylation of Thr 9 in pars intercerebralis major peptide-C (PMP-C) enhances its structural stability and functional ability as a serine protease inhibitor. In order to understand the role of disulfide bonds and glycosylation on the structure and function of PMP-C, we have carried out multiple explicit solvent molecular dynamics (MD) simulations on fucosylated and non-fucosylated forms of PMP-C, both in the presence and absence of the disulfide bonds. Our simulations revealed that there were no significant structural changes in the native disulfide bonded forms of PMP-C due to fucosylation. On the other hand, the non-fucosylated form of PMP-C without disulfide bonds showed larger deviations from the starting structure than the fucosylated form. However, the structural deviations were restricted to the terminal regions while core β-sheet retained its hydrogen bonded structure even in absence of disulfide bonds as well as fucosylation. Interestingly, fucosylation of disulfide bonded native PMP-C led to a decreased thermal flexibility in the residue stretch 29-32 which is known to interact with the active site of the target proteases. Our analysis revealed that disulfide bonds covalently connect the residue stretch 29-32 to the central β-sheet of PMP-C and using a novel network of side chain interactions and disulfide bonds fucosylation at Thr 9 is altering the flexibility of the stretch 29-32 located at a distal site. Thus, our simulations explain for the first time, how presence of disulfide bonds between conserved cysteines and fucosylation enhance the function of PMP-C as a protease inhibitor.

  6. 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

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

    PubMed Central

    Yi, Changhong; Wambo, Thierry O.

    2015-01-01

    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 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

  8. 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.

  9. Molecular dynamics simulations.

    PubMed

    Lindahl, Erik

    2015-01-01

    Molecular dynamics has evolved from a niche method mainly applicable to model systems into a cornerstone in molecular biology. It provides us with a powerful toolbox that enables us to follow and understand structure and dynamics with extreme detail-literally on scales where individual atoms can be tracked. However, with great power comes great responsibility: Simulations will not magically provide valid results, but it requires a skilled researcher. This chapter introduces you to this, and makes you aware of some potential pitfalls. We focus on the two basic and most used methods; optimizing a structure with energy minimization and simulating motion with molecular dynamics. The statistical mechanics theory is covered briefly as well as limitations, for instance the lack of quantum effects and short timescales. As a practical example, we show each step of a simulation of a small protein, including examples of hardware and software, how to obtain a starting structure, immersing it in water, and choosing good simulation parameters. You will learn how to analyze simulations in terms of structure, fluctuations, geometrical features, and how to create ray-traced movies for presentations. With modern GPU acceleration, a desktop can perform μs-scale simulations of small proteins in a day-only 15 years ago this took months on the largest supercomputer in the world. As a final exercise, we show you how to set up, perform, and interpret such a folding simulation.

  10. 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.

  11. Functional roles of a structural element involving Na+-pi interactions in the catalytic site of T1 lipase revealed by molecular dynamics simulations.

    PubMed

    Hagiwara, Yohsuke; Matsumura, Hiroyoshi; Tateno, Masaru

    2009-11-25

    Interactions between metal ions and pi systems (metal-pi interactions) are known to confer significant stabilization energy. However, in biological systems, few structures with metal-pi coordination have been determined; thus, its roles must still be elucidated. The cation-pi interactions are not correctly described by current molecular mechanics even when using a polarizable force field, and thus they require quantum mechanical calculations for accurate estimation. However, the huge computational costs of the latter methodologies prohibit long-time molecular dynamics (MD) simulations. Accordingly, we developed a novel scheme to obtain an effective potential for calculating the interaction energy with an accuracy comparable to that of advanced ab initio calculations at the CCSD(T) levels, and with computational costs comparable to those of conventional MM calculations. Then, to elucidate the functional roles of the Na(+)-phenylalanine (Phe) complex in the catalytic site of T1 lipase, we performed MD simulations in the presence/absence of the accurate Na(+)-pi interaction energy. A comparison of these MD simulations revealed that a significantly large enthalpy gain in Na(+)-Phe16 substantially stabilizes the catalytic site, whereas a water molecule could not be substituted for Na(+) for sufficient stabilization energy. Thus, the cation-pi interaction in the lipase establishes a remarkably stable core structure by combining a hydrophobic aromatic ring and hydrophilic residues, of which the latter form the catalytic triad, thereby contributing to large structural changes from the complex with ligands to the free form of the lipase. This is the first report to elucidate the detailed functional mechanisms of Na(+)-pi interactions.

  12. Molecular dynamics simulations.

    PubMed

    Lindahl, Erik R

    2008-01-01

    Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that, respectively, optimize structure and simulate the natural motion of biological macromolecules. The common theoretical framework based on statistical mechanics is covered briefly as well as limitations of the computational approach, for instance, the lack of quantum effects and limited timescales accessible. As a practical example, a full simulation of the protein lysozyme in water is described step by step, including examples of necessary hardware and software, how to obtain suitable starting molecular structures, immersing it in a solvent, choosing good simulation parameters, and energy minimization. The chapter also describes how to analyze the simulation in terms of potential energies, structural fluctuations, coordinate stability, geometrical features, and, finally, how to create beautiful ray-traced movies that can be used in presentations.

  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. Look-ahead Dynamic Simulation

    SciTech Connect

    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.

  16. 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

  17. Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions.

    PubMed

    Baltoumas, Fotis A; Theodoropoulou, Margarita C; Hamodrakas, Stavros J

    2016-06-01

    A significant amount of experimental evidence suggests that G-protein coupled receptors (GPCRs) do not act exclusively as monomers but also form biologically relevant dimers and oligomers. However, the structural determinants, stoichiometry and functional importance of GPCR oligomerization remain topics of intense speculation. In this study we attempted to evaluate the nature and dynamics of GPCR oligomeric interactions. A representative set of GPCR homodimers were studied through Coarse-Grained Molecular Dynamics simulations, combined with interface analysis and concepts from network theory for the construction and analysis of dynamic structural networks. Our results highlight important structural determinants that seem to govern receptor dimer interactions. A conserved dynamic behavior was observed among different GPCRs, including receptors belonging in different GPCR classes. Specific GPCR regions were highlighted as the core of the interfaces. Finally, correlations of motion were observed between parts of the dimer interface and GPCR segments participating in ligand binding and receptor activation, suggesting the existence of mechanisms through which dimer formation may affect GPCR function. The results of this study can be used to drive experiments aimed at exploring GPCR oligomerization, as well as in the study of transmembrane protein-protein interactions in general.

  18. 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…

  19. Cantera Aerosol Dynamics Simulator

    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. 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.

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

    PubMed Central

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

    2014-01-01

    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. PMID:25362963

  2. Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations.

    PubMed

    Robbins, Timothy J; Wang, Yongmei

    2013-01-01

    Monovalent (Na(+)) and divalent (Mg(2+)) ion distributions around the Dickerson-Drew dodecamer were studied by atomistic molecular dynamics (MD) simulations with AMBER molecular modeling software. Different initial placements of ions were tried and the resulting effects on the ion distributions around DNA were investigated. For monovalent ions, results were found to be nearly independent of initial cation coordinates. However, Mg(2+) ions demonstrated a strong initial coordinate dependent behavior. While some divalent ions initially placed near the DNA formed essentially permanent direct coordination complexes with electronegative DNA atoms, Mg(2+) ions initially placed further away from the duplex formed a full, nonexchanging, octahedral first solvation shell. These fully solvated cations were still capable of binding with DNA with events lasting up to 20 ns, and in comparison were bound much longer than Na(+) ions. Force field parameters were also investigated with modest and little differences arising from ion (ions94 and ions08) and nucleic acid description (ff99, ff99bsc0, and ff10), respectively. Based on known Mg(2+) ion solvation structure, we conclude that in most cases Mg(2+) ions retain their first solvation shell, making only solvent-mediated contacts with DNA duplex. The proper way to simulate Mg(2+) ions around DNA duplex, therefore, should begin with ions placed in the bulk water.

  3. 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…

  4. Molecular dynamics simulations of certain mutant peptide models from staphylococcal nuclease reveal that initial hydrophobic collapse associated with turn propensity drives β-hairpin folding.

    PubMed

    Shukla, Rashmi Tambe; Kumar, Naveen; Sasidhar, Yellamraju U

    2013-08-01

    An important nucleation event during the folding of staphylococcal nuclease involves the formation of a β-hairpin by the sequence (21) DTVKLMYKGQPMTFR(35) . Earlier studies show that the turn sequence 'YKGQP' has an important role in the folding of this β-hairpin. To understand the active or passive nature of the turn sequence 'YKGQP' in the folding of the aforementioned β-hairpin sequence, we studied glycine mutant peptides Ac-(2) DTVKLMYGGQPMTFR(16) -NMe (K9G:15), Ac-(2) DTVKLMYKGGPMTFR(16) -NMe (Q11G:15), Ac-(2) DTVKLMYGGGPMTFR(16) -NMe (K9G/Q11G:15), and Ac-(2) DTVKLMGGGGGMTFR(16) -NMe (penta-G:15) by using molecular dynamics simulations, starting with two different unfolded states, polyproline II and extended conformational forms. Further, 5mer mutant turn peptides Ac-(2) YGGQP(6) -NMe (K3G:5), Ac-(2) YKGGP(6) -NMe (Q5G:5), Ac-(2) YGGGP(6) -NMe (K3G/Q5G:5), and Ac-(2) GGGGG(6) -NMe (penta-G:5) were also studied individually. Our results show that an initial hydrophobic collapse and loop closure occurs in all 15mer mutants, but only K9G:15 mutant forms a stable native-like β-hairpin. In the other 15mer mutants, the hydrophobic collapsed state would not proceed to β-hairpin formation. Of the different simulations performed for the penta-G:15 mutant, in only one simulation a nonnative β-hairpin conformation is sampled with highly flexible loop region ((8) GGGGG(12) ), which has no specific conformational preference as a 5mer. While the sequence 'YGGQP' in the K3G:5 simulation shows relatively higher β-turn propensity, the presence of this sequence in K9G:15 peptide seems to be driving the β-hairpin formation. Thus, these results seem to suggest that for the formation of a stable β-hairpin, the initial hydrophobic collapse is to be assisted by a turn propensity. Initial hydrophobic collapse alone is not sufficient to guide β-hairpin formation.

  5. Mechanism of Inhibition of Hsp90 Dimerization by Gyrase B Inhibitor Coumermycin A1 (C-A1) Revealed by Molecular Dynamics Simulations and Thermodynamic Calculations.

    PubMed

    Cele, Favourite N; Kumalo, Hezekiel; Soliman, Mahmoud E S

    2016-09-01

    Heat shock protein (Hsp) 90 an emerging and attracting target in the anti-HIV drug discovery process due to the key role it plays in the pathogenicity of HIV-1 virus. In this research study, long-range all-atom molecular dynamics simulations were engaged for the bound and the unbound proteins to enhance the understanding of the molecular mechanisms of the Hsp90 dimerization and inhibition. Results evidently showed that coumermycin A1 (C-A1), a recently discovered Hsp90 inhibitor, binds at the dimer's active site of the Hsp90 protein and leads to a substantial parting between dimeric opposed residues, which include Arg591.B, Lys594.A, Ser663.A, Thr653.B, Ala665.A, Thr649.B, Leu646.B and Asn669.A. Significant differences in magnitudes were observed in radius of gyration, root-mean-square deviation and root-mean-square fluctuation, which confirms a reasonably more flexible state in the apo conformation associated with it dimerization. In contrast, the bound conformer of Hsp90 showed less flexibility. This visibly highpoints the inhibition process resulting from the binding of the ligand. These findings were further validated by principal component analysis. We believe that the detailed dynamic analyses of Hsp90 presented in this study, would give an imperative insight and better understanding to the function and mechanisms of inhibition. Furthermore, information obtained from the binding mode of the inhibitor would be of great assistance in the design of more potent inhibitors against the HIV target Hsp90. PMID:27376828

  6. Simul 5 - free dynamic simulator of electrophoresis.

    PubMed

    Hruska, Vlastimil; Jaros, Michal; Gas, Bohuslav

    2006-03-01

    We introduce the mathematical model of electromigration of electrolytes in free solution together with free software Simul, version 5, designed for simulation of electrophoresis. The mathematical model is based on principles of mass conservation, acid-base equilibria, and electroneutrality. It accounts for any number of multivalent electrolytes or ampholytes and yields a complete picture about dynamics of electromigration and diffusion in the separation channel. Additionally, the model accounts for the influence of ionic strength on ionic mobilities and electrolyte activities. The typical use of Simul is: inspection of system peaks (zones), stacking and preconcentrating analytes, resonance phenomena, and optimization of separation conditions, in either CZE, ITP, or IEF.

  7. Dynamic Power Grid Simulation

    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.

  8. Turn-directed α-β conformational transition of α-syn12 peptide at different pH revealed by unbiased molecular dynamics simulations.

    PubMed

    Liu, Lei; Cao, Zanxia

    2013-05-24

    The transition from α-helical to β-hairpin conformations of α-syn12 peptide is characterized here using long timescale, unbiased molecular dynamics (MD) simulations in explicit solvent models at physiological and acidic pH values. Four independent normal MD trajectories, each 2500 ns, are performed at 300 K using the GROMOS 43A1 force field and SPC water model. The most clustered structures at both pH values are β-hairpin but with different turns and hydrogen bonds. Turn9-6 and four hydrogen bonds (HB9-6, HB6-9, HB11-4 and HB4-11) are formed at physiological pH; turn8-5 and five hydrogen bonds (HB8-5, HB5-8, HB10-3, HB3-10 and HB12-1) are formed at acidic pH. A common folding mechanism is observed: the formation of the turn is always before the formation of the hydrogen bonds, which means the turn is always found to be the major determinant in initiating the transition process. Furthermore, two transition paths are observed at physiological pH. One of the transition paths tends to form the most-clustered turn and improper hydrogen bonds at the beginning, and then form the most-clustered hydrogen bonds. Another transition path tends to form the most-clustered turn, and turn5-2 firstly, followed by the formation of part hydrogen bonds, then turn5-2 is extended and more hydrogen bonds are formed. The transition path at acidic pH is as the same as the first path described at physiological pH.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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

  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. 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.

  16. Molecular dynamics simulations reveal fundamental role of water as factor determining affinity of binding of beta-blocker nebivolol to beta(2)-adrenergic receptor.

    PubMed

    Kaszuba, Karol; Róg, Tomasz; Bryl, Krzysztof; Vattulainen, Ilpo; Karttunen, Mikko

    2010-07-01

    The beta-adrenergic antagonists (beta-blockers) constitute a class of drugs that have well-established roles in treatments of various cardiovascular diseases. Despite a 50 year history, there are two clinically important subtypes of beta-adrenergic receptors (betaARs) called beta(1)AR and beta(2)AR that still are promising drug targets. Our study maps the interactions between nebivolol-one of the most efficient beta-blocking agents-and the beta(2)-adrenergic receptor by simulating two optical isomers of nebivolol: ssss-nebivolol and srrr-nebivolol. The srrr-configuration binds preferentially to beta(1)AR and beta(2)AR. The ssss-form has much lower binding affinity to both of them. Our work indicates that water is a very important component of the binding site of the beta(2)AR receptor. We found that the higher stereoselectivity of the srrr-configuration is due to interactions with water molecules, which extensively hydrate the binding site of beta(2)AR. By lowering the energy of binding, water enhanced the affinity of the srrr-form to beta(2)AR. We also address the problem of beta(1)AR/beta(2)AR selectivity. At higher concentrations, all beta-blocking agents lose their specificity and bind nonselectively, causing many adverse effects. Our simulations indicate that PHE194, TYR308, and ILE309 of the beta(2)AR and the corresponding residues of the beta(1)AR receptor may be important determinants of beta(1)AR versus beta(2)AR selectivity.

  17. Dynamic Simulation Nuclear Power Plants

    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

  18. 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.

  19. 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.

  20. 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

  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. 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.

  3. 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.

  4. 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

  5. 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.

  6. Detecting Allosteric Networks Using Molecular Dynamics Simulation.

    PubMed

    Bowerman, S; Wereszczynski, J

    2016-01-01

    Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules. PMID:27497176

  7. Molecular dynamics simulations of wear processes

    NASA Astrophysics Data System (ADS)

    Yu, Hualiang

    Wear has been recognized as a vital problem in many industries. It results in a loss of durability, reliability, and efficiency and costs tens of billions of dollars annually. Significant effort has been devoted in both experimental and theoretical studies. However, the mechanisms of wear are still poorly understood and therefore wear control is far behind its demand. One way to study wear process is via computer simulation, which has become more powerful with the rapid development in computer facilities and efficient algorithms. It allows observation of atomic scale deformation and therefore it is a very good tool to study wear mechanisms at the nano-scale. This study presents a series of molecular dynamic simulation of some nano-scale wear processes, such as indentation and plowing, with the goal of exploring the factors that affect wear and predicting wear for different conditions. Molecular Dynamics simulations were carried out on a system that includes an aluminum substrate and a hard tip. Embedded atom method (EAM) and Lennard-Jones potentials were used to describe interactions between atoms. For nano-indentation simulations, both constant indent force and constant loading speed were applied to study the wear mechanisms as well as material properties. Some phenomenon, such as jump-to-contact, local melting, and dislocation nucleation were observed. More importantly, the effects of system temperature, indent force, substrate orientation, tip-substrate bond, indenter shape, boundary condition, and defect concentrations of the substrate were systematically investigated during indentation. The results are in qualitative agreement with limited experimental data. Similar simulations were carried out for plowing. The effects of plowing force, substrate orientation, the tip-substrate bond, and alloy elements are discussed based on the simulation results. In addition, a simple analytic model of plowing behavior is provided. The model reveals two parameters, static

  8. An Integrated Crustal Dynamics Simulator

    NASA Astrophysics Data System (ADS)

    Xing, H. L.; Mora, P.

    2007-12-01

    Numerical modelling offers an outstanding opportunity to gain an understanding of the crustal dynamics and complex crustal system behaviour. This presentation provides our long-term and ongoing effort on finite element based computational model and software development to simulate the interacting fault system for earthquake forecasting. A R-minimum strategy based finite-element computational model and software tool, PANDAS, for modelling 3-dimensional nonlinear frictional contact behaviour between multiple deformable bodies with the arbitrarily-shaped contact element strategy has been developed by the authors, which builds up a virtual laboratory to simulate interacting fault systems including crustal boundary conditions and various nonlinearities (e.g. from frictional contact, materials, geometry and thermal coupling). It has been successfully applied to large scale computing of the complex nonlinear phenomena in the non-continuum media involving the nonlinear frictional instability, multiple material properties and complex geometries on supercomputers, such as the South Australia (SA) interacting fault system, South California fault model and Sumatra subduction model. It has been also extended and to simulate the hot fractured rock (HFR) geothermal reservoir system in collaboration of Geodynamics Ltd which is constructing the first geothermal reservoir system in Australia and to model the tsunami generation induced by earthquakes. Both are supported by Australian Research Council.

  9. Simulations of Dynamic Relativistic Magnetospheres

    NASA Astrophysics Data System (ADS)

    Parfrey, Kyle Patrick

    Neutron stars and black holes are generally surrounded by magnetospheres of highly conducting plasma in which the magnetic flux density is so high that hydrodynamic forces are irrelevant. In this vanishing-inertia—or ultra-relativistic—limit, magnetohydrodynamics becomes force-free electrodynamics, a system of equations comprising only the magnetic and electric fields, and in which the plasma response is effected by a nonlinear current density term. In this dissertation I describe a new pseudospectral simulation code, designed for studying the dynamic magnetospheres of compact objects. A detailed description of the code and several numerical test problems are given. I first apply the code to the aligned rotator problem, in which a star with a dipole magnetic field is set rotating about its magnetic axis. The solution evolves to a steady state, which is nearly ideal and dissipationless everywhere except in a current sheet, or magnetic field discontinuity, at the equator, into which electromagnetic energy flows and is dissipated. Magnetars are believed to have twisted magnetospheres, due to internal magnetic evolution which deforms the crust, dragging the footpoints of external magnetic field lines. This twisting may be able to explain both magnetars' persistent hard X-ray emission and their energetic bursts and flares. Using the new code, I simulate the evolution of relativistic magnetospheres subjected to slow twisting through large angles. The field lines expand outward, forming a strong current layer; eventually the configuration loses equilibrium and a dynamic rearrangement occurs, involving large-scale rapid magnetic reconnection and dissipation of the free energy of the twisted magnetic field. When the star is rotating, the magnetospheric twisting leads to a large increase in the stellar spin-down rate, which may take place on the long twisting timescale or in brief explosive events, depending on where the twisting is applied and the history of the system

  10. Efficient Simulation of Dissipative Dynamics

    NASA Astrophysics Data System (ADS)

    Noh, Kyungjoo; Albert, Victor V.; Shen, Chao; Jiang, Liang

    Open quantum systems with engineered dissipations may have more than one steady states. These steady states may form a non-trivial decoherence free subspace (DFS) that can store quantum information against major decoherences. Besides unitary operations within DFS, it is also useful to have dissipative/cooling operations within the DFS. We investigate the possibility of using Hamiltonian perturbation to the engineered dissipation to induce an effective dissipative dynamics within the DFS in a controlled manner. The major challenge is to simulate all the Lindblad jump operators in the master equation. By designing the dissipation within the subspace complementary to the DFS, we can simply use the Hamiltonian perturbation to the designed dissipation with a single jump operator to produce an effective dissipation with multiple Lindblad jump operators.

  11. Using Dynamic Graphs to Reveal Student Reasoning

    ERIC Educational Resources Information Center

    Lassak, Marshall

    2009-01-01

    Using dynamic graphs, future secondary mathematics teachers were able to represent and communicate their understanding of a brief mathematical investigation in a way that a symbolic proof of the problem could not. Four different student work samples are discussed. (Contains 6 figures.)

  12. Deuterium reveals the dynamics of notch activation.

    PubMed

    Raphael, Kopan

    2011-04-13

    Notch activation requires unfolding of a juxtamembrane negative regulatory domain (NRR). Tiyanont et al. (2011) analyzed the dynamics of NRR unfolding in the presence of EGTA. As predicted from the crystal structure and deletion analyses, the lin-Notch repeats unfold first, facilitating access by ADAM proteases. Surprisingly, the heterodimerization domain remains stable.

  13. Enabling Strain Hardening Simulations with Dislocation Dynamics

    SciTech Connect

    Arsenlis, A; Cai, W

    2006-12-20

    Numerical algorithms for discrete dislocation dynamics simulations are investigated for the purpose of enabling strain hardening simulations of single crystals on massively parallel computers. The algorithms investigated include the /(N) calculation of forces, the equations of motion, time integration, adaptive mesh refinement, the treatment of dislocation core reactions, and the dynamic distribution of work on parallel computers. A simulation integrating all of these algorithmic elements using the Parallel Dislocation Simulator (ParaDiS) code is performed to understand their behavior in concert, and evaluate the overall numerical performance of dislocation dynamics simulations and their ability to accumulate percents of plastic strain.

  14. Human dynamics revealed through Web analytics

    NASA Astrophysics Data System (ADS)

    Gonçalves, Bruno; Ramasco, José J.

    2008-08-01

    The increasing ubiquity of Internet access and the frequency with which people interact with it raise the possibility of using the Web to better observe, understand, and monitor several aspects of human social behavior. Web sites with large numbers of frequently returning users are ideal for this task. If these sites belong to companies or universities, their usage patterns can furnish information about the working habits of entire populations. In this work, we analyze the properly anonymized logs detailing the access history to Emory University’s Web site. Emory is a medium-sized university located in Atlanta, Georgia. We find interesting structure in the activity patterns of the domain and study in a systematic way the main forces behind the dynamics of the traffic. In particular, we find that linear preferential linking, priority-based queuing, and the decay of interest for the contents of the pages are the essential ingredients to understand the way users navigate the Web.

  15. 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.

  16. Metrics for comparing dynamic earthquake rupture simulations

    USGS Publications Warehouse

    Barall, Michael; Harris, Ruth A.

    2014-01-01

    Earthquakes are complex events that involve a myriad of interactions among multiple geologic features and processes. One of the tools that is available to assist with their study is computer simulation, particularly dynamic rupture simulation. A dynamic rupture simulation is a numerical model of the physical processes that occur during an earthquake. Starting with the fault geometry, friction constitutive law, initial stress conditions, and assumptions about the condition and response of the near‐fault rocks, a dynamic earthquake rupture simulation calculates the evolution of fault slip and stress over time as part of the elastodynamic numerical solution (Ⓔ see the simulation description in the electronic supplement to this article). The complexity of the computations in a dynamic rupture simulation make it challenging to verify that the computer code is operating as intended, because there are no exact analytic solutions against which these codes’ results can be directly compared. One approach for checking if dynamic rupture computer codes are working satisfactorily is to compare each code’s results with the results of other dynamic rupture codes running the same earthquake simulation benchmark. To perform such a comparison consistently, it is necessary to have quantitative metrics. In this paper, we present a new method for quantitatively comparing the results of dynamic earthquake rupture computer simulation codes.

  17. 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

  18. Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations

    PubMed Central

    Gangupomu, Vamshi K.; Wagner, Jeffrey R.; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

    2013-01-01

    All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein’s experimentally established conformational substates. Conformational transition of calmodulin from the Ca2+-bound to the Ca2+-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in

  19. Mapping conformational dynamics of proteins using torsional dynamics simulations.

    PubMed

    Gangupomu, Vamshi K; Wagner, Jeffrey R; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

    2013-05-01

    All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein's experimentally established conformational substates. Conformational transition of calmodulin from the Ca(2+)-bound to the Ca(2+)-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in

  20. Post Flight Dynamic Analysis Simulation

    NASA Technical Reports Server (NTRS)

    Gregory, B. R.

    1970-01-01

    Digital six-degrees-of-freedom, open loop Saturn 5 first stage flight evaluation simulation program obtains post flight simulation of the launch vehicle using actual flight data as input. Results are compared with measured data. For preflight analysis, the program uses predicted flight data as input.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Visualizing Structure and Dynamics of Disaccharide Simulations

    SciTech Connect

    Matthews, J. F.; Beckham, G. T.; Himmel, M. E.; Crowley, M. F.

    2012-01-01

    We examine the effect of several solvent models on the conformational properties and dynamics of disaccharides such as cellobiose and lactose. Significant variation in timescale for large scale conformational transformations are observed. Molecular dynamics simulation provides enough detail to enable insight through visualization of multidimensional data sets. We present a new way to visualize conformational space for disaccharides with Ramachandran plots.

  7. 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.

  8. 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.

  9. 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. PMID:26604800

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Simulation of quantum dynamics with integrated photonics

    NASA Astrophysics Data System (ADS)

    Sansoni, Linda; Sciarrino, Fabio; Mataloni, Paolo; Crespi, Andrea; Ramponi, Roberta; Osellame, Roberto

    2012-12-01

    In recent years, quantum walks have been proposed as promising resources for the simulation of physical quantum systems. In fact it is widely adopted to simulate quantum dynamics. Up to now single particle quantum walks have been experimentally demonstrated by different approaches, while only few experiments involving many-particle quantum walks have been realized. Here we simulate the 2-particle dynamics on a discrete time quantum walk, built on an array of integrated waveguide beam splitters. The polarization independence of the quantum walk circuit allowed us to exploit the polarization entanglement to encode the symmetry of the two-photon wavefunction, thus the bunching-antibunching behavior of non interacting bosons and fermions has been simulated. We have also characterized the possible distinguishability and decoherence effects arising in such a structure. This study is necessary in view of the realization of a quantum simulator based on an integrated optical array built on a large number of beam splitters.

  15. 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

  16. 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

  17. Revealing the Effects of Cognitive Education Programmes through Dynamic Assessment

    ERIC Educational Resources Information Center

    Tzuriel, David

    2011-01-01

    The major objective of this paper is to demonstrate the effectiveness of dynamic assessment (DA) in revealing outcomes of cognitive education programmes. Three programmes based on "mediated learning experience" theory are reviewed: "Feuerstein's Instrumental Enrichment", "Bright Start", and "Peer Mediation with Young Children". In all three…

  18. Dynamical Simulations of HD 69830

    NASA Astrophysics Data System (ADS)

    Payne, Matthew J.; Ford, Eric B.; Wyatt, Mark C.; Booth, Mark

    2009-02-01

    Previous studies have developed models for the growth and migration of three planets orbiting HD 69830. We perform n-body simulations using MERCURY (Chambers 1999) to explore the implications of these models for: 1) the excitation of planetary orbits via planet-planet interactions, 2) the accretion and clearing of a putative planetesimal disk, 3) the distribution of planetesimal orbits following migration, and 4) the implications for the origin of the observed infrared emission from the HD 69830 system. We report preliminary results that suggest new constraints on the formation of HD 69830.

  19. 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

  20. 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.

  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. Dynamic modeling and simulation of planetary rovers

    NASA Astrophysics Data System (ADS)

    Lindemann, Randel A.

    1992-02-01

    This paper documents a preliminary study into the dynamic modeling and computer simulation of wheeled surface vehicles. The research centered on the feasibility of using commercially available multibody dynamics codes running on engineering workstations to perform the analysis. The results indicated that physically representative vehicle mechanics can be modeled and simulated in state-of-the-art Computer Aided Engineering environments, but at excessive cost in modeling and computation time. The results lead to the recommendation for the development of an efficient rover mobility-specific software system. This system would be used for vehicle design and simulation in planetary environments; controls prototyping, design, and testing; as well as local navigation simulation and expectation planning.

  3. 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.

  4. Molecular dynamic simulation methods for anisotropic liquids.

    PubMed

    Aoki, Keiko M; Yoneya, Makoto; Yokoyama, Hiroshi

    2004-03-22

    Methods of molecular dynamics simulations for anisotropic molecules are presented. The new methods, with an anisotropic factor in the cell dynamics, dramatically reduce the artifacts related to cell shapes and overcome the difficulties of simulating anisotropic molecules under constant hydrostatic pressure or constant volume. The methods are especially effective for anisotropic liquids, such as smectic liquid crystals and membranes, of which the stacks of layers are compressible (elastic in direction perpendicular to the layers) while the layer itself is liquid and only elastic under uniform compressive force. The methods can also be used for crystals and isotropic liquids as well.

  5. Molecular Dynamics Simulations of Alpha-synuclein

    NASA Astrophysics Data System (ADS)

    Sammalkorpi, Maria; Schreck, Carl; Nath, Abhinav; Dewitt, David; Rhoades, Elizabeth; O'Hern, Corey

    2011-03-01

    We investigate the conformational dynamics of single alpha-synuclein proteins, which have been implicated in amyloid diseases such as Parkinson's and Alzheimer's disease, in solution using unconstrained and constrained all-atom, explicit solvent molecular dynamics simulations. The constraints on inter-residue separations are obtained from our single-molecule FRET measurements of eleven FRET pairs that span the protein. By comparing the simulation data satisfying different combinations of FRET constraints, we are able to identify those constraints that are most important in determining the radius of gyration and key features of the contact map of the protein.

  6. Dynamic Simulations of Advanced Fuel Cycles

    SciTech Connect

    Steven J. Piet; Brent W. Dixon; Jacob J. Jacobson; Gretchen E. Matthern; David E. Shropshire

    2011-03-01

    Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the U.S. Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe “lessons learned” from dynamic simulations but attempt to answer the “so what” question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof.

  7. 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.

  8. Quantum Simulation for Open-System Dynamics

    NASA Astrophysics Data System (ADS)

    Wang, Dong-Sheng; de Oliveira, Marcos Cesar; Berry, Dominic; Sanders, Barry

    2013-03-01

    Simulations are essential for predicting and explaining properties of physical and mathematical systems yet so far have been restricted to classical and closed quantum systems. Although forays have been made into open-system quantum simulation, the strict algorithmic aspect has not been explored yet is necessary to account fully for resource consumption to deliver bounded-error answers to computational questions. An open-system quantum simulator would encompass classical and closed-system simulation and also solve outstanding problems concerning, e.g. dynamical phase transitions in non-equilibrium systems, establishing long-range order via dissipation, verifying the simulatability of open-system dynamics on a quantum Turing machine. We construct an efficient autonomous algorithm for designing an efficient quantum circuit to simulate many-body open-system dynamics described by a local Hamiltonian plus decoherence due to separate baths for each particle. The execution time and number of gates for the quantum simulator both scale polynomially with the system size. DSW funded by USARO. MCO funded by AITF and Brazilian agencies CNPq and FAPESP through Instituto Nacional de Ciencia e Tecnologia-Informacao Quantica (INCT-IQ). DWB funded by ARC Future Fellowship (FT100100761). BCS funded by AITF, CIFAR, NSERC and USARO.

  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. 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.

  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. 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

  13. 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

  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. Simulating Dynamic Equilibria: A Class Experiment

    NASA Astrophysics Data System (ADS)

    Harrison, John A.; Buckley, Paul D.

    2000-08-01

    A first-order reversible reaction is simulated on an overhead projector using small coins or discs. A simulation is carried out in which initially there are 24 discs representing reactant A and none representing reactant B. At the end of each minute half of the reactant A discs get converted to reactant B, and one quarter of the reactant B discs get converted to reactant A discs. Equilibrium is established with 8 A discs and 16 B discs, and no further net change is observed as the simulation continues. Another simulation beginning with 48 A discs and 0 B discs leads at equilibrium to 16 A discs and 32 B discs. These results illustrate how dynamic equilibria are established and allow the introduction of the concept of an equilibrium constant. Le Châtelier's principle is illustrated by further simulations.

  16. 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

  17. Molecular dynamics simulations of calcium binding in gramicidin A

    NASA Astrophysics Data System (ADS)

    Baştuğ, Turgut; Kuyucak, Serdar

    2006-06-01

    An important issue in molecular dynamics (MD) simulations of biomolecules is whether membrane proteins can be described using nonpolarizable force fields. To shed further light into this question, we study calcium ion binding and blocking of the gramicidin A channel which has not been investigated in MD simulations before. Potential of mean force calculations for calcium and potassium ions using a nonpolarizable force field reveal that calcium binding to the channel is much weaker compared to potassium, and hence calcium block of potassium current cannot be described. Inclusion of polarization interaction in force fields may help to rectify this problem.

  18. 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.

  19. Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers

    PubMed Central

    Koldsø, Heidi; Shorthouse, David; Hélie, Jean; Sansom, Mark S. P.

    2014-01-01

    Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins. PMID:25340788

  20. 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.

  1. 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.

  2. Information field dynamics for simulation scheme construction

    NASA Astrophysics Data System (ADS)

    Enßlin, Torsten A.

    2013-01-01

    Information field dynamics (IFD) is introduced here as a framework to derive numerical schemes for the simulation of physical and other fields without assuming a particular subgrid structure as many schemes do. IFD constructs an ensemble of nonparametric subgrid field configurations from the combination of the data in computer memory, representing constraints on possible field configurations, and prior assumptions on the subgrid field statistics. Each of these field configurations can formally be evolved to a later moment since any differential operator of the dynamics can act on fields living in continuous space. However, these virtually evolved fields need again a representation by data in computer memory. The maximum entropy principle of information theory guides the construction of updated data sets via entropic matching, optimally representing these field configurations at the later time. The field dynamics thereby become represented by a finite set of evolution equations for the data that can be solved numerically. The subgrid dynamics is thereby treated within auxiliary analytic considerations. The resulting scheme acts solely on the data space. It should provide a more accurate description of the physical field dynamics than simulation schemes constructed ad hoc, due to the more rigorous accounting of subgrid physics and the space discretization process. Assimilation of measurement data into an IFD simulation is conceptually straightforward since measurement and simulation data can just be merged. The IFD approach is illustrated using the example of a coarsely discretized representation of a thermally excited classical Klein-Gordon field. This should pave the way towards the construction of schemes for more complex systems like turbulent hydrodynamics.

  3. Information field dynamics for simulation scheme construction.

    PubMed

    Ensslin, Torsten A

    2013-01-01

    Information field dynamics (IFD) is introduced here as a framework to derive numerical schemes for the simulation of physical and other fields without assuming a particular subgrid structure as many schemes do. IFD constructs an ensemble of nonparametric subgrid field configurations from the combination of the data in computer memory, representing constraints on possible field configurations, and prior assumptions on the subgrid field statistics. Each of these field configurations can formally be evolved to a later moment since any differential operator of the dynamics can act on fields living in continuous space. However, these virtually evolved fields need again a representation by data in computer memory. The maximum entropy principle of information theory guides the construction of updated data sets via entropic matching, optimally representing these field configurations at the later time. The field dynamics thereby become represented by a finite set of evolution equations for the data that can be solved numerically. The subgrid dynamics is thereby treated within auxiliary analytic considerations. The resulting scheme acts solely on the data space. It should provide a more accurate description of the physical field dynamics than simulation schemes constructed ad hoc, due to the more rigorous accounting of subgrid physics and the space discretization process. Assimilation of measurement data into an IFD simulation is conceptually straightforward since measurement and simulation data can just be merged. The IFD approach is illustrated using the example of a coarsely discretized representation of a thermally excited classical Klein-Gordon field. This should pave the way towards the construction of schemes for more complex systems like turbulent hydrodynamics.

  4. 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.

  5. Description of the grout system dynamic simulation

    SciTech Connect

    Zimmerman, B.D.

    1993-07-01

    The grout system dynamic computer simulation was created to allow investigation of the ability of the grouting system to meet established milestones, for various assumed system configurations and parameters. The simulation simulates the movement of tank waste through the system versus time, from initial storage tanks, through feed tanks and the grout plant, then finally to a grout vault. The simulation properly accounts for the following (1) time required to perform various actions or processes, (2) delays involved in gaining regulatory approval, (3) random system component failures, (4) limitations on equipment capacities, (5) available parallel components, and (6) different possible strategies for vault filling. The user is allowed to set a variety of system parameters for each simulation run. Currently, the output of a run primarily consists of a plot of projected grouting campaigns completed versus time, for comparison with milestones. Other outputs involving any model component can also be quickly created or deleted as desired. In particular, sensitivity runs where the effect of varying a model parameter (flow rates, delay times, number of feed tanks available, etc.) on the ability of the system to meet milestones can be made easily. The grout system simulation was implemented using the ITHINK* simulation language for Macintosh** computers.

  6. Computer simulations of particle-surface dynamics

    SciTech Connect

    Karo, A.M.; Hiskes, J.R.; DeBoni, T.M.

    1986-10-01

    Our simulations of particle-surface dynamics use the molecular dynamics codes that we have developed over the past several years. The initial state of a molecule and the parameters defining the incoming trajectory can be specifically described or randomly selected. Statistical analyses of the states of the particles and their trajectories following wall collisions are carried out by the code. We have carried out calculations at high center-of-mass energies and low incidence angles and have examined the survival fraction of molecules and the dependence upon the incoming trajectory. We report also on preliminary efforts that are being made to simulate sputtering and recombinant desorption processes, since the recombinant desorption of hydrogen from typical wall materials may be an important source for vibrationally-excited hydrogen in volume sources; for surface sources the presence of occluded hydrogen may affect the concentration of atomic species.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. Molecular Dynamics Simulation of Dynamic Response of Beryllium

    NASA Astrophysics Data System (ADS)

    Thompson, Aidan P.; Lane, J. Matthew D.; Baskes, Michael I.; Desjarlais, Michael P.

    2009-06-01

    The response of beryllium to dynamic loading has been extensively studied, both experimentally and theoretically, due to its importance in several technological areas. Compared to other metals, it is quite challenging to accurately represent the various anomalous behaviors of beryllium using classical interatomic potentials. The spherically-symmetric EAM potential can not reproduce the observed c/a ratio for α-Be under ambient conditions, which is significantly smaller than the ideal HCP value. The directional-dependence of the MEAM potential overcomes this problem, but introduces additional complexity. We will compare predictions of these classical potentials to experimental measurements of beryllium at ambient conditions, and also to theoretical calculations at high temperatures and pressures. Finally, we will present initial results from non-equilibrium molecular dynamics simulations of beryllium under dynamic loading. This work is supported by the Laboratory Directed Research and Development program at Sandia National Laboratories.

  13. 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.

  14. 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.

  15. Molecular dynamics simulation study of methanesulfonic acid.

    PubMed

    Canales, Manel; Alemán, Carlos

    2014-03-27

    A molecular dynamics simulation study of methanesulfonic acid has been carried out using a reliable force field in a large range of temperatures. Several thermodynamic, structural, and dynamical properties have been calculated and compared with the available experimental data. The density, the shear viscosity, the heat of vaporization, and the melting temperature results, calculated from this force field, are in a good agreement with the experimental data. Analysis of the influence of the hydrogen bonds in structural and dynamical properties has also been performed. The continuous and interrupted methodologies to compute hydrogen bonding lifetimes have been applied. The interrupted hydrogen bond lifetimes values are consistent with the diffusion and viscosity coefficients. The activation energies of the self-diffusion, the reorientational motions, and the hydrogen bonding lifetimes are coincident.

  16. Adaptive wavelet simulation of global ocean dynamics

    NASA Astrophysics Data System (ADS)

    Kevlahan, N. K.-R.; Dubos, T.; Aechtner, M.

    2015-07-01

    In order to easily enforce solid-wall boundary conditions in the presence of complex coastlines, we propose a new mass and energy conserving Brinkman penalization for the rotating shallow water equations. This penalization does not lead to higher wave speeds in the solid region. The error estimates for the penalization are derived analytically and verified numerically for linearized one dimensional equations. The penalization is implemented in a conservative dynamically adaptive wavelet method for the rotating shallow water equations on the sphere with bathymetry and coastline data from NOAA's ETOPO1 database. This code could form the dynamical core for a future global ocean model. The potential of the dynamically adaptive ocean model is illustrated by using it to simulate the 2004 Indonesian tsunami and wind-driven gyres.

  17. MDLab: a molecular dynamics simulation prototyping environment.

    PubMed

    Cickovski, Trevor; Chatterjee, Santanu; Wenger, Jacob; Sweet, Christopher R; Izaguirre, Jesús A

    2010-05-01

    Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net.

  18. Dynamic adaptive chemistry for turbulent flame simulations

    NASA Astrophysics Data System (ADS)

    Yang, Hongtao; Ren, Zhuyin; Lu, Tianfeng; Goldin, Graham M.

    2013-02-01

    The use of large chemical mechanisms in flame simulations is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. This study investigates the use of dynamic adaptive chemistry (DAC) for efficient chemistry calculations in turbulent flame simulations. DAC is achieved through the directed relation graph (DRG) method, which is invoked for each computational fluid dynamics cell/particle to obtain a small skeletal mechanism that is valid for the local thermochemical condition. Consequently, during reaction fractional steps, one needs to solve a smaller set of ordinary differential equations governing chemical kinetics. Test calculations are performed in a partially-stirred reactor (PaSR) involving both methane/air premixed and non-premixed combustion with chemistry described by the 53-species GRI-Mech 3.0 mechanism and the 129-species USC-Mech II mechanism augmented with recently updated NO x pathways, respectively. Results show that, in the DAC approach, the DRG reduction threshold effectively controls the incurred errors in the predicted temperature and species concentrations. The computational saving achieved by DAC increases with the size of chemical kinetic mechanisms. For the PaSR simulations, DAC achieves a speedup factor of up to three for GRI-Mech 3.0 and up to six for USC-Mech II in simulation time, while at the same time maintaining good accuracy in temperature and species concentration predictions.

  19. Classical Molecular Dynamics Simulation of Nuclear Fuel

    SciTech Connect

    Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie

    2015-10-10

    Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.

  20. 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.

  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. 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%.

  3. 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.

  4. 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.

  5. The Fermi-Pasta-Ulam problem: Simulation and modern dynamics

    SciTech Connect

    Weissert, T.P.

    1992-01-01

    In 1952, Enrico Fermi, John Pasta and Stanislaw Ulam (FPU) simulated the loaded string model, perturbed with small, nonlinear interaction terms. Because Poincare's theorem guarantees the non-existence of a complete set of integrals for three-body problem, they expected to see the diffusion of energy from its single-mode initial condition to all other modes of the string. But for every combination of initial conditions, the energy remained bounded within the lowest few modes. No theoretical explanation existed for this failure of the underlying hypothesis that erogidicity follows from the lack of a complete set of integrals of the motion in a Hamiltonian model. The author traces the history of this problem from the FPU simulation to the point that a consensus was reached concerning its solution twenty years later. During this period, the simulation of nonlinearly-perturbed integral models became the methodology for a new era in dynamics. Through the use of simulation, dynamicists discovered deterministic chaos, in which the exponential separation of pair orbits generate randomness in deterministic macroscopic systems, and a new kind of structure-related to the KAM theorem-that provides limited order in the absence of analytic integrals of the motions. The author maps the set of conceptually-related journal articles into a chronological inference topology that tracks the understanding of this problem of dynamics. Simulating non-integrable models on a digital computer requires the discretization of time and space. These approximations affect what the simulation can reveal about the model, and the model about reality. Simulations play the role of experiments on mathematical models. A discussion is presented of the issues that emerge with the use of simulation as a heuristic device and the groundwork is laid for an epistemology of simulation.

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

    PubMed

    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. PMID:24345941

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

    PubMed

    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.

  8. 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.

  9. Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties

    SciTech Connect

    Mereghetti, Paolo; Gabdoulline, Razif; Wade, Rebecca C.

    2010-12-01

    The study of solutions of biomacromolecules provides an important basis for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, biochemical reactions, and signal transduction. Here, we describe a Brownian dynamics simulation procedure and its validation for the study of the dynamic and structural properties of protein solutions. In the model used, the proteins are treated as atomically detailed rigid bodies moving in a continuum solvent. The protein-protein interaction forces are described by the sum of electrostatic interaction, electrostatic desolvation, nonpolar desolvation, and soft-core repulsion terms. The linearized Poisson-Boltzmann equation is solved to compute electrostatic terms. Simulations of homogeneous solutions of three different proteins with varying concentrations, pH, and ionic strength were performed. The results were compared to experimental data and theoretical values in terms of long-time self-diffusion coefficients, second virial coefficients, and structure factors. The results agree with the experimental trends and, in many cases, experimental values are reproduced quantitatively. There are no parameters specific to certain protein types in the interaction model, and hence the model should be applicable to the simulation of the behavior of mixtures of macromolecules in cell-like crowded environments.

  10. 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.

  11. 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.

  12. Dynamical simulation of dipolar Janus colloids: dynamical properties.

    PubMed

    Hagy, Matthew C; Hernandez, Rigoberto

    2013-05-14

    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)]. 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. PMID:23676070

  13. 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.

  14. Mobility Laws in Dislocation Dynamics Simulations

    SciTech Connect

    Cai, W; Bulatov, V V

    2003-10-21

    Prediction of the plastic deformation behavior of single crystals based on the collective dynamics of dislocations has been a challenge for computational materials science for a number of years. The difficulty lies in the inability of existing dislocation dynamics (DD) codes to handle a sufficiently large number of dislocation lines, to establish a statistically representative model of crystal plasticity. A new massively-parallel DD code is developed that is capable of modeling million-dislocation systems by employing thousands of processors. We discuss an important ingredient of this code--the mobility laws dictating the behavior of individual dislocations. They are materials input for DD simulations and are constructed based on the understanding of dislocation motion at the atomistic level.

  15. 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.

  16. 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}.

  17. 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..

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

    PubMed

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

    2010-01-01

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

  19. Fracture simulations via massively parallel molecular dynamics

    SciTech Connect

    Holian, B.L.; Abraham, F.F.; Ravelo, R.

    1993-09-01

    Fracture simulations at the atomistic level have heretofore been carried out for relatively small systems of particles, typically 10,000 or less. In order to study anything approaching a macroscopic system, massively parallel molecular dynamics (MD) must be employed. In two spatial dimensions (2D), it is feasible to simulate a sample that is 0.1 {mu}m on a side. We report on recent MD simulations of mode I crack extension under tensile loading at high strain rates. The method of uniaxial, homogeneously expanding periodic boundary conditions was employed to represent tensile stress conditions near the crack tip. The effects of strain rate, temperature, material properties (equation of state and defect energies), and system size were examined. We found that, in order to mimic a bulk sample, several tricks (in addition to expansion boundary conditions) need to be employed: (1) the sample must be pre-strained to nearly the condition at which the crack will spontaneously open; (2) to relieve the stresses at free surfaces, such as the initial notch, annealing by kinetic-energy quenching must be carried out to prevent unwanted rarefactions; (3) sound waves emitted as the crack tip opens and dislocations emitted from the crack tip during blunting must be absorbed by special reservoir regions. The tricks described briefly in this paper will be especially important to carrying out feasible massively parallel 3D simulations via MD.

  20. Coupled nucleotide covariations reveal dynamic RNA interaction patterns.

    PubMed Central

    Gultyaev, A P; Franch, T; Gerdes, K

    2000-01-01

    Evolutionarily conserved structures in related RNA molecules contain coordinated variations (covariations) of paired nucleotides. Analysis of covariations is a very powerful approach to deduce phylogenetically conserved (i.e., functional) conformations, including tertiary interactions. Here we discuss conserved RNA folding pathways that are revealed by covariation patterns. In such pathways, structural requirements for alternative pairings cause some nucleotides to covary with two different partners. Such "coupled" covariations between three or more nucleotides were found in various types of RNAs. The analysis of coupled covariations can unravel important features of RNA folding dynamics and improve phylogeny reconstruction in some cases. Importantly, it is necessary to distinguish between multiple covariations determined by mutually exclusive structures and those determined by tertiary contacts. PMID:11105748

  1. 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.

  2. Local RNA Conformational Dynamics Revealed by 2-Aminopurine Solvent Accessibility†

    PubMed Central

    Ballin, Jeff D.; Prevas, James P.; Bharill, Shashank; Gryczynski, Ignacy; Gryczynski, Zygmunt; Wilson, Gerald M.

    2008-01-01

    Acrylamide quenching is widely used to monitor the solvent exposure of fluorescent probes in vitro. Here, we tested the utility of this technique to discriminate local RNA secondary structures using the fluorescent adenine analogue 2-aminopurine (2-AP). Under native conditions, the solvent accessibilities of most 2-AP-labeled RNA substrates were poorly resolved by classical single population models; rather, a two-state quencher accessibility algorithm was required to model acrylamide-dependent changes in 2-AP fluorescence in structured RNA contexts. Comparing 2-AP quenching parameters between structured and unstructured RNA substrates permitted the effects of local RNA structure on 2-AP solvent exposure to be distinguished from nearest neighbor effects or environmental influences on intrinsic 2-AP photophysics. Using this strategy, the fractional accessibility of 2-AP for acrylamide (fa) was found to be highly sensitive to local RNA structure. Base-paired 2-AP exhibited relatively poor accessibility, consistent with extensive shielding by adjacent bases. 2-AP in a single base bulge was uniformly accessible to solvent, whereas the fractional accessibility of 2-AP in a hexanucleotide loop was indistinguishable from that of an unstructured RNA. However, these studies also provided evidence that the fa parameter reflects local conformational dynamics in base-paired RNA. Enhanced base pair dynamics at elevated temperatures were accompanied by increased fa values, while restricting local RNA breathing by adding a C-G base pair clamp or positioning 2-AP within extended RNA duplexes significantly decreased this parameter. Together, these studies show that 2-AP quenching studies can reveal local RNA structural and dynamic features beyond those measurable by conventional spectroscopic approaches. PMID:18543944

  3. 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.

  4. 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

  5. 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.

  6. Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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 1ππ∗, 1nπ∗, 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 1ππ∗ system. The first is the diabatic ESIPT process along the 1ππ∗ potential energy profile. The generated 1ππ∗ keto species then decays to the S0 state via the keto 1ππ∗/gs conical intersection. The second is internal conversion to the dark 1nπ∗ state near the 1ππ∗ /1nπ∗ crossing point in the course of the diabatic 1ππ∗ ESIPT process. Our following dynamics simulations have shown that the ESIPT and 1ππ∗ → S0 internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the 1ππ∗ → S0 internal conversion in the keto region, the 1ππ∗ → 1nπ∗ internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone.

  7. 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

  8. 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.

  9. Molecular dynamics simulations of unsaturated lipid bilayers

    NASA Astrophysics Data System (ADS)

    Rabinovich, Alexander L.; Balabaev, Nikolay K.

    2001-02-01

    Molecular dynamics simulations were carried out for bilayers of lipid molecules having stearic acid (C18:0) chain in position '3-D' (using the nomenclature of M. Sundaralingam, 1972) and fatty acid chain C18:0, C18:1(omega 9), C18:2(omega 6), C18:3(omega 3), C20:4(omega 6) or C22:6(omega 3) in position '2-D'. To investigate the properties of the bilayers two models were considered. In the first model, the simulation cells of the bilayers consisted of 96 phosphatidylcholine (PC) molecules and 2304 water molecules: 48 lipid molecules per layer and 24 H2O molecules per lipid. The water was modeled by explicit TIP3P water molecules. In the second model, the head group of the lipid molecules was treated as an effective sphere -- diacylglycerolipids (DGs) were considered, the interface of each monolayer was modeled by a flat surface; no water molecules were present explicitly. The bilayers consisted of 48 X 2 equals 96 glycerolipids arranged in a rectangular simulation cell. Various properties of the bilayers -- the C-H bond order parameter -SCH profiles of the hydrocarbon tails, the root-mean-square values of the positional fluctuations of the lipid chain carbons, mass density distributions of lipid molecules and water along the normals were investigated.

  10. Molecular dynamics simulations of unsaturated lipid bilayers

    NASA Astrophysics Data System (ADS)

    Rabinovich, Alexander L.; Balabaev, Nikolay K.

    2000-02-01

    Molecular dynamics simulations were carried out for bilayers of lipid molecules having stearic acid (C18:0) chain in position '3-D' (using the nomenclature of M. Sundaralingam, 1972) and fatty acid chain C18:0, C18:1(omega 9), C18:2(omega 6), C18:3(omega 3), C20:4(omega 6) or C22:6(omega 3) in position '2-D'. To investigate the properties of the bilayers two models were considered. In the first model, the simulation cells of the bilayers consisted of 96 phosphatidylcholine (PC) molecules and 2304 water molecules: 48 lipid molecules per layer and 24 H2O molecules per lipid. The water was modeled by explicit TIP3P water molecules. In the second model, the head group of the lipid molecules was treated as an effective sphere -- diacylglycerolipids (DGs) were considered, the interface of each monolayer was modeled by a flat surface; no water molecules were present explicitly. The bilayers consisted of 48 X 2 equals 96 glycerolipids arranged in a rectangular simulation cell. Various properties of the bilayers -- the C-H bond order parameter -SCH profiles of the hydrocarbon tails, the root-mean-square values of the positional fluctuations of the lipid chain carbons, mass density distributions of lipid molecules and water along the normals were investigated.

  11. Digital system for structural dynamics simulation

    SciTech Connect

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

    1982-11-01

    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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. GBT Dynamic Scheduling System: Algorithms, Metrics, and Simulations

    NASA Astrophysics Data System (ADS)

    Balser, D. S.; Bignell, C.; Braatz, J.; Clark, M.; Condon, J.; Harnett, J.; O'Neil, K.; Maddalena, R.; Marganian, P.; McCarty, M.; Sessoms, E.; Shelton, A.

    2009-09-01

    We discuss the scoring algorithm of the Robert C. Byrd Green Bank Telescope (GBT) Dynamic Scheduling System (DSS). Since the GBT is located in a continental, mid-latitude region where weather is dominated by water vapor and small-scale effects, the weather plays an important role in optimizing the observing efficiency of the GBT. We score observing sessions as a product of many factors. Some are continuous functions while others are binary limits taking values of 0 or 1, any one of which can eliminate a candidate session by forcing the score to zero. Others reflect management decisions to expedite observations by visiting observers, ensure the timely completion of projects, etc. Simulations indicate that dynamic scheduling can increase the effective observing time at frequencies higher than 10 GHz by about 50% over one full year. Beta tests of the DSS during Summer 2008 revealed the significance of various scheduling constraints and telescope overhead time to the overall observing efficiency.

  18. Dynamics of rhenium photocatalysts revealed through ultrafast multidimensional spectroscopy.

    PubMed

    Kiefer, Laura M; King, John T; Kubarych, Kevin J

    2015-04-21

    Rhenium catalysts have shown promise to promote carbon neutrality by reducing a prominent greenhouse gas, CO2, to CO and other starting materials. Much research has focused on identifying intermediates in the photocatalysis mechanism as well as time scales of relevant ultrafast processes. Recent studies have implemented multidimensional spectroscopies to characterize the catalyst's ultrafast dynamics as it undergoes the many steps of its photocycle. Two-dimensional infrared (2D-IR) spectroscopy is a powerful method to obtain molecular structure information while extracting time scales of dynamical processes with ultrafast resolution. Many observables result from 2D-IR experiments including vibrational lifetimes, intramolecular redistribution time scales, and, unique to 2D-IR, spectral diffusion, which is highly sensitive to solute-solvent interactions and motional dynamics. Spectral diffusion, a measure of how long a vibrational mode takes to sample its frequency space due to multiple solvent configurations, has various contributing factors. Properties of the solvent, the solute's structural flexibility, and electronic properties, as well as interactions between the solvent and solute, complicate identifying the origin of the spectral diffusion. With carefully chosen experiments, however, the source of the spectral diffusion can be unveiled. Within the context of a considerable body of previous work, here we discuss the spectral diffusion of several rhenium catalysts at multiple stages in the catalysis. These studies were performed in multiple polar liquids to aid in discovering the contributions of the solvent. We also performed electronic ground state 2D-IR and electronic excited state transient-2D-IR experiments to observe how spectral diffusion changes upon electronic excitation. Our results indicate that with the original Lehn catalyst in THF, relative to the ground state, the spectral diffusion slows by a factor of 3 in the equilibrated triplet metal

  19. Forced reptation revealed by chain pull-out simulations.

    PubMed

    Bulacu, Monica; van der Giessen, Erik

    2009-08-14

    We report computation results obtained from extensive molecular dynamics simulations of tensile disentanglement of connector chains placed at the interface between two polymer bulks. Each polymer chain (either belonging to the bulks or being a connector) is treated as a sequence of beads interconnected by springs, using a coarse-grained representation based on the Kremer-Grest model, extended to account for stiffness along the chain backbone. Forced reptation of the connectors was observed during their disentanglement from the bulk chains. The extracted chains are clearly seen following an imaginary "tube" inside the bulks as they are pulled out. The entropic and energetic responses to the external deformation are investigated by monitoring the connector conformation tensor and the modifications of the internal parameters (bonds, bending, and torsion angles along the connectors). The work needed to separate the two bulks is computed from the tensile force induced during debonding in the connector chains. The value of the work reached at total separation is considered as the debonding energy G. The most important parameters controlling G are the length (n) of the chains placed at the interface and their areal density. Our in silico experiments are performed at relatively low areal density and are disregarded if chain scission occurs during disentanglement. As predicted by the reptation theory, for this pure pull-out regime, the power exponent from the scaling G proportional, variant n(a) is a approximately 2, irrespective of chain stiffness. Small variations are found when the connectors form different number of stitches at the interface, or when their length is randomly distributed in between the two bulks. Our results show that the effects of the number of stitches and of the randomness of the block lengths have to be considered together, especially when comparing with experiments where they cannot be controlled rigorously. These results may be significant for

  20. Forced reptation revealed by chain pull-out simulations

    NASA Astrophysics Data System (ADS)

    Bulacu, Monica; van der Giessen, Erik

    2009-08-01

    We report computation results obtained from extensive molecular dynamics simulations of tensile disentanglement of connector chains placed at the interface between two polymer bulks. Each polymer chain (either belonging to the bulks or being a connector) is treated as a sequence of beads interconnected by springs, using a coarse-grained representation based on the Kremer-Grest model, extended to account for stiffness along the chain backbone. Forced reptation of the connectors was observed during their disentanglement from the bulk chains. The extracted chains are clearly seen following an imaginary "tube" inside the bulks as they are pulled out. The entropic and energetic responses to the external deformation are investigated by monitoring the connector conformation tensor and the modifications of the internal parameters (bonds, bending, and torsion angles along the connectors). The work needed to separate the two bulks is computed from the tensile force induced during debonding in the connector chains. The value of the work reached at total separation is considered as the debonding energy G. The most important parameters controlling G are the length (n) of the chains placed at the interface and their areal density. Our in silico experiments are performed at relatively low areal density and are disregarded if chain scission occurs during disentanglement. As predicted by the reptation theory, for this pure pull-out regime, the power exponent from the scaling G ∝na is a ≈2, irrespective of chain stiffness. Small variations are found when the connectors form different number of stitches at the interface, or when their length is randomly distributed in between the two bulks. Our results show that the effects of the number of stitches and of the randomness of the block lengths have to be considered together, especially when comparing with experiments where they cannot be controlled rigorously. These results may be significant for industrial applications, such

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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

  9. Molecular dynamics simulations of gold nanomaterials

    NASA Astrophysics Data System (ADS)

    Wang, Yanting

    We have carried out Molecular Dynamics simulations to study the thermal stability and melting behavior of gold nanoclusters and gold nanorods. The surface is found to play a very important role in both gold nanomaterials. Upon cooling from the liquid, we find that gold nanoclusters with 600-3000 atoms crystallize into a Mackay icosahedron. Upon heating, the {111} facets on the surface of the Mackay icosahedral gold nanoclusters soften but do not premelt below the bulk melting temperature. We attribute this surface softening to the increasing mobility of vertex and edge atoms with temperature, which leads to inter-layer and intra-layer diffusion, and a shrinkage of the average facet size. Upon heating, our simulated gold nanorods undergo a shape transformation preceding the melting transition. The shape transformation is induced by a minimization of the surface free energy, and is accompanied by a complete reconstruction of the internal structure driven by the surface change. During the transformation, the atoms on the end caps of the rod move to the sides of the rods, leading the rods to be shorter and wider. After the transformation, the surface of the stable intermediate state rod is mostly covered by the more stable {111} facets, other than the less stable {110} and {100} facets covering the sides of the initial constructed rod.

  10. 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.

  11. 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.

  12. 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.

  13. Thermostat for nonequilibrium multiparticle-collision-dynamics simulations.

    PubMed

    Huang, Chien-Cheng; Varghese, Anoop; Gompper, Gerhard; Winkler, Roland G

    2015-01-01

    Multiparticle collision dynamics (MPC), a particle-based mesoscale simulation technique for complex fluid, is widely employed in nonequilibrium simulations of soft matter systems. To maintain a defined thermodynamic state, thermalization of the fluid is often required for certain MPC variants. We investigate the influence of three thermostats on the nonequilibrium properties of a MPC fluid under shear or in Poiseuille flow. In all cases, the local velocities are scaled by a factor, which is either determined via a local simple scaling approach (LSS), a Monte Carlo-like procedure (MCS), or by the Maxwell-Boltzmann distribution of kinetic energy (MBS). We find that the various scaling schemes leave the flow profile unchanged and maintain the local temperature well. The fluid viscosities extracted from the various simulations are in close agreement. Moreover, the numerically determined viscosities are in remarkably good agreement with the respective theoretically predicted values. At equilibrium, the calculation of the dynamic structure factor reveals that the MBS method closely resembles an isothermal ensemble, whereas the MCS procedure exhibits signatures of an adiabatic system at larger collision-time steps. Since the velocity distribution of the LSS approach is non-Gaussian, we recommend to apply the MBS thermostat, which has been shown to produce the correct velocity distribution even under nonequilibrium conditions.

  14. Frontiers in molecular dynamics simulations of DNA.

    PubMed

    Pérez, Alberto; Luque, F Javier; Orozco, Modesto

    2012-02-21

    It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global

  15. The Dynamics of Miscible Interfaces: Simulations

    NASA Technical Reports Server (NTRS)

    Meiburg, Eckart

    2002-01-01

    The goal of this experimental/computational investigation (joint with Prof Maxworthy at USC) has been to study the dynamics of miscible interfaces, both from a scientific and a practical point of view, and to prepare a related experiment to be flown on the International Space Station. In order to address these effects, we have focused experimental and computational investigations on miscible displacements in cylindrical capillary tubes, as well as in Hele-Shaw cells. Regarding the flow in a capillary tube, the question was addressed as to whether Korteweg stresses and/or divergence effects can potentially account for discrepancies observed between conventional Stokes flow simulations and experiments for miscible flows in capillary tubes. An estimate of the vorticity and streamfunction fields induced by the Kortewegs stresses was derived, which shows these stresses to result in the formation of a vortex ring structure near the tip of the concentration front. Through this mechanism the propagation velocity of the concentration front is reduced, in agreement with the experimental observations. Divergence effects, on the other hand, were seen to be very small, and they have a negligible influence on the tip velocity. As a result, it can be concluded that they are not responsible for the discrepancies between experiments and conventional Stokes simulations. A further part of our investigation focussed on the development of high-accuracy three-dimensional spectral element simulation techniques for miscible flows in capillary tubes, including the effects of variable density and viscosity. Towards this end, the conservation equations are treated in cylindrical coordinates.

  16. PACO: PArticle COunting Method To Enforce Concentrations in Dynamic Simulations.

    PubMed

    Berti, Claudio; Furini, Simone; Gillespie, Dirk

    2016-03-01

    We present PACO, a computationally efficient method for concentration boundary conditions in nonequilibrium particle simulations. Because it requires only particle counting, its computational effort is significantly smaller than other methods. PACO enables Brownian dynamics simulations of micromolar electrolytes (3 orders of magnitude lower than previously simulated). PACO for Brownian dynamics is integrated in the BROWNIES package (www.phys.rush.edu/BROWNIES). We also introduce a molecular dynamics PACO implementation that allows for very accurate control of concentration gradients.

  17. 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...

  18. 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.

  19. Lytic Water Dynamics Reveal Evolutionarily Conserved Mechanisms of ATP Hydrolysis by TIP49 AAA+ ATPases

    PubMed Central

    Afanasyeva, Arina; Hirtreiter, Angela; Schreiber, Anne; Grohmann, Dina; Pobegalov, Georgii; McKay, Adam R.; Tsaneva, Irina; Petukhov, Michael; Käs, Emmanuel; Grigoriev, Mikhail; Werner, Finn

    2014-01-01

    Summary Eukaryotic TIP49a (Pontin) and TIP49b (Reptin) AAA+ ATPases play essential roles in key cellular processes. How their weak ATPase activity contributes to their important functions remains largely unknown and difficult to analyze because of the divergent properties of TIP49a and TIP49b proteins and of their homo- and hetero-oligomeric assemblies. To circumvent these complexities, we have analyzed the single ancient TIP49 ortholog found in the archaeon Methanopyrus kandleri (mkTIP49). All-atom homology modeling and molecular dynamics simulations validated by biochemical assays reveal highly conserved organizational principles and identify key residues for ATP hydrolysis. An unanticipated crosstalk between Walker B and Sensor I motifs impacts the dynamics of water molecules and highlights a critical role of trans-acting aspartates in the lytic water activation step that is essential for the associative mechanism of ATP hydrolysis. PMID:24613487

  20. 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

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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

  6. Molecular dynamics simulations of water droplets on polymer surfaces.

    PubMed

    Hirvi, Janne T; Pakkanen, Tapani A

    2006-10-14

    Molecular dynamics simulations were used to study the wetting of polymer surfaces with water. Contact angles of water droplets on crystalline and two amorphous polyethylene (PE) and poly(vinyl chloride) (PVC) surfaces were extracted from atomistic simulations. Crystalline surfaces were produced by duplicating the unit cell of an experimental crystal structure, and amorphous surfaces by pressing the bulk polymer step by step at elevated temperature between two repulsive grid surfaces to a target density. Different-sized water droplets on the crystalline PE surface revealed a slightly positive line tension on the order of 10(-12)-10(-11) N, whereas droplets on crystalline PVC did not yield a definite line tension. Microscopic contact angles produced by the simple point charge (SPC) water model were mostly a few degrees smaller than those produced by the extended SPC model, which, as the model with lowest bulk energy, presents an upper boundary for contact angles. The macroscopic contact angle for the SPC model was 94 degrees on crystalline PVC and 113 degrees on crystalline PE. Amorphicity of the surface increased the water contact angle on PE but decreased it on PVC, for both water models. If the simulated contact angles on crystalline and amorphous surfaces are combined in proportion to the crystallinity of the polymer in question, simulated values in relatively good agreement with measured values are obtained.

  7. 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

  8. 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.

  9. 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.

  10. Simulation of Chemical Isomerization Reaction Dynamics on a NMR Quantum Simulator

    NASA Astrophysics Data System (ADS)

    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.

  11. 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)

  12. Staggered solution procedures for multibody dynamics simulation

    NASA Astrophysics Data System (ADS)

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

    1990-04-01

    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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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…

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations

    PubMed Central

    Chang, Le; Takada, Shoji

    2016-01-01

    Histone tail acetylation is a key epigenetic marker that tends to open chromatin folding and activate transcription. Despite intensive studies, precise roles of individual lysine acetylation in chromatin folding have only been poorly understood. Here, we revealed structural dynamics of tri-nucleosomes with several histone tail acetylation states and analyzed histone tail interactions with DNA by performing molecular simulations at an unprecedentedly high resolution. We found versatile acetylation-dependent landscapes of tri-nucleosome. The H4 and H2A tail acetylation reduced the contact between the first and third nucleosomes mediated by the histone tails. The H3 tail acetylation reduced its interaction with neighboring linker DNAs resulting in increase of the distance between consecutive nucleosomes. Notably, two copies of the same histone in a single nucleosome have markedly asymmetric interactions with DNAs, suggesting specific pattern of nucleosome docking albeit high inherent flexibility. Estimated transcription factor accessibility was significantly high for the H4 tail acetylated structures. PMID:27698366

  4. Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics

    PubMed Central

    Ben Imeddourene, Akli; Elbahnsi, Ahmad; Guéroult, Marc; Oguey, Christophe; Foloppe, Nicolas; Hartmann, Brigitte

    2015-01-01

    The accurate prediction of the structure and dynamics of DNA remains a major challenge in computational biology due to the dearth of precise experimental information on DNA free in solution and limitations in the DNA force-fields underpinning the simulations. A new generation of force-fields has been developed to better represent the sequence-dependent B-DNA intrinsic mechanics, in particular with respect to the BI ↔ BII backbone equilibrium, which is essential to understand the B-DNA properties. Here, the performance of MD simulations with the newly updated force-fields Parmbsc0εζOLI and CHARMM36 was tested against a large ensemble of recent NMR data collected on four DNA dodecamers involved in nucleosome positioning. We find impressive progress towards a coherent, realistic representation of B-DNA in solution, despite residual shortcomings. This improved representation allows new and deeper interpretation of the experimental observables, including regarding the behavior of facing phosphate groups in complementary dinucleotides, and their modulation by the sequence. It also provides the opportunity to extensively revisit and refine the coupling between backbone states and inter base pair parameters, which emerges as a common theme across all the complementary dinucleotides. In sum, the global agreement between simulations and experiment reveals new aspects of intrinsic DNA mechanics, a key component of DNA-protein recognition. PMID:26657165

  5. Swimming patterns and dynamics of simulated Escherichia coli bacteria.

    PubMed

    Zonia, Laura; Bray, Dennis

    2009-11-01

    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.

  6. 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

  7. 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.

  8. High speed simulation of flexible multibody dynamics

    NASA Technical Reports Server (NTRS)

    Jacot, A. D.; Jones, R. E.; Juengst, C. D.

    1987-01-01

    A multiflexible body dynamics code intended for fast turnaround control design trades is described. Nonlinear rigid body dynamics and linearized flexible dynamics combine to provide efficient solution of the equations of motion. Comparison with results from the DISCOS code provide verification of accuracy.

  9. 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.

  10. Mechanics of severing for large microtubule complexes revealed by coarse-grained simulations

    NASA Astrophysics Data System (ADS)

    Theisen, Kelly E.; Desai, Neha J.; Volski, Allison M.; Dima, Ruxandra I.

    2013-09-01

    We investigate the mechanical behavior of microtubule (MT) protofilaments under the action of bending forces, ramped up linearly in time, to provide insight into the severing of MTs by microtubule associated proteins (MAPs). We used the self-organized polymer model which employs a coarse-grained description of the protein chain and ran Brownian dynamics simulations accelerated on graphics processing units that allow us to follow the dynamics of a MT system on experimental timescales. Our study focused on the role played in the MT depolymerization dynamics by the inter-tubulin contacts a protofilament experiences when embedded in the MT lattice, and the number of binding sites of MAPs on MTs. We found that proteins inducing breaking of MTs must have at least three attachment points on any tubulin dimer from an isolated protofilament. In contrast, two points of contact would suffice when dimers are located in an intact MT lattice, in accord with experimental findings on MT severing proteins. Our results show that confinement of a protofilament in the MT lattice leads to a drastic reduction in the energy required for the removal of tubulin dimers, due to the drastic reduction in entropy. We further showed that there are differences in the energetic requirements based on the location of the dimer to be removed by severing. Comparing the energy of tubulin dimers removal revealed by our simulations with the amount of energy resulting from one ATP hydrolysis, which is the source of energy for all MAPs, we provided strong evidence for the experimental finding that severing proteins do not bind uniformly along the MT wall.

  11. Simulating fiction: individual differences in literature comprehension revealed with FMRI.

    PubMed

    Nijhof, Annabel D; Willems, Roel M

    2015-01-01

    When we read literary fiction, we are transported to fictional places, and we feel and think along with the characters. Despite the importance of narrative in adult life and during development, the neurocognitive mechanisms underlying fiction comprehension are unclear. We used functional magnetic resonance imaging (fMRI) to investigate how individuals differently employ neural networks important for understanding others' beliefs and intentions (mentalizing), and for sensori-motor simulation while listening to excerpts from literary novels. Localizer tasks were used to localize both the cortical motor network and the mentalizing network in participants after they listened to excerpts from literary novels. Results show that participants who had high activation in anterior medial prefrontal cortex (aMPFC; part of the mentalizing network) when listening to mentalizing content of literary fiction, had lower motor cortex activity when they listened to action-related content of the story, and vice versa. This qualifies how people differ in their engagement with fiction: some people are mostly drawn into a story by mentalizing about the thoughts and beliefs of others, whereas others engage in literature by simulating more concrete events such as actions. This study provides on-line neural evidence for the existence of qualitatively different styles of moving into literary worlds, and adds to a growing body of literature showing the potential to study narrative comprehension with neuroimaging methods. PMID:25671708

  12. Simulating fiction: individual differences in literature comprehension revealed with FMRI.

    PubMed

    Nijhof, Annabel D; Willems, Roel M

    2015-01-01

    When we read literary fiction, we are transported to fictional places, and we feel and think along with the characters. Despite the importance of narrative in adult life and during development, the neurocognitive mechanisms underlying fiction comprehension are unclear. We used functional magnetic resonance imaging (fMRI) to investigate how individuals differently employ neural networks important for understanding others' beliefs and intentions (mentalizing), and for sensori-motor simulation while listening to excerpts from literary novels. Localizer tasks were used to localize both the cortical motor network and the mentalizing network in participants after they listened to excerpts from literary novels. Results show that participants who had high activation in anterior medial prefrontal cortex (aMPFC; part of the mentalizing network) when listening to mentalizing content of literary fiction, had lower motor cortex activity when they listened to action-related content of the story, and vice versa. This qualifies how people differ in their engagement with fiction: some people are mostly drawn into a story by mentalizing about the thoughts and beliefs of others, whereas others engage in literature by simulating more concrete events such as actions. This study provides on-line neural evidence for the existence of qualitatively different styles of moving into literary worlds, and adds to a growing body of literature showing the potential to study narrative comprehension with neuroimaging methods.

  13. 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…

  14. Molecular dynamics simulation of liquid water confined inside graphite channels: dielectric and dynamical properties.

    PubMed

    Martí, J; Nagy, G; Guàrdia, E; Gordillo, M C

    2006-11-30

    Electric and dielectric properties and microscopic dynamics of liquid water confined between graphite slabs are analyzed by means of molecular dynamics simulations for several graphite-graphite separations at ambient conditions. The electric potential across the interface shows oscillations due to water layering, and the overall potential drop is about -0.28 V. The total dielectric constant is larger than the corresponding value for the bulklike internal region of the system. This is mainly due to the preferential orientations of water nearest the graphite walls. Estimation of the capacitance of the system is reported, indicating large variations for the different adsorption layers. The main trend observed concerning water diffusion is 2-fold: on one hand, the overall diffusion of water is markedly smaller for the closest graphite-graphite separations, and on the other hand, water molecules diffuse in interfaces slightly slower than those in the bulklike internal areas. Molecular reorientational times are generally larger than those corresponding to those of unconstrained bulk water. The analysis of spectral densities revealed significant spectral shifts, compared to the bands in unconstrained water, in different frequency regions, and associated to confinement effects. These findings are important because of the scarce information available from experimental, theoretical, and computer simulation research into the dielectric and dynamical properties of confined water.

  15. 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.

  16. 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.

  17. Rhodopsin photoactivation dynamics revealed by quasi-elastic neutron scattering

    DOE PAGESBeta

    Bhowmik, Debsindhu; Shrestha, Utsab; Perera, Suchithranga M.d.c.; Chawla, Udeep; Mamontov, Eugene; Brown, Michael F.; Chu, Xiang -Qiang

    2015-01-27

    Rhodopsin is a G-protein-coupled receptor (GPCR) responsible for vision under dim light conditions. During rhodopsin photoactivation, the chromophore retinal undergoes cis-trans isomerization, and subsequently dissociates from the protein yielding the opsin apoprotein [1]. What are the changes in protein dynamics that occur during the rhodopsin photoactivation process? Here, we studied the microscopic dynamics of the dark-state rhodopsin and the ligand-free opsin using quasi-elastic neutron scattering (QENS). The QENS technique tracks the individual hydrogen atom motions in the protein molecules, because the neutron scattering cross-section of hydrogen is much higher than other atoms [2-4]. We used protein (rhodopsin/opsin) samples with CHAPSmore » detergent hydrated with heavy water. The solvent signal is suppressed due to the heavy water, so that only the signals from proteins and detergents are detected. The activation of proteins is confirmed at low temperatures up to 300 K by the mean-square displacement (MSD) analysis. Our QENS experiments conducted at temperatures ranging from 220 K to 300 K clearly indicate that the protein dynamic behavior increases with temperature. The relaxation time for the ligand-bound protein rhodopsin was longer 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 forms a band around the protein molecule in the micelle. Unlike the protein, the CHAPS detergent manifests localized motions that are the same as in the bulk empty micelles. Furthermore QENS provides unique understanding of the key dynamics involved in the activation of the GPCR involved in the visual process.« less

  18. Rhodopsin photoactivation dynamics revealed by quasi-elastic neutron scattering

    SciTech Connect

    Bhowmik, Debsindhu; Shrestha, Utsab; Perera, Suchithranga M.d.c.; Chawla, Udeep; Mamontov, Eugene; Brown, Michael F.; Chu, Xiang -Qiang

    2015-01-27

    Rhodopsin is a G-protein-coupled receptor (GPCR) responsible for vision under dim light conditions. During rhodopsin photoactivation, the chromophore retinal undergoes cis-trans isomerization, and subsequently dissociates from the protein yielding the opsin apoprotein [1]. What are the changes in protein dynamics that occur during the rhodopsin photoactivation process? Here, we studied the microscopic dynamics of the dark-state rhodopsin and the ligand-free opsin using quasi-elastic neutron scattering (QENS). The QENS technique tracks the individual hydrogen atom motions in the protein molecules, because the neutron scattering cross-section of hydrogen is much higher than other atoms [2-4]. We used protein (rhodopsin/opsin) samples with CHAPS detergent hydrated with heavy water. The solvent signal is suppressed due to the heavy water, so that only the signals from proteins and detergents are detected. The activation of proteins is confirmed at low temperatures up to 300 K by the mean-square displacement (MSD) analysis. Our QENS experiments conducted at temperatures ranging from 220 K to 300 K clearly indicate that the protein dynamic behavior increases with temperature. The relaxation time for the ligand-bound protein rhodopsin was longer 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 forms a band around the protein molecule in the micelle. Unlike the protein, the CHAPS detergent manifests localized motions that are the same as in the bulk empty micelles. Furthermore QENS provides unique understanding of the key dynamics involved in the activation of the GPCR involved in the visual process.

  19. Sub-structure of laser generated harmonics reveals plasma dynamics of a relativistically oscillating mirror

    SciTech Connect

    Braenzel, J.; Schnürer, M.; Steinke, S.; Priebe, G.; Sandner, W.; Andreev, A.; Platonov, K.

    2013-08-15

    Theoretical and experimental investigations of the dynamics of a relativistically oscillating plasma slab reveal spectral line splitting in laser driven harmonic spectra, leading to double harmonic series. Both series are well characterized with harmonics arising by two fundamental frequencies. While a relativistic oscillation of the critical density drives the harmonic emission, the splitting is a result of an additional acceleration during the laser pulse duration. In comparison with the oscillatory movement, this acceleration is rather weak and can be described by a plasma shock wave driven by the pressure of light. We introduce particle in cell simulations and an analytical model explaining the harmonic line splitting. The derived analytical formula gives direct access between the splitting in the harmonic spectrum and the acceleration of the plasma surface.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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

  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. 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.

  8. 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.

  9. The conformational transition pathway of ATP binding cassette transporter MsbA revealed by atomistic simulations.

    PubMed

    Weng, Jing-Wei; Fan, Kang-Nian; Wang, Wen-Ning

    2010-01-29

    ATP binding cassette transporters are integral membrane proteins that use the energy released from ATP hydrolysis at the two nucleotide binding domains (NBDs) to translocate a wide variety of substrates through a channel at the two transmembrane domains (TMDs) across the cell membranes. MsbA from Gram-negative bacteria is a lipid and multidrug resistance ATP binding cassette exporter that can undergo large scale conformational changes between the outward-facing and the inward-facing conformations revealed by crystal structures in different states. Here, we use targeted molecular dynamics simulation methods to explore the atomic details of the conformational transition from the outward-facing to the inward-facing states of MsbA. The molecular dynamics trajectories revealed a clear spatiotemporal order of the conformational movements. The disruption of the nucleotide binding sites at the NBD dimer interface is the very first event that initiates the following conformational changes, verifying the assumption that the conformational conversion is triggered by ATP hydrolysis. The conserved x-loops of the NBDs were identified to participate in the interaction network that stabilizes the cytoplasmic tetrahelix bundle of the TMDs and play an important role in mediating the cross-talk between the NBD and TMD. The movement of the NBD dimer is transmitted through x-loops to break the tetrahelix bundle, inducing the packing rearrangements of the transmembrane helices at the cytoplasmic side and the periplasmic side sequentially. The packing rearrangement within each periplasmic wing of TMD that results in exposure of the substrate binding sites occurred at the end stage of the trajectory, preventing the wrong timing of the binding site accessibility.

  10. 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.

  11. Near-membrane protein dynamics revealed by evanescent field microscopy

    NASA Astrophysics Data System (ADS)

    Bezzerides, Vassilios J.; Clapham, David E.

    2004-05-01

    Evanescent Field (EF) microscopy is used to investigate the spatial and temporal dynamics of proteins in living cells. A genetically engineered ion channel fused to a fluorescent tag is expressed in cells and imaged with an objective-based EF microscope. Images are obtained from a CCD and analyzed to determine fluorescence and velocity of individual protein containing vesicles. An inverse correlation between fluorescent intensity and average motility provides a method for determination of membrane localization. Stimulation and subsequent decrease in ion channel activity is correlated with loss of protein from membrane as shown by EF microscopy and patch-clamp electrophysiology.

  12. Better HMC integrators for dynamical simulations

    SciTech Connect

    M.A. Clark, Balint Joo, A.D. Kennedy, P.J. Silva

    2010-06-01

    We show how to improve the molecular dynamics step of Hybrid Monte Carlo, both by tuning the integrator using Poisson brackets measurements and by the use of force gradient integrators. We present results for moderate lattice sizes.

  13. 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.

  14. 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

  15. Energetics and dynamics in MbCN: CN--vibrational relaxation from molecular dynamics simulations.

    PubMed

    Danielsson, Jonas; Meuwly, Markus

    2007-01-11

    The dynamics of the cyanide anion bound to sperm-whale myoglobin is investigated using atomistic simulations. With density-functional theory, a 2D potential energy surface for the cyanide-heme complex is calculated. Two deep minima with a stabilization energy of approximately 50 kcal/mol corresponding to two different binding orientations (Fe-CN and Fe-NC) of the ligand are found. The Fe-CN conformation is favored over Fe-NC by several kcal/mol. Mixed quantum mechanics/molecular mechanics calculations show that the binding orientation affects the bond strength of the ligand, with a significantly different bond length and a 25 cm-1 shift in the fundamental CN-frequency. For the molecular dynamics (MD) simulations, a 3-center fluctuating charge model for the Fe-CN unit is developed that captures polarization and ligand-metal charge transfer. Stability arguments based on the energetics around the active site and the CN- frequency shifts suggest that the Fe-CN conformation with epsilon-protonation of His epsilon 64 are most likely, which is in agreement with experiment. Both equilibrium and nonequilibrium MD simulations are carried out to investigate the relaxation time scale and possible relaxation pathways in bound MbCN. The nonequilibrium MD simulations with a vibrationally excited ligand reveal that vibrational relaxation takes place on a time scale of hundreds of picoseconds within the active site. This finding supports the hypothesis that the experimentally observed relaxation rate (3.6 ps) reflects the repopulation of the electronic ground state.

  16. 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.

  17. 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

  18. 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

  19. Large-Scale Hybrid Dynamic Simulation Employing Field Measurements

    SciTech Connect

    Huang, Zhenyu; Guttromson, Ross T.; Hauer, John F.

    2004-06-30

    Simulation and measurements are two primary ways for power engineers to gain understanding of system behaviors and thus accomplish tasks in system planning and operation. Many well-developed simulation tools are available in today's market. On the other hand, large amount of measured data can be obtained from traditional SCADA systems and currently fast growing phasor networks. However, simulation and measurement are still two separate worlds. There is a need to combine the advantages of simulation and measurements. In view of this, this paper proposes the concept of hybrid dynamic simulation which opens up traditional simulation by providing entries for measurements. A method is presented to implement hybrid simulation with PSLF/PSDS. Test studies show the validity of the proposed hybrid simulation method. Applications of such hybrid simulation include system event playback, model validation, and software validation.

  20. 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.

  1. Dynamic simulator for anaerobic digestion processes.

    PubMed

    Kleinstreuer, C; Poweigha, T

    1982-09-01

    A transient, two-culture model simulating methane production from biomass has been developed. The simulator, based partially on the work by Andrews and McCarty, is capable of calculating the hydrolysis products of several common organic materials, accommodating various substrate feeding modes, and simulating the transient physico-biochemical transport and conversion processes occurring in the biological, liquid, and gaseous phases of a well-mixed reactor. The mathematical representation of this bioconversion system consists of a set of 11 coupled, nonlinear first-order rate equations based on the principles of mass conservation and biochemical reaction kinetics. The model can be used in conjunction with laboratory investigations and as a simulator for evaluating process control strategies and cost developments.

  2. The Dynamical Structure of Planetary Nebulae Revealed by Gaia

    NASA Astrophysics Data System (ADS)

    Walton, Nicholas; Rejkuba, Marina; Walsh, Jeremy

    2015-08-01

    Planetary Nebulae (PN) are a brief evolutionary stage through which low and intermediate mass stars pass towards the end of their evolution, between red giant and white dwarf. They play an important role in the processing of a number of elements into the surrounding interstellar medium. They act as useful probes of kinematical structure of the Milky Way, and provide insights into the chemical evolution history of the Galaxy. Understanding the global role of PN is limited due to large uncertainties in individual distances and to a detailed knowledge of the dynamics of their nebulae. These factors in turn constrain the absolute parameters of PN, such as their sizes, luminosities, masses, lifetimes and determination of the overall Galactic PN population.The ESA Gaia satellite was launched in December 2013. Over the 5 years of its nominal mission it will map the positions, motions, and parallaxes (hence distances) to some billion stars in the Milky Way. It is sensitive to objects to a limiting Gaia magnitude of G=20.7, achieving parallax errors of a few tens of microarcsecs for G=15 Solar type stars.Gaia is optimised for the detection of point sources, and in general is not sensitive to extended objects (with sizes >0.5 arcsec). However, Gaia is able to resolve structure within extended objects, with the sampling points enabling a detailed view of extended structure. This is demonstrated by early observations of the large PN NGC 6543, where the complex nebula is decomposed by Gaia into thousands of individual mapping points. With nominal lifetime Gaia astrometry, it will be possible to accurately map the evolution of the plane of sky expansion of NGC 6543 and from line of sight velocities, the complex dynamical structure of the expanding nebula.In this presentation, we will discuss the potential of Gaia in mapping the complex dynamics of many extended Galactic PN throughout the Milky Way. This will set precise limits on the expansion rates in a representative sample of

  3. 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

  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. 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

  7. 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.

  8. Revealing the dynamics of polymicrobial infections: implications for antibiotic therapy

    PubMed Central

    Rogers, Geraint B.; Hoffman, Lucas R.; Whiteley, Marvin; Daniels, Thomas W.V.; Carroll, Mary P.; Bruce, Kenneth D.

    2011-01-01

    As a new generation of culture-independent analytical strategies emerge, the amount of data on polymicrobial infections will increase dramatically. For these data to inform clinical thinking, and in turn to maximise benefits for patients, an appropriate framework for their interpretation is required. Here, we use cystic fibrosis (CF) lower airway infections as a model system to examine how conceptual and technological advances can address two clinical questions that are central to improved management of CF respiratory disease. Firstly, can markers of the microbial community be identified that predict a change in infection dynamics and clinical outcomes? Secondly, can these new strategies directly characterize the impact of antimicrobial therapies, allowing treatment efficacy to be both assessed and optimized? PMID:20554204

  9. New Autophagy Reporter Mice Reveal Dynamics of Proximal Tubular Autophagy

    PubMed Central

    Li, Ling; Wang, Zhao V.

    2014-01-01

    The accumulation of autophagosomes in postischemic kidneys may be renoprotective, but whether this accumulation results from the induction of autophagy or from obstruction within the autophagic process is unknown. Utilizing the differential pH sensitivities of red fluorescent protein (RFP; pKa 4.5) and enhanced green fluorescent protein (EGFP; pKa 5.9), we generated CAG-RFP-EGFP-LC3 mice to distinguish early autophagic vacuoles from autolysosomes. In vitro and in vivo studies confirmed that in response to nutrient deprivation, renal epithelial cells in CAG-RFP-EGFP-LC3 mice produce autophagic vacuoles expressing RFP and EGFP puncta. EGFP fluorescence diminished substantially in the acidic environment of the autolysosomes, whereas bright RFP signals remained. Under normal conditions, nephrons expressed few EGFP and RFP puncta, but ischemia-reperfusion injury (IRI) led to dynamic changes in the proximal tubules, with increased numbers of RFP and EGFP puncta that peaked at 1 day after IRI. The number of EGFP puncta returned to control levels at 3 days after IRI, whereas the high levels of RFP puncta persisted, indicating autophagy initiation at day 1 and autophagosome clearance during renal recovery at day 3. Notably, proliferation decreased in cells containing RFP puncta, suggesting that autophagic cells are less likely to divide for tubular repair. Furthermore, 87% of proximal tubular cells with activated mechanistic target of rapamycin (mTOR), which prevents autophagy, contained no RFP puncta. Conversely, inhibition of mTOR complex 1 induced RFP and EGFP expression and decreased cell proliferation. In summary, our results highlight the dynamic regulation of autophagy in postischemic kidneys and suggest a role of mTOR in autophagy resolution during renal repair. PMID:24179166

  10. Cyclic dynamics in simulated plant populations.

    PubMed Central

    Bauer, Silke; Berger, Uta; Hildenbrandt, Hanno; Grimm, Volker

    2002-01-01

    Despite the general interest in nonlinear dynamics in animal populations, plant populations are supposed to show a stable equilibrium that is attributed to fundamental differences compared with animals. Some studies find more complex dynamics, but empirical studies usually are too short and most modelling studies ignore important spatial aspects of local competition and establishment. Therefore, we used a spatially explicit individual-based model of a hypothetical, non-clonal perennial to explore which mechanisms might generate complex dynamics, i.e. cycles. The model is based on the field-of-neighbourhood approach that describes local competition and establishment in a phenomenological manner. We found cyclic population dynamics for a wide spectrum of model variants, provided that mortality is determined by local competition and recruitment is virtually completely suppressed within the zone of influence of established plants. This destabilizing effect of local processes within plant populations might have wide-ranging implications for the understanding of plant community dynamics and coexistence. PMID:12495487

  11. 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

  12. Dynamics of nitrogen dissociation from direct molecular simulation

    NASA Astrophysics Data System (ADS)

    Valentini, Paolo; Schwartzentruber, Thomas E.; Bender, Jason D.; Candler, Graham V.

    2016-08-01

    dissociating nitrogen systems involving both atomic and molecular nitrogen. Such direct comparisons also illustrate how the DMS method is able to reveal all relevant nonequilibrium physics without the need to compute large numbers of state-transition probabilities. In this manner, DMS presents an accurate and tractable approach to construct models for direct-simulation Monte Carlo and computational fluid dynamics simulations from first principles.

  13. 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.

  14. Exploration of ice growth through molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Rozmanov, Dmitri

    Ice is the solid form of water, the most important chemical compound for life. A large number of atmospherically and biologically relevant processes occur at interfaces between these two phases. At the molecular level, crystallization in general, and ice growth in particular, is a less complex example of a natural process of self-assembling, where an ordered crystal is created from a disordered and mobile liquid. This thesis describes efforts to extend our understanding of the process of ice crystal growth by employing the technique of molecular simulations. Molecular simulations have become a de facto standard for these kinds of studies due to fundamental technical difficulties for experimental methods to probe growing interfaces. The study described in this thesis was done as a series of self-contained and relatively independent investigations linked together by one general goal of extending our understanding of the ice growth process. A new general simulation code was developed to answer technical demands of the project. This simulation code was used to perform all the simulations reported in here. The formal development necessary for this work lead to the publication of two new methods of integration of rotational equations of motion, as well as new simulation and data analysis techniques. An investigation of the diffusive behaviour of the TIP4P-2005 model of water was necessary for interpretation of our initial ice growth study and resulted in another research project component; which results provided information necessary for the analysis of ice growth kinetics and also revealed new details of the translational and rotational dynamics of the TIP4P-2005 model in liquid phase. The main body of work directly addressing the primary objective of the project, the process of ice growth, was done as four separate simulation studies which are described in this thesis in detail. The main results of this thesis can be summarized as follows. The molecular dynamics

  15. 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.

  16. Bridging fluctuating hydrodynamics and molecular dynamics simulations of fluids.

    PubMed

    Voulgarakis, Nikolaos K; Chu, Jhih-Wei

    2009-04-01

    A new multiscale coarse-graining (CG) methodology is developed to bridge molecular and hydrodynamic models of a fluid. The hydrodynamic representation considered in this work is based on the equations of fluctuating hydrodynamics (FH). The essence of this method is a mapping from the position and velocity vectors of a snapshot of a molecular dynamics (MD) simulation to the field variables on Eulerian cells of a hydrodynamic representation. By explicit consideration of the effective lengthscale d(mol) that characterizes the volume of a molecule, the computed density fluctuations from MD via our mapping procedure have volume dependence that corresponds to a grand canonical ensemble of a cold liquid even when a small cell length (5-10 A) is used in a hydrodynamic representation. For TIP3P water at 300 K and 1 atm, d(mol) is found to be 2.4 A, corresponding to the excluded radius of a water molecule as revealed by its center-of-mass radial distribution function. By matching the density fluctuations and autocorrelation functions of momentum fields computed from solving the FH equations with those computed from MD simulation, the sound velocity and shear and bulk viscosities of a CG hydrodynamic model can be determined directly from MD. Furthermore, a novel staggered discretization scheme is developed for solving the FH equations of an isothermal compressive fluid in a three dimensional space with a central difference method. This scheme demonstrates high accuracy in satisfying the fluctuation-dissipation theorem. Since the causative relationship between field variables and fluxes is captured, we demonstrate that the staggered discretization scheme also predicts correct physical behaviors in simulating transient fluid flows. The techniques presented in this work may also be employed to design multiscale strategies for modeling complex fluids and macromolecules in solution. PMID:19355721

  17. Modes of embayed beach dynamics: analysis reveals emergent timescales

    NASA Astrophysics Data System (ADS)

    Murray, K. T.; Murray, A.; Limber, P. W.; Ells, K. D.

    2013-12-01

    Embayed beaches, or beaches positioned between rocky headlands, exhibit morphologic changes over many length and time scales. Beach sediment is transported as a result of the day-to-day wave forcing, causing patterns of erosion and accretion. We use the Rocky Coastline Evolution Model (RCEM) to investigate how patterns of shoreline change depend on wave climate (the distribution of wave-approach angles) and beach characteristics. Measuring changes in beach width through time allows us to track the evolution of the shape of the beach and the movement of sand within it. By using Principle Component Analysis (PCA), these changes can be categorized into modes, where the first few modes explain the majority of the variation in the time series. We analyze these modes and how they vary as a function of wave climate and headland/bay aspect ratio. In the purposefully simple RCEM, sediment transport is wave-driven and affected by wave shadowing behind the headlands. The rock elements in our model experiments (including the headlands) are fixed and unerodable so that this analysis can focus purely on sand dynamics between the headlands, without a sand contribution from the headlands or cliffs behind the beach. The wave climate is characterized by dictating the percentage of offshore waves arriving from the left and the percentage of waves arriving from high angles (very oblique to the coastline orientation). A high-angle dominated wave climate tends to amplify coastline perturbations, whereas a lower-angle wave climate is diffusive. By changing the headland/bay aspect ratio and wave climate, we can perform PCA analysis of generalized embayed beaches with differing anatomy and wave climate forcings. Previous work using PCA analysis of embayed beaches focused on specific locations and shorter timescales (<30 years; Short and Trembanis, 2004). By using the RCEM, we can more broadly characterize beach dynamics over longer timescales. The first two PCA modes, which explain a

  18. 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.

  19. Intermyofilament dynamics of myocytes revealed by second harmonic generation microscopy.

    PubMed

    Prent, Nicole; Green, Chantal; Greenhalgh, Catherine; Cisek, Richard; Major, Arkady; Stewart, Bryan; Barzda, Virginijus

    2008-01-01

    Drosophila melanogaster larva myocytes are imaged with second harmonic generation (SHG) microscopy undergoing forced stretching and rhythmic contractions to determine the nature of the SHG signal. During stretching, double peaked SHG profiles of the anisotropic (A-) bands evolve into single peaks with a higher SHG intensity. The dip in the intensity profile at the center of the A-band is attributed to destructive interference from out-of-phase second harmonic radiating myosin molecules that, in the central region of myofilaments, are arranged antiparallel. An intensity increase at the center of the A-band appears during forced stretching due to a small, less than 100 nm, intermyofilament separation of the antiparallel myosin molecules leading to constructive interference of the SHG radiation. In addition, the same phenomenon occurs during periodic contractions of the myocyte, where an SHG intensity increase with the lengthening of sarcomeres is observed. The SHG intensity dependence on sarcomere length can be used for imaging myocyte contractions with low resolution microscopy, and can be applied for the development of diagnostic tools where monitoring of muscle contraction dynamics is required.

  20. 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

  1. Alternative variable transformation for simulation of multibody dynamic systems

    NASA Astrophysics Data System (ADS)

    Yang, Li-Farn

    1995-03-01

    An alternative variable transformation is proposed and analyzed for the simulation of multibody dynamic systems. The developed alternative variable transformation matrix intended to work directly with the multibody equations of motion without altering the inherent dynamic characteristics also eliminates the need for expensive computation of inversion of a large mass matrix required for the simulation of multibody dynamic systems. From the analytical derivation of an articulated multibody model, it was found that the computation can be saved (3n + 1/4)-fold due to the computational merits associated with the band matrix.

  2. 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.

  3. SLM-based optical simulator for dynamic speckle analysis

    NASA Astrophysics Data System (ADS)

    Berberova, Nataliya; Stoykova, Elena; Ivanov, Branimir

    2014-08-01

    The phenomenon of dynamic speckle allows for non-invasive whole-field detection of physical or biological activity in objects through statistical description of laser speckle dynamics. Effective way to improve the statistical analysis is generation of controlled speckle patterns. SLM implementation of an optical simulator of dynamic speckle patterns is proposed by feeding a correlated sequence of 2D random phase distributions to the phase-only SLM. Atthevarying in space correlation radius of the phase fluctuations in the successive frames, the SLM produces regions of different activity on a screen under laser illumination. Feasibility of the proposed approach is proved both by simulation and experiment.

  4. CQESTR Simulations of soil organic carbon dynamics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A processed-based carbon (C) model, CQESTR (sequester), was used to predict soil organic carbon (SOC) dynamics and examine the effect of agricultural management practices on SOC accretion in three diverse regions of the USA. The three regions chosen had long-term experiments (LTEs) ranging from 23 t...

  5. 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.

  6. AceCloud: Molecular Dynamics Simulations in the Cloud.

    PubMed

    Harvey, M J; De Fabritiis, G

    2015-05-26

    We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

  7. 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).

  8. 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.

  9. Test and validation for robot arm control dynamics simulation

    NASA Technical Reports Server (NTRS)

    Yae, K. Harold; Kim, Sung-Soo; Haug, Edward J.; Seering, Warren; Sundaram, Kamala; Thompson, Bruce; Turner, James; Chun, Hon; Frisch, Harold P.; Schnurr, Richard

    1989-01-01

    The Flight Telerobotic Servicer (FTS) program will require an ability to develop, in a cost effective manner, many simulation models for design, analysis, performance evaluation, and crew training. Computational speed and the degree of modeling fidelity associated with each simulation must be commensurate with problem objectives. To demonstrate evolving state-of-the-art general purpose multibody modeling capabilities, to validate these by laboratory testing, and to expose their modeling shortcomings, two focus problems at the opposite ends of the simulation spectrum are defined: (1) Coarse Acquisition Control Dynamics. Create a real time man-in-the-control-loop simulator. Provide animated graphical display of robot arm dynamics and tactile feedback sufficient for cueing the operator. Interface simulator software with human operated tactile feedback controller; i.e., the Kraft mini-master. (2) Fine, Precision Mode Control Dynamics. Create a high speed, high fidelity simulation model for the design, analysis, and performance evaluation of autonomous 7 degree-of-freedom (DOF) trajectory control algorithms. This model must contain detail dynamic models for all significant dynamics elements within the robot arm, such as joint drive mechanisms.

  10. 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.

  11. 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…

  12. 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...

  13. 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

  14. 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.

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

    PubMed

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

    2015-05-19

    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.

  16. 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.

  17. Persistent predator–prey dynamics revealed by mass extinction

    PubMed Central

    Sallan, Lauren Cole; Kammer, Thomas W.; Ausich, William I.; Cook, Lewis A.

    2011-01-01

    Predator–prey interactions are thought by many researchers to define both modern ecosystems and past macroevolutionary events. In modern ecosystems, experimental removal or addition of taxa is often used to determine trophic relationships and predator identity. Both characteristics are notoriously difficult to infer in the fossil record, where evidence of predation is usually limited to damage from failed attacks, individual stomach contents, one-sided escalation, or modern analogs. As a result, the role of predation in macroevolution is often dismissed in favor of competition and abiotic factors. Here we show that the end-Devonian Hangenberg event (359 Mya) was a natural experiment in which vertebrate predators were both removed and added to an otherwise stable prey fauna, revealing specific and persistent trophic interactions. Despite apparently favorable environmental conditions, crinoids diversified only after removal of their vertebrate consumers, exhibiting predatory release on a geological time scale. In contrast, later Mississippian (359–318 Mya) camerate crinoids declined precipitously in the face of increasing predation pressure from new durophagous fishes. Camerate failure is linked to the retention of obsolete defenses or “legacy adaptations” that prevented coevolutionary escalation. Our results suggest that major crinoid evolutionary phenomena, including rapid diversification, faunal turnover, and species selection, might be linked to vertebrate predation. Thus, interactions observed in small ecosystems, such as Lotka-Volterra cycles and trophic cascades, could operate at geologic time scales and higher taxonomic ranks. Both trophic knock-on effects and retention of obsolete traits might be common in the aftermath of predator extinction. PMID:21536875

  18. 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.

  19. 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

  20. Simulations of the dynamics of entangled polymer melts

    NASA Astrophysics Data System (ADS)

    McCormick, Julie Ann

    2002-04-01

    The objective of this thesis is to increase our understanding of the basic physical principles governing the dynamics of entangled polymer melts. Discontinuous molecular dynamics simulations are performed on dense systems containing 32 hard chains of length 192 to investigate their dynamic properties. The mean squared displacements of the chain center of mass, the inner, outer, and intermediate segments along the chain, the end-to-end vector autocorrelation function, and the apparent self-diffusion coefficient are calculated over the course of the simulations. First, the relaxation and release of entanglements is compared with that predicted by the tube model and that associated with the release of interchain entanglements, or knots. The initial relaxation of chain segments occurs from the ends toward the middle as the tube model predicts; however, the final relaxation occurs at the chain ends, compatible with interchain entanglement release. The results provide evidence for a proposed mechanism of interchain entanglement relaxation consisting of initial relaxation, memory, and final release from a chain end. Next, the effect of position along the chain on the segmental mean squared displacement is investigated. The results reveal that small blocks provide a greater difference between the mean squared displacements of middle blocks, end blocks, and the whole chain than larger equal-sized blocks. A large portion of the chain displays middle behavior, while a small portion displays end behavior. The relaxation of small blocks of segments along the chain starts at the chain ends and progresses toward the chain middle. Finally, the time scale is extended, and the diffusive and stress relaxation behaviors of individual chains are explored. Increased time averaging causes the anomalous relaxation-memory-release behavior to smooth out of the system results; however, anomalous behavior is still exhibited by individual chains. They display super-diffusive, diffusive, and

  1. Hybrid Dynamics Simulation Engine for Metalloproteins

    PubMed Central

    Sparta, Manuel; Shirvanyants, David; Ding, Feng; Dokholyan, Nikolay V.; Alexandrova, Anastassia N.

    2012-01-01

    Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete molecular dynamics (DMD) (QM/DMD). DMD samples the entire protein, including the backbone, and most of the active site, except for the immediate coordination region of the metal. QM operates on the part of the protein of electronic and chemical significance, which may include tens to hundreds of atoms. The breathing quantum-classical boundary provides a continuous mutual feedback between the two machineries. We test QM/DMD using the Fe-containing electron transporter protein, rubredoxin, and its three mutants as a model. QM/DMD can provide a reliable balanced description of metalloproteins’ structure, dynamics, and electronic structure in a reasonable amount of time. As an illustration of QM/DMD capabilities, we then predict the structure of the Ca2+ form of the enzyme catechol O-methyl transferase, which, unlike the native Mg2+ form, is catalytically inactive. The Mg2+ site is ochtahedral, but the Ca2+ is 7-coordinate and features the misalignment of the reacting parts of the system. The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight. PMID:22947938

  2. Quantum simulation of dynamical maps with trapped ions

    NASA Astrophysics Data System (ADS)

    Schindler, P.; Müller, M.; Nigg, D.; Barreiro, J. T.; Martinez, E. A.; Hennrich, M.; Monz, T.; Diehl, S.; Zoller, P.; Blatt, R.

    2013-06-01

    Dynamical maps describe general transformations of the state of a physical system--their iteration interpreted as generating a discrete time evolution. Prime examples include classical nonlinear systems undergoing transitions to chaos. Quantum mechanical counterparts show intriguing phenomena such as dynamical localization on the single-particle level. Here we extend the concept of dynamical maps to a many-particle context, where the time evolution involves both coherent and dissipative elements: we experimentally explore the stroboscopic dynamics of a complex many-body spin model with a universal trapped ion quantum simulator. We generate long-range phase coherence of spin by an iteration of purely dissipative quantum maps and demonstrate the characteristics of competition between combined coherent and dissipative non-equilibrium evolution--the hallmark of a previously unobserved dynamical phase transition. We assess the influence of experimental errors in the quantum simulation and tackle this problem by developing an efficient error detection and reduction toolbox based on quantum feedback.

  3. Comparison of mode-coupling theory with molecular dynamics simulations from a unified point of view.

    PubMed

    Narumi, Takayuki; Tokuyama, Michio

    2011-08-01

    We study the tagged-particle dynamics by solving equations of the mode-coupling theory (MCT). The numerical solutions are compared with results obtained by the molecular dynamics (MD) simulations from a unified point of view proposed by Tokuyama [Phys. Rev. E 80, 031503 (2009)]. We propose a way of comparison in which the reduced long-time self-diffusion coefficient is used to characterize states of the system. The comparison reveals that the tagged-particle dynamics calculated from MCT qualitatively deviates from that obtained by MD. Our results suggest that the deviation originates from the starting equation of MCT.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. The role of hydrogen bonds in an aqueous solution of acetylsalicylic acid: a molecular dynamics simulation study.

    PubMed

    Donnamaria, Maria Cristina; de Xammar Oro, Juan Roberto

    2011-10-01

    This work focuses on the role of the dynamic hydrogen bonds (HB) formed in an aqueous solution of aspirin using molecular dynamics simulation. The statistics reveal the existence of internal HB that inhibit the rotational movements of the acetyl and the carboxylic acid groups, forcing the molecule to adopt a closed conformer structure in water, and playing an important role in stabilizing this conformation.

  10. An approach to validation of a leg simulation by the comparison of two dynamic models.

    PubMed

    Cocatre-Zilgien, J H; Delcomyn, F; Hall, L V; Pijanowski, G J

    1995-05-01

    The dynamics of a jointed leg were simulated using two different models, one based on a recursive Newton-Euler method and one on a closed-form Lagrange method. To validate the models, the simulations were run in parallel and the intermediate steps and output of the two methods were compared to one another to reveal the presence and locations of errors. Sources of error and the use of this method for the detection of errors are discussed. Some errors could not have been detected using only a single simulation.

  11. 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.

  12. Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study

    PubMed Central

    Wan, Hua; Chang, Shan; Hu, Jian-ping; Tian, Xu-hong

    2016-01-01

    TAL effectors (TALEs) contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations for the crystal structure of DNA-bound TALE AvrBs3 lacking the last half repeat and its modeled structure having the last half repeat. The structural stability analysis indicates that the modeled system is more stable than the nonmodeled system. Based on the principle component analysis, it is found that the AvrBs3 increases its structural compactness in the presence of the last half repeat. The comparison of DNA groove parameters of the two systems implies that the last half repeat also causes the change of DNA major groove binding efficiency. The following calculation of hydrogen bond reveals that, by stabilizing the phosphate binding with DNA at the C-terminus, the last half repeat helps to adopt a compact conformation at the protein-DNA interface. It further mediates more contacts between TAL repeats and DNA nucleotide bases. Finally, we suggest that the last half repeat is required for the high-efficient recognition of DNA by TALE. PMID:27803930

  13. Quantum simulation of non-equilibrium dynamical maps with trapped ions

    NASA Astrophysics Data System (ADS)

    Schindler, Philipp; Müller, Markus; Nigg, Daniel; Monz, Thomas; Barreiro, Julio; Martinez, Esteban; Hennrich, Markus; Diehl, Sebastian; Zoller, Peter; Blatt, Rainer

    2013-03-01

    Dynamical maps are central for the understanding of general state transformations of physical systems. Prime examples include classical nonlinear systems undergoing transitions to chaos, or single particle quantum mechanical counterparts showing intriguing phenomena such as dynamical localization. Here, we extend the concept of dynamical maps to an open-system, many-particle context and experimentally explore the stroboscopic dynamics of a complex many-body spin model in a universal quantum simulator using up to five ions. We generate quantum mechanical long range order by an iteration of purely dissipative maps, reveal the characteristic features of a combined coherent and dissipative non-equilibrium evolution, and develop and implement various error detection and reduction techniques that will facilitate the faithful quantum simulation of larger systems.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. Homology model and molecular dynamics simulation of carp ovum cystatin.

    PubMed

    Su, Yuan-Chen; Lin, Jin-Chung; Liu, Hsuan-Liang

    2005-01-01

    In this study, a homology model of carp ovum cystatin was constructed based on the crystal structure of chicken egg white cystatin. The results of amino acid sequence alignment indicate that these two proteins exhibit 36.11% of sequence identity. The resultant homology model reveals that carp ovum cystatin shares similar folds as chicken egg white cystatin, particularly in the conserved regions of Q48-V49-G52 and P98-W99 and the locations of two disulfide bonds, C67-C76 and C90-C110. However, the results of 1 ns molecular dynamics simulations show that carp ovum cystatin exhibits less structural integrity than chicken egg white cystatin in explicit water at 300 K. The relatively hydrophilic Met62 of carp ovum cystatin, corresponding to the hydrophobic Leu68 of human cystatin C and Ile66 of chicken egg white cystatin, may destabilize the hydrophobic core and form a dimeric structure more easily through domain swapping. A total of 16 positively charged residues are equally distributed on the surface of carp ovum cystatin, resulting in agglutination with the negatively charged spermatozoa via electrostatic interaction. Thus, carp ovum cystatin is considered to be important in preventing carp eggs from polyspermy.

  20. 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.

  1. Accelerated Molecular Dynamics Simulation of Alkane Desorption

    NASA Astrophysics Data System (ADS)

    McLaughlin, Kelly; Fichthorn, Kristen

    2006-03-01

    Thermal desorption has been the focus of much surface science research. Studies of alkanes on graphite^1 and gold^2 have shown prefactors that are constant with alkane chain length but vary by over six orders of magnitude. Other studies on magnesium oxide^3 and gold^4 show a prefactor that increases with increasing chain length. We have developed an all-atom model to study alkane desorption from graphite. Transition state theory is used to obtain rate constants from the simulation. Accelerated MD is used to extend the desorption simulation to experimentally relevant temperatures. Our results show a prefactor that increases with increasing chain length. We predict that it will become constant as internal conformational changes occur significantly. We examine the effect of desorption environment through varying the alkane surface coverage. 1. K.R. Paserba and A.J. Gellman, J. Chem. Phys. 115, 6737 (2001). 2. S.M. Wetterer et al., J. Phys. Chem. 102, 9266 (1998). 3. S.L. Tait et al., J. Chem. Phys. 122, 164707 (2005). 4. K.A. Fichthorn and R.A. Miron, Phys. Rev. Lett. 89, 196103 (2002).

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Molecular Dynamics Simulations of Lignin Peroxidase in Solution

    PubMed Central

    Francesca Gerini, M.; Roccatano, Danilo; Baciocchi, Enrico; Nola, Alfredo Di

    2003-01-01

    The dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant have been investigated in aqueous solution using molecular dynamics (MD) simulations. In both cases, the enzyme retained its overall backbone structure and all its noncovalent interactions in the course of the MD simulations. Very interestingly, the analysis of the MD trajectories showed the presence of large fluctuations in correspondence of the residues forming the heme access channel; these movements enlarge the opening and facilitate the access of substrates to the enzyme active site. Moreover, steered molecular dynamics docking simulations have shown that lignin peroxidase natural substrate (veratryl alcohol) can easily approach the heme edge through the access channel. PMID:12770894

  7. Design and development of an unconstrained dynamic knee simulator.

    PubMed

    McLean, C A; Ahmed, A M

    1993-05-01

    A dynamic knee simulator has been developed to allow in-vitro investigation of the mechanical response of the joint corresponding to dynamic functional activities, e.g., walking. In the simulator, the controlled inputs are the time-histories of three parameters of a given dynamic activity: the flexion angle, and the flexion/extension moment and tibial axial force components of the foot-to-floor reaction. A combination of stepping motors and electro-hydraulic actuators is used to apply to a knee specimen, simultaneously and independently, the specified load and/or displacement inputs while allowing unconstrained relative motion between the joint members. Satisfactory performance of the simulator has been established for walking gait conditions based on measurements on three fresh-frozen specimens.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Thermal Conductivity of Natural Rubber Using Molecular Dynamics Simulation.

    PubMed

    He, Yan; Ma, Lian-Xiang; Tang, Yuan-Zheng; Wang, Ze-Peng; Li, Wei; Kukulka, David

    2015-04-01

    Thermal conductivity of natural rubber has been studied by classic molecular dynamics simulations. These simulations are performed on natural rubber models using the adaptive intermolecular reactive empirical bond order (AIREBO) and the Green-Kubo molecular dynamics (MD) simulations. Thermal conductivity results are found to be very sensitive to the time step used in the simulations. For a time step of 0.1 fs, the converged thermal conductivity is 0.35 W/mK. Additionally the anisotropic thermal conductivity of a specially-modeled natural rubber model with straight molecular chains was studied and values of thermal conductivity parallel to the molecular chains was found to be 1.71 W/mK and the anisotropy, 2Kz/(Kx + Ky), was 2.67.

  13. 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.

  14. 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.

  15. Simulation of Naval Guns' Breechblock System Dynamics Based on ADAMS

    NASA Astrophysics Data System (ADS)

    Tan, Bo; Liu, Hui-Min; Liu, Kai

    In order to study the dynamical characteristics of the breechblock system during gun firing, a virtual prototype model was established based on ADAMS, in which motion and force transmission among mechanisms are realized by collision. By simulation, kinematics and dynamics properties of main components are obtained, and the relationships between the motion of breechblock and the position of breechblock opening plate are analyzed. According to the simulation results, the collision among the breechblock opening plate and the roller is discontinuous, which may make the breechblock system fail to hitch the breechblock reliably. And within allowable scope of the structure, the breechblock opening template should be installed near the upside as much as possible.

  16. 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.

  17. 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.

  18. A nonequilibrium model for dynamic simulation of tray distillation columns

    SciTech Connect

    Kooijman, H.A.; Taylor, R.

    1995-08-01

    A nonequilibrium model for the dynamic simulation of distillation columns is described. The nonequilibrium model includes the direct calculation of the rates of mass and energy transfer and is better able to model the actual physical processes occurring on a real distillation tray than is the conventional equilibrium stage model. Example calculations show that heat-transfer limitations and the vapor holdup above the froth cannot be neglected at elevated pressures. Back-computed Murphree tray efficiencies are not constant over time, which implies that the equilibrium model should not be used for dynamic simulations.

  19. Dynamical simulations of superionicity in alkaline-earth halides

    NASA Astrophysics Data System (ADS)

    Zhou, L. X.; Hardy, J. R.; Cao, H. Z.

    1996-04-01

    Superionicity in alkaline-earth halides CaF 2, SrF 2 and BaF 2 has been studied by molecular dynamical simulations using Gordon-Kim potentials. These dynamical simulations employ a novel technique to monitor the motion of ions which clearly demonstrates the nature of the superionic phases in these crystals. While in the superionic phase, the Ca 2+, Ba 2+, and Sr 2+ ions maintain ideal lattice positions, the F - ions flow between them in a correlated linear manner closely related to that proposed previously by Boyer.

  20. 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.

  1. Lessons Learned From Dynamic Simulations of Advanced Fuel Cycles

    SciTech Connect

    Steven J. Piet; Brent W. Dixon; Jacob J. Jacobson; Gretchen E. Matthern; David E. Shropshire

    2009-04-01

    Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe “lessons learned” from dynamic simulations but attempt to answer the “so what” question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof.

  2. 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.

  3. 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.

  4. Effect of acetone accumulation on structure and dynamics of lipid membranes studied by molecular dynamics simulations.

    PubMed

    Posokhov, Yevgen O; Kyrychenko, Alexander

    2013-10-01

    The modulation of the properties and function of cell membranes by small volatile substances is important for many biomedical applications. Despite available experimental results, molecular mechanisms of action of inhalants and organic solvents, such as acetone, on lipid membranes remain not well understood. To gain a better understanding of how acetone interacts with membranes, we have performed a series of molecular dynamics (MD) simulations of a POPC bilayer in aqueous solution in the presence of acetone, whose concentration was varied from 2.8 to 11.2 mol%. The MD simulations of passive distribution of acetone between a bulk water phase and a lipid bilayer show that acetone favors partitioning into the water-free region of the bilayer, located near the carbonyl groups of the phospholipids and at the beginning of the hydrocarbon core of the lipid membrane. Using MD umbrella sampling, we found that the permeability barrier of ~0.5 kcal/mol exists for acetone partitioning into the membrane. In addition, a Gibbs free energy profile of the acetone penetration across a bilayer demonstrates a favorable potential energy well of -3.6 kcal/mol, located at 15-16Å from the bilayer center. The analysis of the structural and dynamics properties of the model membrane revealed that the POPC bilayer can tolerate the presence of acetone in the concentration range of 2.8-5.6 mol%. The accumulation of the higher acetone concentration of 11.2 mol% results, however, in drastic disordering of phospholipid packing and the increase in the membrane fluidity. The acetone molecules push the lipid heads apart and, hence, act as spacers in the headgroup region. This effect leads to the increase in the average headgroup area per molecule. In addition, the acyl tail region of the membrane also becomes less dense. We suggest, therefore, that the molecular mechanism of acetone action on the phospholipid bilayer has many common features with the effects of short chain alcohols, DMSO, and

  5. Dynamical QCD+QED simulation with staggered quarks

    SciTech Connect

    Zhou, Ran; Gottlieb, Steven

    2014-11-15

    Electromagnetic effects play an important role in many phenomena such as isospin-symmetry breaking in the hadron spectrum and the hadronic contributions to g-2. We have generalized the MILC QCD code to include the electromagnetic field. In this work, we focus on simulations including charged sea quarks using the RHMC algorithm. We show details of the dynamical QCD+QED simulation algorithm with compact QED. We analyze the code performance and results for hadron-spectrum observables.

  6. 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.

  7. 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.

  8. Fast Simulation on Flexible Multibody Dynamics Using Domain Decomposition Technique

    NASA Astrophysics Data System (ADS)

    Imanishi, Etsujiro; Nanjo, Takao; Hirooka, Eiko; Sugano, Naoki

    Recently, HILS (Hardware in the Loop Simulation) has been investigated in the field of the multibody dynamics (MBD). The fast calculation is necessary for the HILS system in order to require the real time simulation. This paper presents a fast simulation technique using the domain decomposition method. The domain decomposition method is widely used in the dynamic simulation for the mechanical system involving the hydraulic control system. This method is, however, not absolutely stable as the numerical integration. Fujikawa proposed a numerical stable solution scheme by introducing the iteration calculation. This paper applies the method to actual simulations of flexible multibody system in which the flexible linkage system and the hydraulic drive system are coupled with each other, and examines the speedup by parallel computing with the common memory in the calculation time. It is shown that using the present method in a multi-degrees-of freedom model can shorten the computing time. The present method is effective for the speedup in the calculation time by applying the dynamic simulation of the actual digging works on the hydraulic excavator.

  9. 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.

  10. Flight Simulation of Taketombo Based on Computational Fluid Dynamics and Computational Flight Dynamics

    NASA Astrophysics Data System (ADS)

    Kawamura, Kohei; Ueno, Yosuke; Nakamura, Yoshiaki

    In the present study we have developed a numerical method to simulate the flight dynamics of a small flying body with unsteady motion, where both aerodynamics and flight dynamics are fully considered. A key point of this numerical code is to use computational fluid dynamics and computational flight dynamics at the same time, which is referred to as CFD2, or double CFDs, where several new ideas are adopted in the governing equations, the method to make each quantity nondimensional, and the coupling method between aerodynamics and flight dynamics. This numerical code can be applied to simulate the unsteady motion of small vehicles such as micro air vehicles (MAV). As a sample calculation, we take up Taketombo, or a bamboo dragonfly, and its free flight in the air is demonstrated. The eventual aim of this research is to virtually fly an aircraft with arbitrary motion to obtain aerodynamic and flight dynamic data, which cannot be taken in the conventional wind tunnel.

  11. 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

  12. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

    PubMed

    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.

  13. 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.

  14. 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

  15. 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.

  16. Selection of solar simulator for solar dynamic ground test

    NASA Astrophysics Data System (ADS)

    Tolbert, Carol M.

    1994-08-01

    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.

  17. 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

  18. 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.

  19. Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics

    PubMed Central

    Riley, Blake T.; Ilyichova, Olga; Costa, Mauricio G. S.; Porebski, Benjamin T.; de Veer, Simon J.; Swedberg, Joakim E.; Kass, Itamar; Harris, Jonathan M.; Hoke, David E.; Buckle, Ashley M.

    2016-01-01

    The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (~1 Å) resolution, as well as with bound nickel. These structures offer a structural rationalization for the potency and selectivity of these inhibitors, and together with MD simulation and computational analysis, reveal a dynamic pathway between the metal binding exosite and the active site, providing key details of a previously proposed allosteric mode of inhibition. Collectively, this work provides insight into both direct and indirect mechanisms of inhibition for KLK4 that have broad implications for the enzymology of the serine protease superfamily, and may potentially be exploited for the design of therapeutic inhibitors. PMID:27767076

  20. Dynamical Network of HIV-1 Protease Mutants Reveals the Mechanism of Drug Resistance and Unhindered Activity.

    PubMed

    Appadurai, Rajeswari; Senapati, Sanjib

    2016-03-15

    HIV-1 protease variants resist drugs by active and non-active-site mutations. The active-site mutations, which are the primary or first set of mutations, hamper the stability of the enzyme and resist the drugs minimally. As a result, secondary mutations that not only increase protein stability for unhindered catalytic activity but also resist drugs very effectively arise. While the mechanism of drug resistance of the active-site mutations is through modulating the active-site pocket volume, the mechanism of drug resistance of the non-active-site mutations is unclear. Moreover, how these allosteric mutations, which are 8-21 Å distant, communicate to the active site for drug efflux is completely unexplored. Results from molecular dynamics simulations suggest that the primary mechanism of drug resistance of the secondary mutations involves opening of the flexible protease flaps. Results from both residue- and community-based network analyses reveal that this precise action of protease is accomplished by the presence of robust communication paths between the mutational sites and the functionally relevant regions: active site and flaps. While the communication is more direct in the wild type, it traverses across multiple intermediate residues in mutants, leading to weak signaling and unregulated motions of flaps. The global integrity of the protease network is, however, maintained through the neighboring residues, which exhibit high degrees of conservation, consistent with clinical data and mutagenesis studies. PMID:26892689

  1. 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

  2. Parallel-in-time molecular-dynamics simulations.

    PubMed

    Baffico, L; Bernard, S; Maday, Y; Turinici, G; Zérah, G

    2002-11-01

    While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations. PMID:12513644

  3. Parallel-in-time molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Baffico, L.; Bernard, S.; Maday, Y.; Turinici, G.; Zérah, G.

    2002-11-01

    While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations.

  4. 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…

  5. Brownian dynamics simulations of nanosheet solutions under shear.

    PubMed

    Xu, Yueyi; Green, Micah J

    2014-07-14

    The flow-induced conformation dynamics of nanosheets are simulated using a Brownian Dynamics (BD) formulation applied to a bead-rod sheetlike molecular model. This is the first-ever use of BD to simulate flow-induced dynamics of two-dimensional structures. Using this framework, we simulate dilute suspensions of coarse-grained nanosheets and compute conformation dynamics for simple shear flow. The data show power law scaling relationships between nanosheet parameters (such as bending moduli and molecular weight) and the resulting intrinsic viscosity and conformation. For nonzero bending moduli, an effective dimension of 2.77 at equilibrium is calculated from the scaling relationship between radius of gyration and molecular weight. We also find that intrinsic viscosity varies with molecular weight with an exponent of 2.12 ± 0.23; this dependence is significantly larger than those found for linear polymers. Weak shear thinning is observed at high Weissenberg number (Wi). This simulation method provides a computational basis for developing manufacturing processes for nanosheet-derived materials by relating flow forces and nanosheet parameters to the resulting material morphology.

  6. Molecular dynamics simulation of size segregation in three dimensions

    NASA Astrophysics Data System (ADS)

    Gallas, Jason A. C.; Herrmann, Hans J.; Pöschel, Thorsten; Sokołowski, Stefan

    1996-01-01

    We report the first three-dimensional molecular dynamics simulation of particle segregation by shaking. Two different containers are considered: one cylindrical and another with periodic boundary conditions. The dependence of the time evolution of a test particle inside the material is studied as a function of the shaking frequency and amplitude, damping coefficients, and dispersivity.

  7. 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.

  8. 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.

  9. 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

  10. Fast Quantum Molecular Dynamics Simulations of Simple Organic Liquids under Shock Compression

    NASA Astrophysics Data System (ADS)

    Cawkwell, Marc; Niklasson, Anders; Manner, Virginia; McGrane, Shawn; Dattelbaum, Dana

    2013-06-01

    The responses of liquid formic acid, acrylonitrile, and nitromethane to shock compression have been studied using quantum-based molecular dynamics simulations with the self-consistent tight-binding code LATTE. Microcanonical Born-Oppenheimer trajectories with precise energy conservation were computed without relying on an iterative self-consistent field optimization of the electronic degrees of freedom at each time step via the Fast Quantum Mechanical Molecular Dynamics formalism. The input shock pressures required to initiate chemistry in our simulations agree very well with recent laser- and flyer-plate-driven shock compression experiments. On-the-fly analysis of the electronic structure of the liquids over hundreds of picoseconds after dynamic compression revealed that their reactivity is strongly correlated with the temperature and pressure dependence of their HOMO-LUMO gap.

  11. 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.

  12. Molecular dynamics simulation: A tool for exploration and discovery

    NASA Astrophysics Data System (ADS)

    Rapaport, Dennis C.

    2009-03-01

    The exploratory and didactic aspects of science both benefit from the ever-growing role played by computer simulation. One particularly important simulational approach is the molecular dynamics method, used for studying the nature of matter from the molecular to much larger scales. The effectiveness of molecular dynamics can be enhanced considerably by employing visualization and interactivity during the course of the computation and afterwards, allowing the modeler not only to observe the detailed behavior of the systems simulated in different ways, but also to steer the computations in alternative directions by manipulating parameters that govern the actual behavior. This facilitates the creation of potentially rich simulational environments for examining a multitude of complex phenomena, as well as offering an opportunity for enriching the learning process. A series of relatively advanced examples involving molecular dynamics will be used to demonstrate the value of this approach, in particular, atomistic simulations of spontaneously emergent structured fluid flows (the classic Rayleigh--B'enard and Taylor--Couette problems), supramolecular self-assembly of highly symmetric shell structures (involved in the formation of viral capsids), and that most counterintuitive of phenomena, granular segregation (e.g., axial and radial separation in a rotating cylinder).

  13. 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

  14. Extended event driven molecular dynamics for simulating dense granular matter

    NASA Astrophysics Data System (ADS)

    González, S.; Risso, D.; Soto, R.

    2009-12-01

    A new numerical method is presented to efficiently simulate the inelastic hard sphere (IHS) model for granular media, when fluid and frozen regions coexist in the presence of gravity. The IHS model is extended by allowing particles to change their dynamics into either a frozen state or back to the normal collisional state, while computing the dynamics only for the particles in the normal state. Careful criteria, local in time and space, are designed such that particles become frozen only at mechanically stable positions. The homogeneous deposition over a static surface and the dynamics of a rotating drum are studied as test cases. The simulations agree with previous experimental results. The model is much more efficient than the usual event driven method and allows to overcome some of the difficulties of the standard IHS model, such as the existence of a static limit.

  15. Temperature-accelerated dynamics for simulation of infrequent events

    SciTech Connect

    Soerensen, Mads R.; Voter, Arthur F.

    2000-06-01

    We present a method for accelerating dynamic simulations of activated processes in solids. By raising the temperature, but allowing only those events that should occur at the original temperature, the time scale of a simulation is extended by orders of magnitude compared to ordinary molecular dynamics, while preserving the correct dynamics at the original temperature. The main assumption behind the method is harmonic transition state theory. Importantly, the method does not require any prior knowledge about the transition mechanisms. As an example, the method is applied to a study of surface diffusion, where concerted processes play a key role. In the example, times of hours are achieved at a temperature of 150 K. (c) 2000 American Institute of Physics.

  16. 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).

  17. 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.

  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. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Linear Optics Simulation of Quantum Non-Markovian Dynamics

    PubMed Central

    Chiuri, Andrea; Greganti, Chiara; Mazzola, Laura; Paternostro, Mauro; Mataloni, Paolo

    2012-01-01

    The simulation of open quantum dynamics has recently allowed the direct investigation of the features of system-environment interaction and of their consequences on the evolution of a quantum system. Such interaction threatens the quantum properties of the system, spoiling them and causing the phenomenon of decoherence. Sometimes however a coherent exchange of information takes place between system and environment, memory effects arise and the dynamics of the system becomes non-Markovian. Here we report the experimental realisation of a non-Markovian process where system and environment are coupled through a simulated transverse Ising model. By engineering the evolution in a photonic quantum simulator, we demonstrate the role played by system-environment correlations in the emergence of memory effects. PMID:23236588

  6. 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.

  7. 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.

  8. 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.

  9. Information diversity in structure and dynamics of simulated neuronal networks.

    PubMed

    Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena

    2011-01-01

    Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and dynamics in neuronal networks. Information diversity within the structure and dynamics of a neuronal network is studied using the normalized compression distance. To describe the structure, a scheme for generating distance-dependent networks with identical in-degree distribution but variable strength of dependence on distance is presented. The resulting network structure classes possess differing path length and clustering coefficient distributions. In parallel, comparable realistic neuronal networks are generated with NETMORPH simulator and similar analysis is done on them. To describe the dynamics, network spike trains are simulated using different network structures and their bursting behaviors are analyzed. For the simulation of the network activity the Izhikevich model of spiking neurons is used together with the Tsodyks model of dynamical synapses. We show that the structure of the simulated neuronal networks affects the spontaneous bursting activity when measured with bursting frequency and a set of intraburst measures: the more locally connected networks produce more and longer bursts than the more random networks. The information diversity of the structure of a network is greatest in the most locally connected networks, smallest in random networks, and somewhere in between in the networks between order and disorder. As for the dynamics, the most locally connected networks and some of the in-between networks produce the most complex intraburst spike trains. The same result also holds for sparser of the two considered network densities in the case of full spike trains.

  10. Optimal estimation of dynamically consistent kinematics and kinetics for forward dynamic simulation of gait.

    PubMed

    Remy, C David; Thelen, Darryl G

    2009-03-01

    Forward dynamic simulation provides a powerful framework for characterizing internal loads and for predicting changes in movement due to injury, impairment or surgical intervention. However, the computational challenge of generating simulations has greatly limited the use and application of forward dynamic models for simulating human gait. In this study, we introduce an optimal estimation approach to efficiently solve for generalized accelerations that satisfy the overall equations of motion and best agree with measured kinematics and ground reaction forces. The estimated accelerations are numerically integrated to enforce dynamic consistency over time, resulting in a forward dynamic simulation. Numerical optimization is then used to determine a set of initial generalized coordinates and speeds that produce a simulation that is most consistent with the measured motion over a full cycle of gait. The proposed method was evaluated with synthetically created kinematics and force plate data in which both random noise and bias errors were introduced. We also applied the method to experimental gait data collected from five young healthy adults walking at a preferred speed. We show that the proposed residual elimination algorithm (REA) converges to an accurate solution, reduces the detrimental effects of kinematic measurement errors on joint moments, and eliminates the need for residual forces that arise in standard inverse dynamics. The greatest improvements in joint kinetics were observed proximally, with the algorithm reducing joint moment errors due to marker noise by over 20% at the hip and over 50% at the low back. Simulated joint angles were generally within 1 deg of recorded values when REA was used to generate a simulation from experimental gait data. REA can thus be used as a basis for generating accurate simulations of subject-specific gait dynamics.

  11. 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.

  12. Simulation of Nitroxide Electron Paramagnetic Resonance Spectra from Brownian Trajectories and Molecular Dynamics Simulations

    PubMed Central

    DeSensi, Susan C.; Rangel, David P.; Beth, Albert H.; Lybrand, Terry P.; Hustedt, Eric J.

    2008-01-01

    A simulated continuous wave electron paramagnetic resonance spectrum of a nitroxide spin label can be obtained from the Fourier transform of a free induction decay. It has been previously shown that the free induction decay can be calculated by solving the time-dependent stochastic Liouville equation for a set of Brownian trajectories defining the rotational dynamics of the label. In this work, a quaternion-based Monte Carlo algorithm has been developed to generate Brownian trajectories describing the global rotational diffusion of a spin-labeled protein. Also, molecular dynamics simulations of two spin-labeled mutants of T4 lysozyme, T4L F153R1, and T4L K65R1 have been used to generate trajectories describing the internal dynamics of the protein and the local dynamics of the spin-label side chain. Trajectories from the molecular dynamics simulations combined with trajectories describing the global rotational diffusion of the protein are used to account for all of the dynamics of a spin-labeled protein. Spectra calculated from these combined trajectories correspond well to the experimental spectra for the buried site T4L F153R1 and the helix surface site T4L K65R1. This work provides a framework to further explore the modeling of the dynamics of the spin-label side chain in the wide variety of labeling environments encountered in site-directed spin labeling studies. PMID:18234808

  13. 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.

  14. 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.

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

    PubMed

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

    2010-11-01

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

  16. Ab initio centroid molecular dynamics: a fully quantum method for condensed-phase dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pavese, Marc; Berard, Daniel R.; Voth, Gregory A.

    1999-01-01

    A fully quantum molecular dynamics method is presented which combines ab initio Car-Parrinello molecular dynamics with centroid molecular dynamics. The first technique allows the forces on the atoms to be obtained from ab initio electronic structure. The second technique, given the forces on the atoms, allows one to calculate an approximate quantum time evolution for the nuclei. The combination of the two, therefore, represents the first feasible approach to simulating the fully quantum dynamics of a many-body system. An application to excess proton translocation along a model water wire will be presented.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. Characterization of 4-HNE modified L-FABP reveals alterations in structural and functional dynamics.

    PubMed

    Smathers, Rebecca L; Fritz, Kristofer S; Galligan, James J; Shearn, Colin T; Reigan, Philip; Marks, Michael J; Petersen, Dennis R

    2012-01-01

    4-Hydroxynonenal (4-HNE) is a reactive α,β-unsaturated aldehyde produced during oxidative stress and subsequent lipid peroxidation of polyunsaturated fatty acids. The reactivity of 4-HNE towards DNA and nucleophilic amino acids has been well established. In this report, using proteomic approaches, liver fatty acid-binding protein (L-FABP) is identified as a target for modification by 4-HNE. This lipid binding protein mediates the uptake and trafficking of hydrophobic ligands throughout cellular compartments. Ethanol caused a significant decrease in L-FABP protein (P<0.001) and mRNA (P<0.05), as well as increased poly-ubiquitinated L-FABP (P<0.001). Sites of 4-HNE adduction on mouse recombinant L-FABP were mapped using MALDI-TOF/TOF mass spectrometry on apo (Lys57 and Cys69) and holo (Lys6, Lys31, His43, Lys46, Lys57 and Cys69) L-FABP. The impact of 4-HNE adduction was found to occur in a concentration-dependent manner; affinity for the fluorescent ligand, anilinonaphthalene-8-sulfonic acid, was reduced from 0.347 µM to Kd(1) = 0.395 µM and Kd(2) = 34.20 µM. Saturation analyses revealed that capacity for ligand is reduced by approximately 50% when adducted by 4-HNE. Thermal stability curves of apo L-FABP was also found to be significantly affected by 4-HNE adduction (ΔTm = 5.44°C, P<0.01). Computational-based molecular modeling simulations of adducted protein revealed minor conformational changes in global protein structure of apo and holo L-FABP while more apparent differences were observed within the internal binding pocket, revealing reduced area and structural integrity. New solvent accessible portals on the periphery of the protein were observed following 4-HNE modification in both the apo and holo state, suggesting an adaptive response to carbonylation. The results from this study detail the dynamic process associated with L-FABP modification by 4-HNE and provide insight as to how alterations in structural integrity and ligand binding may a

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. Dynamical systems model and discrete element simulations of a tapped granular column

    NASA Astrophysics Data System (ADS)

    Rosato, A. D.; Blackmore, D.; Tricoche, X. M.; Urban, K.; Zuo, L.

    2013-06-01

    We present an approximate dynamical systems model for the mass center trajectory of a tapped column of N uniform, inelastic, spheres (diameter d), in which collisional energy loss is governed by the Walton-Braun linear loading-unloading soft interaction. Rigorous analysis of the model, akin to the equations for the motion of a single bouncing ball on a vibrating plate, reveals a parameter γ≔2aω2(1+e)/g that gauges the dynamical regimes and their transitions. In particular, we find bifurcations from periodic to chaotic dynamics that depend on frequency ω, amplitude a/d of the tap. Dynamics predicted by the model are also qualitatively observed in discrete element simulations carried out over a broad range of the tap parameters.

  9. 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

  10. Analysis of utilization of desert habitats with dynamic simulation

    USGS Publications Warehouse

    Williams, B.K.

    1986-01-01

    The effects of climate and herbivores on cool desert shrubs in north-western Utah were investigated with a dynamic simulation model. Cool desert shrublands are extensively managed as grazing lands, and are defoliated annually by domestic livestock. A primary production model was used to simulate harvest yields and shrub responses under a variety of climatic regimes and defoliation patterns. The model consists of six plant components, and it is based on equations of growth analysis. Plant responses were simulated under various combinations of 20 annual weather patterns and 14 defoliation strategies. Results of the simulations exhibit some unexpected linearities in model behavior, and emphasize the importance of both the pattern of climate and the level of plant vigor in determining optimal harvest strategies. Model behaviors are interpreted in terms of shrub morphology, physiology and ecology.

  11. Molecular dynamics simulation of amplitude modulation atomic force microscopy.

    PubMed

    Hu, Xiaoli; Egberts, Philip; Dong, Yalin; Martini, Ashlie

    2015-06-12

    Molecular dynamics (MD) simulations were used to model amplitude modulation atomic force microscopy (AM-AFM). In this novel simulation, the model AFM tip responds to both tip-substrate interactions and to a sinusoidal excitation signal. The amplitude and phase shift of the tip oscillation observed in the simulation and their variation with tip-sample distance were found to be consistent with previously reported trends from experiments and theory. These simulation results were also fit to an expression enabling estimation of the energy dissipation, which was found to be smaller than that in a corresponding experiment. The difference was analyzed in terms of the effects of tip size and substrate thickness. Development of this model is the first step toward using MD to gain insight into the atomic-scale phenomena that occur during an AM-AFM measurement.

  12. 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.

  13. Molecular Dynamics Simulation of a Microvillus in a Cross Flow

    NASA Astrophysics Data System (ADS)

    Chen, X. Y.; Liu, Y.; So, R. M. C.; Yang, J. M.

    One of the functions of microvilli in the microvessel endothelial glycocalyx is molecular filtering. The microvillus behaves as a mechanosensory system which may sense the fluid shear and drag forces. The permeability of small particles in microvessel is crucial for drug design and drug delivery. Therefore a better understanding of flow field around microvillus is important to simulate accurately the particle penetration in microvessel. Since the dimension of the microvilli is about ~10 nm, the conventional Navier-Stokes equation may not be good enough to simulate the fluid flow in such microscale and nanoscale structures. Molecular dynamics (MD) simulation is a powerful method to simulate the fluid flow at the molecular level. As a first attempt, the microvillus is reduced as a two-dimensional cylinder which is in a cross flow. The detailed drag and lift together with flow field are obtained and compared with available data.

  14. 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.

  15. 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.

  16. 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

  17. Spotting the difference in molecular dynamics simulations of biomolecules

    NASA Astrophysics Data System (ADS)

    Sakuraba, Shun; Kono, Hidetoshi

    2016-08-01

    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.

  18. Simulating soil phosphorus dynamics for a phosphorus loss quantification tool.

    PubMed

    Vadas, Peter A; Joern, Brad C; Moore, Philip A

    2012-01-01

    Pollution of fresh waters by agricultural phosphorus (P) is a water quality concern. Because soils can contribute significantly to P loss in runoff, it is important to assess how management affects soil P status over time, which is often done with models. Our objective was to describe and validate soil P dynamics in the Annual P Loss Estimator (APLE) model. APLE is a user-friendly spreadsheet model that simulates P loss in runoff and soil P dynamics over 10 yr for a given set of runoff, erosion, and management conditions. For soil P dynamics, APLE simulates two layers in the topsoil, each with three inorganic P pools and one organic P pool. It simulates P additions to soil from manure and fertilizer, distribution among pools, mixing between layers due to tillage and bioturbation, leaching between and out of layers, crop P removal, and loss by surface runoff and erosion. We used soil P data from 25 published studies to validate APLE's soil P processes. Our results show that APLE reliably simulated soil P dynamics for a wide range of soil properties, soil depths, P application sources and rates, durations, soil P contents, and management practices. We validated APLE specifically for situations where soil P was increasing from excessive P inputs, where soil P was decreasing due to greater outputs than inputs, and where soil P stratification occurred in no-till and pasture soils. Successful simulations demonstrate APLE's potential to be applied to major management scenarios related to soil P loss in runoff and erosion. PMID:23128732

  19. Quantifying the Heterogeneous Dynamics of a Simulated Dipalmitoylphosphatidylcholine (DPPC) Membrane.

    PubMed

    Shafique, Neha; Kennedy, Kiley E; Douglas, Jack F; Starr, Francis W

    2016-06-16

    Heterogeneity of dynamics plays a vital role in membrane function, but the methods for quantifying this heterogeneity are still being developed. Here we examine membrane dynamical heterogeneity via molecular simulations of a single-component dipalmitoylphosphatidylcholine (DPPC) lipid bilayer using the MARTINI force field. We draw upon well-established analysis methods developed in the study of glass-forming fluids and find significant changes in lipid dynamics between the fluid (Lα), and gel (Lβ) phases. In particular, we distinguish two mobility groups in the more ordered Lβ phase: (i) lipids that are transiently trapped by their neighbors and (ii) lipids with displacements on the scale of the intermolecular spacing. These distinct mobility groups spatially segregate, forming dynamic clusters that have characteristic time (1-2 μs) and length (1-10 nm) scales comparable to those of proteins and other biomolecules. We suggest that these dynamic clusters could couple to biomolecules within the membrane and thus may play a role in many membrane functions. In the equilibrium membrane, lipid molecules dynamically exchange between the mobility groups, and the resulting clusters are not associated with a thermodynamic phase separation. Dynamical clusters having similar characteristics arise in many other condensed phase materials, placing membranes in a broad class of materials with strong intermolecular interactions. PMID:27223339

  20. Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lu, Yan; Salsbury, Freddie R.

    2015-01-01

    ERG, an ETS-family transcription factor, acts as a regulator of differentiation of early hematopoietic cells. It contains an autoinhibitory domain, which negatively regulates DNA-binding. The mechanism of autoinhibitory is still illusive. To understand the mechanism, we study the dynamical properties of ERG protein by molecular dynamics simulations. These simulations suggest that DNA binding autoinhibition associates with the internal dynamics of ERG. Specifically, we find that (1), The N-C terminal correlation in the inhibited ERG is larger than that in uninhibited ERG that contributes to the autoinhibition of DNA-binding. (2), DNA-binding changes the property of the N-C terminal correlation from being anti-correlated to correlated, that is, changing the relative direction of the correlated motions and (3), For the Ets-domain specifically, the inhibited and uninhibited forms exhibit essentially the same dynamics, but the binding of the DNA decreases the fluctuation of the Ets-domain. We also find from PCA analysis that the three systems, even with quite different dynamics, do have highly similar free energy surfaces, indicating that they share similar conformations.

  1. Beam Dynamics Design and Simulation in Ion Linear Accelerators (

    2006-08-01

    Orginally, the ray tracing code TRACK has been developed to fulfill the many special requirements for the Rare Isotope Accelerator Facility known as RIA. Since no available beam-dynamics code met all the necessary requirements, modifications to the code TRACK were introduced to allow end-to-end (from the ion souce to the production target) simulations of the RIA machine, TRACK is a general beam-dynamics code and can be applied for the design, commissioning and operation of modernmore » ion linear accelerators and beam transport systems.« less

  2. Molecular dynamical simulations of melting behaviors of metal clusters

    SciTech Connect

    Hamid, Ilyar; Fang, Meng; Duan, Haiming

    2015-04-15

    The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002)] for the statically stable structures.

  3. Beam Dynamics Design and Simulation in Ion Linear Accelerators (

    SciTech Connect

    Ostroumov, Peter N.; Asseev, Vladislav N.; Mustapha, and Brahim

    2006-08-01

    Orginally, the ray tracing code TRACK has been developed to fulfill the many special requirements for the Rare Isotope Accelerator Facility known as RIA. Since no available beam-dynamics code met all the necessary requirements, modifications to the code TRACK were introduced to allow end-to-end (from the ion souce to the production target) simulations of the RIA machine, TRACK is a general beam-dynamics code and can be applied for the design, commissioning and operation of modern ion linear accelerators and beam transport systems.

  4. Process Modeling and Dynamic Simulation for EAST Helium Refrigerator

    NASA Astrophysics Data System (ADS)

    Lu, Xiaofei; Fu, Peng; Zhuang, Ming; Qiu, Lilong; Hu, Liangbing

    2016-06-01

    In this paper, the process modeling and dynamic simulation for the EAST helium refrigerator has been completed. The cryogenic process model is described and the main components are customized in detail. The process model is controlled by the PLC simulator, and the realtime communication between the process model and the controllers is achieved by a customized interface. Validation of the process model has been confirmed based on EAST experimental data during the cool down process of 300-80 K. Simulation results indicate that this process simulator is able to reproduce dynamic behaviors of the EAST helium refrigerator very well for the operation of long pulsed plasma discharge. The cryogenic process simulator based on control architecture is available for operation optimization and control design of EAST cryogenic systems to cope with the long pulsed heat loads in the future. supported by National Natural Science Foundation of China (No. 51306195) and Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, CAS (No. CRYO201408)

  5. Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott

    2015-01-01

    We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.

  6. Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics

    SciTech Connect

    Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott

    2015-01-28

    We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.

  7. Process Modeling and Dynamic Simulation for EAST Helium Refrigerator

    NASA Astrophysics Data System (ADS)

    Lu, Xiaofei; Fu, Peng; Zhuang, Ming; Qiu, Lilong; Hu, Liangbing

    2016-06-01

    In this paper, the process modeling and dynamic simulation for the EAST helium refrigerator has been completed. The cryogenic process model is described and the main components are customized in detail. The process model is controlled by the PLC simulator, and the realtime communication between the process model and the controllers is achieved by a customized interface. Validation of the process model has been confirmed based on EAST experimental data during the cool down process of 300–80 K. Simulation results indicate that this process simulator is able to reproduce dynamic behaviors of the EAST helium refrigerator very well for the operation of long pulsed plasma discharge. The cryogenic process simulator based on control architecture is available for operation optimization and control design of EAST cryogenic systems to cope with the long pulsed heat loads in the future. supported by National Natural Science Foundation of China (No. 51306195) and Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, CAS (No. CRYO201408)

  8. Quantum dynamical simulations of local field enhancement in metal nanoparticles.

    PubMed

    Negre, Christian F A; Perassi, Eduardo M; Coronado, Eduardo A; Sánchez, Cristián G

    2013-03-27

    Field enhancements (Γ) around small Ag nanoparticles (NPs) are calculated using a quantum dynamical simulation formalism and the results are compared with electrodynamic simulations using the discrete dipole approximation (DDA) in order to address the important issue of the intrinsic atomistic structure of NPs. Quite remarkably, in both quantum and classical approaches the highest values of Γ are located in the same regions around single NPs. However, by introducing a complete atomistic description of the metallic NPs in optical simulations, a different pattern of the Γ distribution is obtained. Knowing the correct pattern of the Γ distribution around NPs is crucial for understanding the spectroscopic features of molecules inside hot spots. The enhancement produced by surface plasmon coupling is studied by using both approaches in NP dimers for different inter-particle distances. The results show that the trend of the variation of Γ versus inter-particle distance is different for classical and quantum simulations. This difference is explained in terms of a charge transfer mechanism that cannot be obtained with classical electrodynamics. Finally, time dependent distribution of the enhancement factor is simulated by introducing a time dependent field perturbation into the Hamiltonian, allowing an assessment of the localized surface plasmon resonance quantum dynamics.

  9. Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

    NASA Astrophysics Data System (ADS)

    Zobač, Vladmír; Lewis, James P.; Jelínek, Pavel

    2016-07-01

    We report non-adiabatic molecular dynamic simulations of the ring opening reaction of diarylethene (DAE) derivative molecules, both free standing and embedded between gold electrodes. Simulations are performed by the surface hopping method employing density functional theory. Typically, the free-standing molecules exhibit large quantum yields to open and close; however the process is quenched for the molecules embedded between electrodes. Our simulations reveal the importance of the DAE side chemical groups, which explain the efficiency of the quenching process. Namely, delocalization of the LUMO state contributes to electronic coupling between the molecule and electrodes, suppressing or enhancing the reaction process. The simulations indicate that a proper choice of the chemical side group, which provides the strong localization of the LUMO state, can substantially diminish the quenching mechanism. Additionally, we analyze a strong dependency of the quantum yield of the opening reaction coming from the mechanical strength of the molecules.

  10. Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions.

    PubMed

    Zobač, Vladmír; Lewis, James P; Jelínek, Pavel

    2016-07-15

    We report non-adiabatic molecular dynamic simulations of the ring opening reaction of diarylethene (DAE) derivative molecules, both free standing and embedded between gold electrodes. Simulations are performed by the surface hopping method employing density functional theory. Typically, the free-standing molecules exhibit large quantum yields to open and close; however the process is quenched for the molecules embedded between electrodes. Our simulations reveal the importance of the DAE side chemical groups, which explain the efficiency of the quenching process. Namely, delocalization of the LUMO state contributes to electronic coupling between the molecule and electrodes, suppressing or enhancing the reaction process. The simulations indicate that a proper choice of the chemical side group, which provides the strong localization of the LUMO state, can substantially diminish the quenching mechanism. Additionally, we analyze a strong dependency of the quantum yield of the opening reaction coming from the mechanical strength of the molecules. PMID:27255903

  11. 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

  12. Research of TREETOPS Structural Dynamics Controls Simulation Upgrade

    NASA Technical Reports Server (NTRS)

    Yates, Rose M.

    1996-01-01

    Under the provisions of contract number NAS8-40194, which was entitled 'TREETOPS Structural Dynamics and Controls Simulation System Upgrade', Oakwood College contracted to produce an upgrade to the existing TREETOPS suite of analysis tools. This suite includes the main simulation program, TREETOPS, two interactive preprocessors, TREESET and TREEFLX, an interactive post processor, TREEPLOT, and an adjunct program, TREESEL. A 'Software Design Document', which provides descriptions of the argument lists and internal variables for each subroutine in the TREETOPS suite, was established. Additionally, installation guides for both DOS and UNIX platforms were developed. Finally, updated User's Manuals, as well as a Theory Manual, were generated.

  13. The very local Hubble flow: Computer simulations of dynamical history

    NASA Astrophysics Data System (ADS)

    Chernin, A. D.; Karachentsev, I. D.; Valtonen, M. J.; Dolgachev, V. P.; Domozhilova, L. M.; Makarov, D. I.

    2004-02-01

    The phenomenon of the very local (≤3 Mpc) Hubble flow is studied on the basis of the data of recent precision observations. A set of computer simulations is performed to trace the trajectories of the flow galaxies back in time to the epoch of the formation of the Local Group. It is found that the ``initial conditions'' of the flow are drastically different from the linear velocity-distance relation. The simulations enable one also to recognize the major trends of the flow evolution and identify the dynamical role of universal antigravity produced by the cosmic vacuum.

  14. Structural considerations for a software life cycle dynamic simulation model

    NASA Technical Reports Server (NTRS)

    Tausworthe, R. C.; Mckenzie, M.; Lin, C. Y.

    1983-01-01

    This paper presents the results of a preliminary study into the prospects for simulating the software implementation and maintenance life cycle process, with the aim of producing a computerized tool for use by management and software engineering personnel in project planning, tradeoff studies involving product, environmental, situational, and technological factors, and training. The approach taken is the modular application of a 'flow of resource' concept to the systems dynamics simulation modeling technique. The software life cycle process is represented as a number of stochastic, time-varying, interacting work tasks that each achieves one of the project milestones. Each task is characterized by the item produced, the personnel applied, and the budgetary profile.

  15. Simulating Hamiltonian dynamics with a truncated Taylor series.

    PubMed

    Berry, Dominic W; Childs, Andrew M; Cleve, Richard; Kothari, Robin; Somma, Rolando D

    2015-03-01

    We describe a simple, efficient method for simulating Hamiltonian dynamics on a quantum computer by approximating the truncated Taylor series of the evolution operator. Our method can simulate the time evolution of a wide variety of physical systems. As in another recent algorithm, the cost of our method depends only logarithmically on the inverse of the desired precision, which is optimal. However, we simplify the algorithm and its analysis by using a method for implementing linear combinations of unitary operations together with a robust form of oblivious amplitude amplification. PMID:25793789

  16. Large-scale molecular dynamics simulations of fracture and deformation

    NASA Astrophysics Data System (ADS)

    Zhou, S. J.; Beazley, D. M.; Lomdahl, P. S.; Holian, B. L.

    1996-08-01

    We have discussed the prospects of applying massively parallel molecular dynamics simulation to investigate brittle versus ductile fracture behaviors and dislocation intersection. This idea is illustrated by simulating dislocation emission from a three-dimensional crack. Unprecedentedly, the dislocation loops emitted from the crack fronts have been observed. It is found that dislocation-emission modes, jogging or blunting, are very sensitive to boundary conditions and interatomic potentials. These 3D phenomena can be effectively visualized and analyzed by a new technique, namely, plotting only those atoms within the certain ranges of local potential energies.

  17. Dynamic focusing approach to mixed-level simulation

    NASA Astrophysics Data System (ADS)

    Fall, Thomas C.

    1997-06-01

    The dynamic focusing approach (DFA) has been under development for several years. Its intent is to address several of the issues of mixed level simulations, particularly the aggregational issues. Though the approach requires that the system be able to be modeled within certain constraints, many systems of interest fit well within them. This approach combines a hierarchical representation of knowledge with a stochastic propagation mechanism; this provides capability to gracefully move from coarse granularity to fine granularity under user guidance. Prototype tools have been developed for engineering analysis, combat simulation and TQM process implementation. This paper gives an overview of the approach and its current status.

  18. Dislocation dynamics simulations of plasticity at small scales

    SciTech Connect

    Zhou, Caizhi

    2010-01-01

    As metallic structures and devices are being created on a dimension comparable to the length scales of the underlying dislocation microstructures, the mechanical properties of them change drastically. Since such small structures are increasingly common in modern technologies, there is an emergent need to understand the critical roles of elasticity, plasticity, and fracture in small structures. Dislocation dynamics (DD) simulations, in which the dislocations are the simulated entities, offer a way to extend length scales beyond those of atomistic simulations and the results from DD simulations can be directly compared with the micromechanical tests. The primary objective of this research is to use 3-D DD simulations to study the plastic deformation of nano- and micro-scale materials and understand the correlation between dislocation motion, interactions and the mechanical response. Specifically, to identify what critical events (i.e., dislocation multiplication, cross-slip, storage, nucleation, junction and dipole formation, pinning etc.) determine the deformation response and how these change from bulk behavior as the system decreases in size and correlate and improve our current knowledge of bulk plasticity with the knowledge gained from the direct observations of small-scale plasticity. Our simulation results on single crystal micropillars and polycrystalline thin films can march the experiment results well and capture the essential features in small-scale plasticity. Furthermore, several simple and accurate models have been developed following our simulation results and can reasonably predict the plastic behavior of small scale materials.

  19. 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

  20. Effects of antimicrobial peptide revealed by simulations: translocation, pore formation, membrane corrugation and euler buckling.

    PubMed

    Chen, Licui; Jia, Nana; Gao, Lianghui; Fang, Weihai; Golubovic, Leonardo

    2013-04-11

    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.

  1. 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

  2. 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.

  3. Simulation of Spin-orbit Dynamics in Storage Rings

    NASA Astrophysics Data System (ADS)

    Ivanov, A.; Andrianov, S.; Senichev, Yu.

    2016-09-01

    In the article a mapping approach based on nonlinear matrix integration for longterm spin-orbit dynamics simulation is briefly described. Using this technique the nonlinear effects of spin dynamics in an electrostatics storage ring are investigated. Namely, the fringe fields, the energy conservation law and the random field errors are considered. The necessity of examination of such effects arises, for example, in the storage ring design for search the Electrical Dipole Moment of proton and deuteron. The EDM ring is proposed to measure EDM using the spin transformation of polarized particle in the magneto-electrostatic elements of the ring. The article consists of short description of the spin-orbit simulation results based on the nonlinear model.

  4. Extrapolated gradientlike algorithms for molecular dynamics and celestial mechanics simulations.

    PubMed

    Omelyan, I P

    2006-09-01

    A class of symplectic algorithms is introduced to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an advanced gradientlike decomposition approach. Its main advantage over the standard gradient scheme is the avoidance of time-consuming evaluations of force gradients by force extrapolation without any loss of precision. As a result, the efficiency of the integration improves significantly. The algorithms obtained are analyzed and optimized using an error-function theory. The best among them are tested in actual molecular dynamics and celestial mechanics simulations for comparison with well-known nongradient and gradient algorithms such as the Störmer-Verlet, Runge-Kutta, Cowell-Numerov, Forest-Ruth, Suzuki-Chin, and others. It is demonstrated that for moderate and high accuracy, the extrapolated algorithms should be considered as the most efficient for the integration of motion in molecular dynamics simulations. PMID:17025782

  5. Extrapolated gradientlike algorithms for molecular dynamics and celestial mechanics simulations.

    PubMed

    Omelyan, I P

    2006-09-01

    A class of symplectic algorithms is introduced to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an advanced gradientlike decomposition approach. Its main advantage over the standard gradient scheme is the avoidance of time-consuming evaluations of force gradients by force extrapolation without any loss of precision. As a result, the efficiency of the integration improves significantly. The algorithms obtained are analyzed and optimized using an error-function theory. The best among them are tested in actual molecular dynamics and celestial mechanics simulations for comparison with well-known nongradient and gradient algorithms such as the Störmer-Verlet, Runge-Kutta, Cowell-Numerov, Forest-Ruth, Suzuki-Chin, and others. It is demonstrated that for moderate and high accuracy, the extrapolated algorithms should be considered as the most efficient for the integration of motion in molecular dynamics simulations.

  6. Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics.

    PubMed

    Petsev, Nikolai D; Leal, L Gary; Shell, M Scott

    2016-02-28

    Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales. PMID:26931689

  7. Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott

    2016-02-01

    Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales.

  8. Reduced order component models for flexible multibody dynamics simulations

    NASA Technical Reports Server (NTRS)

    Tsuha, Walter S.; Spanos, John T.

    1990-01-01

    Many flexible multibody dynamics simulation codes require some form of component description that properly characterizes the dynamic behavior of the system. A model reduction procedure for producing low order component models for flexible multibody simulation is described. Referred to as projection and assembly, the method is a Rayleigh-Ritz approach that uses partitions of the system modal matrix as component Ritz transformation matrices. It is shown that the projection and assembly method yields a reduced system model that preserves a specified set of the full order system modes. Unlike classical component mode synthesis methods, the exactness of the method described is obtained at the expense of having to compute the full order system modes. The paper provides a comprehensive description of the method, a proof of exactness, and numerical results demonstrating the method's effectiveness.

  9. Spin dynamics simulations for a nanoscale Heisenberg antiferromagnet

    NASA Astrophysics Data System (ADS)

    Hou, Zhuofei; Landau, D. P.; Brown, G.; Stocks, G. M.

    2010-03-01

    Thermoinduced magnetization(TiM) is a novel response which was predicted to occur in nanoscale antiferromagnetic materials. Extensive Monte Carlo simulations footnotetextG. Brown, A. Janotti, M. Eisenbach, and G. M. Stocks, Phys.Rev.B 72, 140405(2005) have shown that TiM is an intrinsic property of the antiferromagnetic classical Heisenberg model below the Neel temperature. To obtain a fundamental understanding of TiM, spin dynamics(SD) simulations are performed to study the spin wave behavior, which seems to be the cause of TiM. A classical Heisenberg model with an antiferromagnetic nearest-neighbor exchange interaction and uniaxial single-site anisotropy is studied. Simple-cubic lattices with free boundary conditions are used. We employed the fast spin dynamics algorithms with fourth-order Suzuki-Trotter decompositions of the exponential operator. Additional small excitation peaks due to surface effects are found in transverse S(q,w).

  10. Dislocation dynamics: simulation of plastic flow of bcc metals

    SciTech Connect

    Lassila, D H

    2001-02-20

    This is the final report for the LDRD strategic initiative entitled ''Dislocation Dynamic: Simulation of Plastic Flow of bcc Metals'' (tracking code: 00-SI-011). This report is comprised of 6 individual sections. The first is an executive summary of the project and describes the overall project goal, which is to establish an experimentally validated 3D dislocation dynamics simulation. This first section also gives some information of LLNL's multi-scale modeling efforts associated with the plasticity of bcc metals, and the role of this LDRD project in the multiscale modeling program. The last five sections of this report are journal articles that were produced during the course of the FY-2000 efforts.

  11. Algorithm for simulation of quantum many-body dynamics using dynamical coarse-graining

    SciTech Connect

    Khasin, M.; Kosloff, R.

    2010-04-15

    An algorithm for simulation of quantum many-body dynamics having su(2) spectrum-generating algebra is developed. The algorithm is based on the idea of dynamical coarse-graining. The original unitary dynamics of the target observables--the elements of the spectrum-generating algebra--is simulated by a surrogate open-system dynamics, which can be interpreted as weak measurement of the target observables, performed on the evolving system. The open-system state can be represented by a mixture of pure states, localized in the phase space. The localization reduces the scaling of the computational resources with the Hilbert-space dimension n by factor n{sup 3/2}(ln n){sup -1} compared to conventional sparse-matrix methods. The guidelines for the choice of parameters for the simulation are presented and the scaling of the computational resources with the Hilbert-space dimension of the system is estimated. The algorithm is applied to the simulation of the dynamics of systems of 2x10{sup 4} and 2x10{sup 6} cold atoms in a double-well trap, described by the two-site Bose-Hubbard model.

  12. Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association.

    PubMed

    Butler, Brandon M; Gerek, Z Nevin; Kumar, Sudhir; Ozkan, S Banu

    2015-03-01

    Recent studies have shown that the protein interface sites between individual monomeric units in biological assemblies are enriched in disease-associated non-synonymous single nucleotide variants (nsSNVs). To elucidate the mechanistic underpinning of this observation, we investigated the conformational dynamic properties of protein interface sites through a site-specific structural dynamic flexibility metric (dfi) for 333 multimeric protein assemblies. dfi measures the dynamic resilience of a single residue to perturbations that occurred in the rest of the protein structure and identifies sites contributing the most to functionally critical dynamics. Analysis of dfi profiles of over a thousand positions harboring variation revealed that amino acid residues at interfaces have lower average dfi (31%) than those present at non-interfaces (50%), which means that protein interfaces have less dynamic flexibility. Interestingly, interface sites with disease-associated nsSNVs have significantly lower average dfi (23%) as compared to those of neutral nsSNVs (42%), which directly relates structural dynamics to functional importance. We found that less conserved interface positions show much lower dfi for disease nsSNVs as compared to neutral nsSNVs. In this case, dfi is better as compared to the accessible surface area metric, which is based on the static protein structure. Overall, our proteome-wide conformational dynamic analysis indicates that certain interface sites play a critical role in functionally related dynamics (i.e., those with low dfi values), therefore mutations at those sites are more likely to be associated with disease.

  13. Applying Parallel Processing Techniques to Tether Dynamics Simulation

    NASA Technical Reports Server (NTRS)

    Wells, B. Earl

    1996-01-01

    The focus of this research has been to determine the effectiveness of applying parallel processing techniques to a sizable real-world problem, the simulation of the dynamics associated with a tether which connects two objects in low earth orbit, and to explore the degree to which the parallelization process can be automated through the creation of new software tools. The goal has been to utilize this specific application problem as a base to develop more generally applicable techniques.

  14. Phase transitions of methane using molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    El-Sheikh, S. M.; Barakat, K.; Salem, N. M.

    2006-03-01

    Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.

  15. Phase transitions of methane using molecular dynamics simulations.

    PubMed

    El-Sheikh, S M; Barakat, K; Salem, N M

    2006-03-28

    Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4 under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256 molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.

  16. Simulated dynamic response of a servovalve controlled hydraulic actuator

    NASA Technical Reports Server (NTRS)

    Babcock, Dale A.

    1990-01-01

    A general purpose math model of a servovalve controlled hydraulic actuator system is derived. The system consists of a linear actuator with unequal piston areas, a single stage servovalve, a gas charged hydraulic accumulator, and the interconnecting piping. The state equations are integrated using the Advanced Continuous Simulation Language (ACSL) for determining the system's dynamic response characteristics. Using this generalized hydraulic actuator system model, response characteristics were determined for various servovalve commands.

  17. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

    PubMed

    Rapaport, D C

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

  18. Molecular dynamics simulations of ordering of polydimethylsiloxane under uniaxial extension

    SciTech Connect

    Lacevic, N M; Gee, R H

    2005-03-11

    Molecular dynamics simulations of a bulk melts of polydimethylsiloxane (PDMS) are utilized to study chain conformation and ordering under constant uniaxial tension. We find that large extensions induce chain ordering in the direction of applied tension. We also find that voids are created via a cavitation mechanism. This study represents a validation of the current model for PDMS and benchmark for the future study of mechanical properties of PDMS melts enriched with fillers under tension.

  19. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

    PubMed

    Rapaport, D C

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency. PMID:19518394

  20. Simulation of dynamic material response with the PAGOSA code

    SciTech Connect

    Holian, K.S.; Adams, T.F.

    1993-08-01

    The 3D Eulerian PAGOSA hydrocode is being run on the massively parallel Connection Machine (CM) to simulate the response of materials to dynamic loading, such as by high explosives or high velocity impact. The code has a variety of equation of state forms, plastic yield models, and fracture and fragmentation models. The numerical algorithms in PAGOSA and the implementation of material models are discussed briefly.