Transition Pathway and Its Free-Energy Profile: A Protocol for Protein Folding Simulations

PubMed Central

Lee, In-Ho; Kim, Seung-Yeon; Lee, Jooyoung

2013-01-01

We propose a protocol that provides a systematic definition of reaction coordinate and related free-energy profile as the function of temperature for the protein-folding simulation. First, using action-derived molecular dynamics (ADMD), we investigate the dynamic folding pathway model of a protein between a fixed extended conformation and a compact conformation. We choose the pathway model to be the reaction coordinate, and the folding and unfolding processes are characterized by the ADMD step index, in contrast to the common a priori reaction coordinate as used in conventional studies. Second, we calculate free-energy profile as the function of temperature, by employing the replica-exchange molecular dynamics (REMD) method. The current method provides efficient exploration of conformational space and proper characterization of protein folding/unfolding dynamics from/to an arbitrary extended conformation. We demonstrate that combination of the two simulation methods, ADMD and REMD, provides understanding on molecular conformational changes in proteins. The protocol is tested on a small protein, penta-peptide of met-enkephalin. For the neuropeptide met-enkephalin system, folded, extended, and intermediate sates are well-defined through the free-energy profile over the reaction coordinate. Results are consistent with those in the literature. PMID:23917881

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.

PubMed

Mishra, Sushil Kumar; Kara, Mahmut; Zacharias, Martin; Koca, Jaroslav

2014-01-01

Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.

Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models.

PubMed

Fan, Hao; Periole, Xavier; Mark, Alan E

2012-07-01

The efficiency of using a variant of Hamiltonian replica-exchange molecular dynamics (Chaperone H-replica-exchange molecular dynamics [CH-REMD]) for the refinement of protein structural models generated de novo is investigated. In CH-REMD, the interaction between the protein and its environment, specifically, the electrostatic interaction between the protein and the solvating water, is varied leading to cycles of partial unfolding and refolding mimicking some aspects of folding chaperones. In 10 of the 15 cases examined, the CH-REMD approach sampled structures in which the root-mean-square deviation (RMSD) of secondary structure elements (SSE-RMSD) with respect to the experimental structure was more than 1.0 Å lower than the initial de novo model. In 14 of the 15 cases, the improvement was more than 0.5 Å. The ability of three different statistical potentials to identify near-native conformations was also examined. Little correlation between the SSE-RMSD of the sampled structures with respect to the experimental structure and any of the scoring functions tested was found. The most effective scoring function tested was the DFIRE potential. Using the DFIRE potential, the SSE-RMSD of the best scoring structures was on average 0.3 Å lower than the initial model. Overall the work demonstrates that targeted enhanced-sampling techniques such as CH-REMD can lead to the systematic refinement of protein structural models generated de novo but that improved potentials for the identification of near-native structures are still needed. Copyright © 2012 Wiley Periodicals, Inc.

Interaction of the Disordered Yersinia Effector Protein YopE with Its Cognate Chaperone SycE

DTIC Science & Technology

2009-01-01

structures of YopECBD were molten globules with a hydrophobic core. Molecular dynamics (MD) simulations indi- cated that the structure remained compact at...ensembles of unfolded conformations of the Yersinia effector YopE using REMD simulations and docked them to the chaper- one SycE using a multistep protein...disordered state but transitions into an ordered state upon binding to its cognate chaperone (7). The dynamics of the disordered effector protein and

The molecular mechanism of fullerene-inhibited aggregation of Alzheimer's β-amyloid peptide fragment

NASA Astrophysics Data System (ADS)

Xie, Luogang; Luo, Yin; Lin, Dongdong; Xi, Wenhui; Yang, Xinju; Wei, Guanghong

2014-07-01

Amyloid deposits are implicated in the pathogenesis of many neurodegenerative diseases such as Alzheimer's disease (AD). The inhibition of β-sheet formation has been considered as the primary therapeutic strategy for AD. Increasing data show that nanoparticles can retard or promote the fibrillation of amyloid-β (Aβ) peptides depending on the physicochemical properties of nanoparticles, however, the underlying molecular mechanism remains elusive. In this study, our replica exchange molecular dynamics (REMD) simulations show that fullerene nanoparticle - C60 (with a fullerene : peptide molar ratio greater than 1 : 8) can dramatically prevent β-sheet formation of Aβ(16-22) peptides. Atomic force microscopy (AFM) experiments further confirm the inhibitory effect of C60 on Aβ(16-22) fibrillation, in support of our REMD simulations. An important finding from our REMD simulations is that fullerene C180, albeit with the same number of carbon atoms as three C60 molecules (3C60) and smaller surface area than 3C60, displays an unexpected stronger inhibitory effect on the β-sheet formation of Aβ(16-22) peptides. A detailed analysis of the fullerene-peptide interaction reveals that the stronger inhibition of β-sheet formation by C180 results from the strong hydrophobic and aromatic-stacking interactions of the fullerene hexagonal rings with the Phe rings relative to the pentagonal rings. The strong interactions between the fullerene nanoparticles and Aβ(16-22) peptides significantly weaken the peptide-peptide interaction that is important for β-sheet formation, thus retarding Aβ(16-22) fibrillation. Overall, our studies reveal the significant role of fullerene hexagonal rings in the inhibition of Aβ(16-22) fibrillation and provide novel insight into the development of drug candidates against Alzheimer's disease.Amyloid deposits are implicated in the pathogenesis of many neurodegenerative diseases such as Alzheimer's disease (AD). The inhibition of β-sheet formation has been considered as the primary therapeutic strategy for AD. Increasing data show that nanoparticles can retard or promote the fibrillation of amyloid-β (Aβ) peptides depending on the physicochemical properties of nanoparticles, however, the underlying molecular mechanism remains elusive. In this study, our replica exchange molecular dynamics (REMD) simulations show that fullerene nanoparticle - C60 (with a fullerene : peptide molar ratio greater than 1 : 8) can dramatically prevent β-sheet formation of Aβ(16-22) peptides. Atomic force microscopy (AFM) experiments further confirm the inhibitory effect of C60 on Aβ(16-22) fibrillation, in support of our REMD simulations. An important finding from our REMD simulations is that fullerene C180, albeit with the same number of carbon atoms as three C60 molecules (3C60) and smaller surface area than 3C60, displays an unexpected stronger inhibitory effect on the β-sheet formation of Aβ(16-22) peptides. A detailed analysis of the fullerene-peptide interaction reveals that the stronger inhibition of β-sheet formation by C180 results from the strong hydrophobic and aromatic-stacking interactions of the fullerene hexagonal rings with the Phe rings relative to the pentagonal rings. The strong interactions between the fullerene nanoparticles and Aβ(16-22) peptides significantly weaken the peptide-peptide interaction that is important for β-sheet formation, thus retarding Aβ(16-22) fibrillation. Overall, our studies reveal the significant role of fullerene hexagonal rings in the inhibition of Aβ(16-22) fibrillation and provide novel insight into the development of drug candidates against Alzheimer's disease. Electronic supplementary information (ESI) available: The description of REMD simulations, analysis parameters, and AFM imaging of Aβ(16-22) aggregation with and without C60 nanoparticles, and three figures. The figures show the initial states, the convergence check for all the REMD runs, the PDF of the centroid distance (d) between the aromatic rings of Phe and its closest carbon ring, and the PDF of the angle between the two rings with a centroid distance of d <= 0.65 nm. See DOI: 10.1039/c4nr01005a

Computational investigation of the conformational profile of the four stereomers of Ac-L-Pro-c3Phe-NHMe (c3Phe= 2,3-methanophenylalanine).

PubMed

Rodriguez, Alejandro; Canto, Josep; Corcho, Francesc J; Perez, Juan J

2009-01-01

The present report regards a computational study aimed at assessing the conformational profile of the four stereoisomers of the peptide Ace-Pro-c3Phe-NMe, previously reported to exhibit beta-turn structures in dichloromethane with different type I/type II beta-turn profiles. Molecular systems were represented at the molecular mechanics level using the parm96 parameterization of the AMBER force field. Calculations were carried out in dichloromethane using an implicit solvent approach. Characterization of the conformational features of the peptide analogs was carried out using simulated annealing (SA), molecular dynamics (MD) and replica exchange molecular dynamics (REMD). Present results show that MD calculations do not provide a reasonable sampling after 300 ns. In contrast, both SA and REMD provide similar results and agree well with experimental observations. Copyright 2009 Wiley Periodicals, Inc.

The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations.

PubMed

Wang, Moye; Hu, Jie; Zhang, Zhuqing

2016-04-26

As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5-10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.

The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations

PubMed Central

Wang, Moye; Hu, Jie; Zhang, Zhuqing

2016-01-01

As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5–10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design. PMID:27128902

Communication: Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering

NASA Astrophysics Data System (ADS)

Arefi, Hadi H.; Yamamoto, Takeshi

2017-12-01

Conventional molecular-dynamics (cMD) simulation has a well-known limitation in accessible time and length scales, and thus various enhanced sampling techniques have been proposed to alleviate the problem. In this paper, we explore the utility of replica exchange with solute tempering (REST) (i.e., a variant of Hamiltonian replica exchange methods) to simulate the self-assembly of a supramolecular polymer in explicit solvent and compare the performance with temperature-based replica exchange MD (T-REMD) as well as cMD. As a test system, we consider a relatively simple all-atom model of supramolecular polymerization (namely, benzene-1,3,5-tricarboxamides in methylcyclohexane solvent). Our results show that both REST and T-REMD are able to predict highly ordered polymer structures with helical H-bonding patterns, in contrast to cMD which completely fails to obtain such a structure for the present model. At the same time, we have also experienced some technical challenge (i.e., aggregation-dispersion transition and the resulting bottleneck for replica traversal), which is illustrated numerically. Since the computational cost of REST scales more moderately than T-REMD, we expect that REST will be useful for studying the self-assembly of larger systems in solution with enhanced rearrangement of monomers.

Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation.

PubMed

Kasahara, Kota; Sakuraba, Shun; Fukuda, Ikuo

2018-03-08

We investigate the problem of artifacts caused by the periodic boundary conditions (PBC) used in molecular simulation studies. Despite the long history of simulations with PBCs, the existence of measurable artifacts originating from PBCs applied to inherently nonperiodic physical systems remains controversial. Specifically, these artifacts appear as differences between simulations of the same system but with different simulation-cell sizes. Earlier studies have implied that, even in the simple case of a small model peptide in water, sampling inefficiency is a major obstacle to understanding these artifacts. In this study, we have resolved the sampling issue using the replica exchange molecular dynamics (REMD) enhanced-sampling method to explore PBC artifacts. Explicitly solvated zwitterionic polyalanine octapeptides with three different cubic-cells, having dimensions of L = 30, 40, and 50 Å, were investigated to elucidate the differences with 64 replica × 500 ns REMD simulations using the AMBER parm99SB force field. The differences among them were not large overall, and the results for the L = 30 and 40 Å simulations in the conformational free energy landscape were found to be very similar at room temperature. However, a small but statistically significant difference was seen for L = 50 Å. We observed that extended conformations were slightly overstabilized in the smaller systems. The origin of these artifacts is discussed by comparison to an electrostatic calculation method without PBCs.

Multiscale implementation of infinite-swap replica exchange molecular dynamics.

PubMed

Yu, Tang-Qing; Lu, Jianfeng; Abrams, Cameron F; Vanden-Eijnden, Eric

2016-10-18

Replica exchange molecular dynamics (REMD) is a popular method to accelerate conformational sampling of complex molecular systems. The idea is to run several replicas of the system in parallel at different temperatures that are swapped periodically. These swaps are typically attempted every few MD steps and accepted or rejected according to a Metropolis-Hastings criterion. This guarantees that the joint distribution of the composite system of replicas is the normalized sum of the symmetrized product of the canonical distributions of these replicas at the different temperatures. Here we propose a different implementation of REMD in which (i) the swaps obey a continuous-time Markov jump process implemented via Gillespie's stochastic simulation algorithm (SSA), which also samples exactly the aforementioned joint distribution and has the advantage of being rejection free, and (ii) this REMD-SSA is combined with the heterogeneous multiscale method to accelerate the rate of the swaps and reach the so-called infinite-swap limit that is known to optimize sampling efficiency. The method is easy to implement and can be trivially parallelized. Here we illustrate its accuracy and efficiency on the examples of alanine dipeptide in vacuum and C-terminal β-hairpin of protein G in explicit solvent. In this latter example, our results indicate that the landscape of the protein is a triple funnel with two folded structures and one misfolded structure that are stabilized by H-bonds.

Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch

PubMed Central

Eichhorn, Catherine D.; Feng, Jun; Suddala, Krishna C.; Walter, Nils G.; Brooks, Charles L.; Al-Hashimi, Hashim M.

2012-01-01

Single-stranded RNAs (ssRNAs) are ubiquitous RNA elements that serve diverse functional roles. Much of our understanding of ssRNA conformational behavior is limited to structures in which ssRNA directly engages in tertiary interactions or is recognized by proteins. Little is known about the structural and dynamic behavior of free ssRNAs at atomic resolution. Here, we report the collaborative application of nuclear magnetic resonance (NMR) and replica exchange molecular dynamics (REMD) simulations to characterize the 12 nt ssRNA tail derived from the prequeuosine riboswitch. NMR carbon spin relaxation data and residual dipolar coupling measurements reveal a flexible yet stacked core adopting an A-form-like conformation, with the level of order decreasing toward the terminal ends. An A-to-C mutation within the polyadenine tract alters the observed dynamics consistent with the introduction of a dynamic kink. Pre-ordering of the tail may increase the efficacy of ligand binding above that achieved by a random-coil ssRNA. The REMD simulations recapitulate important trends in the NMR data, but suggest more internal motions than inferred from the NMR analysis. Our study unmasks a previously unappreciated level of complexity in ssRNA, which we believe will also serve as an excellent model system for testing and developing computational force fields. PMID:22009676

Role of mutation on fibril formation in small peptides by REMD

NASA Astrophysics Data System (ADS)

Mahmoudinobar, Farbod; Dias, Cristiano

Amyloid fibrils are now recognized as a common form of protein structure. They have wide implications for neurological diseases and entities involved in the survival of living organisms, e.g., silkmoth eggshells. Biological functions of these entities are often related to the superior mechanical strength of fibrils that persists over a broad range of chemical and thermal conditions desirable for various biotechnological applications, e.g., to encapsulate drugs. Mechanical properties of fibrils was shown to depend strongly on the amino acid sequence of its constituent peptides whereby bending rigidities can vary by two orders of magnitude. Therefore, the rational design of new fibril-prone peptides with tailored properties depends on our understanding of the relation between amino acid sequence and its propensity to fibrillize. In this presentation I will show results from extensive Replica Exchange Molecular Dynamics (REMD) simulations of a 12-residue peptide containing the fibril-prone motif KFFE and its mutants. Simulations are performed on monomers, dimers, and tetramers. I will discuss effects of side chain packing, hydrophobicity, charges and beta-sheet propensity on fibril formation. Physics Department, University Heights, Newark, New Jersey, 07102-1982, USA.

A flexible docking scheme to explore the binding selectivity of PDZ domains.

PubMed

Gerek, Z Nevin; Ozkan, S Banu

2010-05-01

Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using ROSETTALIGAND, we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density-95/Dlg/ZO-1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 A. We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately.

A flexible docking scheme to explore the binding selectivity of PDZ domains

PubMed Central

Gerek, Z Nevin; Ozkan, S Banu

2010-01-01

Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using RosettaLigand, we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density-95/Dlg/ZO-1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 Å. We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately. PMID:20196074

Efficient parallel implementations of QM/MM-REMD (quantum mechanical/molecular mechanics-replica-exchange MD) and umbrella sampling: isomerization of H2O2 in aqueous solution.

PubMed

Fedorov, Dmitri G; Sugita, Yuji; Choi, Cheol Ho

2013-07-03

An efficient parallel implementation of QM/MM-based replica-exchange molecular dynamics (REMD) as well as umbrella samplings techniques was proposed by adopting the generalized distributed data interface (GDDI). Parallelization speed-up of 40.5 on 48 cores was achieved, making our QM/MM-MD engine a robust tool for studying complex chemical dynamics in solution. They were comparatively used to study the torsional isomerization of hydrogen peroxide in aqueous solution. All results by QM/MM-REMD and QM/MM umbrella sampling techniques yielded nearly identical potentials of mean force (PMFs) regardless of the particular QM theories for solute, showing that the overall dynamics are mainly determined by solvation. Although the entropic penalty of solvent rearrangements exists in cisoid conformers, it was found that both strong intermolecular hydrogen bonding and dipole-dipole interactions preferentially stabilize them in solution, reducing the torsional free-energy barrier at 0° by about 3 kcal/mol as compared to that in gas phase.

Computational Insights into the Stability and Folding Pathways of Human Telomeric DNA G-Quadruplexes.

PubMed

Luo, Di; Mu, Yuguang

2016-06-09

G-quadruplex is a noncanonical yet crucial secondary structure of nucleic acids, which has proven its importance in cell aging, anticancer therapies, gene expression, and genome stability. In this study, the stability and folding dynamics of human telomeric DNA G-quadruplexes were investigated via enhanced sampling techniques. First, temperature-replica exchange MD (REMD) simulations were employed to compare the thermal stabilities among the five established folding topologies. The hybrid-2 type adopted by extended human telomeric sequence is revealed to be the most stable conformation in our simulations. Next, the free energy landscapes and folding intermediates of the hybrid-1 and -2 types were investigated with parallel tempering metadynamics simulations in the well-tempered ensemble. It was observed that the N-glycosidic conformations of guanines can flip over to accommodate into the cyclic Hoogsteen H-bonding on G-tetrads in which they were not originally involved. Furthermore, a hairpin and a triplex intermediate were identified for the folding of the hybrid-1 type conformation, whereas for the hybrid-2 type, there were no folding intermediates observed from its free energy surface. However, the energy barrier from its native topology to the transition structure is found to be extremely high compared to that of the hybrid-1 type, which is consistent with our stability predictions from the REMD simulations. We hope the insights presented in this work can help to complement current understanding on the stability and dynamics of G-quadruplexes, which is necessary not only to stabilize the structures but also to intervene their formation in genome.

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.

PubMed

Voelz, Vincent A; Dill, Ken A; Chorny, Ilya

2011-01-01

To test the accuracy of existing AMBER force field models in predicting peptoid conformation and dynamics, we simulated a set of model peptoid molecules recently examined by Butterfoss et al. (JACS 2009, 131, 16798-16807) using QM methods as well as three peptoid sequences with experimentally determined structures. We found that AMBER force fields, when used with a Generalized Born/Surface Area (GBSA) implicit solvation model, could accurately reproduce the peptoid torsional landscape as well as the major conformers of known peptoid structures. Enhanced sampling by replica exchange molecular dynamics (REMD) using temperatures from 300 to 800 K was used to sample over cis-trans isomerization barriers. Compared to (Nrch)5 and cyclo-octasarcosyl, the free energy of N-(2-nitro-3-hydroxyl phenyl)glycine-N-(phenyl)glycine has the most "foldable" free energy landscape, due to deep trans-amide minima dictated by N-aryl sidechains. For peptoids with (S)-N (1-phenylethyl) (Nspe) side chains, we observe a discrepancy in backbone dihedral propensities between molecular simulations and QM calculations, which may be due to force field effects or the inability to capture n --> n* interactions. For these residues, an empirical phi-angle biasing potential can "rescue" the backbone propensities seen in QM. This approach can serve as a general strategy for addressing force fields without resorting to a complete reparameterization. Overall, this study demonstrates the utility of implicit-solvent REMD simulations for efficient sampling to predict peptoid conformational landscapes, providing a potential tool for first-principles design of sequences with specific folding properties.

Recipes for free energy calculations in biomolecular systems.

PubMed

Moradi, Mahmoud; Babin, Volodymyr; Sagui, Celeste; Roland, Christopher

2013-01-01

During the last decade, several methods for sampling phase space and calculating various free energies in biomolecular systems have been devised or refined for molecular dynamics (MD) simulations. Thus, state-of-the-art methodology and the ever increasing computer power allow calculations that were forbidden a decade ago. These calculations, however, are not trivial as they require knowledge of the methods, insight into the system under study, and, quite often, an artful combination of different methodologies in order to avoid the various traps inherent in an unknown free energy landscape. In this chapter, we illustrate some of these concepts with two relatively simple systems, a sugar ring and proline oligopeptides, whose free energy landscapes still offer considerable challenges. In order to explore the configurational space of these systems, and to surmount the various free energy barriers, we combine three complementary methods: a nonequilibrium umbrella sampling method (adaptively biased MD, or ABMD), replica-exchange molecular dynamics (REMD), and steered molecular dynamics (SMD). In particular, ABMD is used to compute the free energy surface of a set of collective variables; REMD is used to improve the performance of ABMD, to carry out sampling in space complementary to the collective variables, and to sample equilibrium configurations directly; and SMD is used to study different transition mechanisms.

Comparative characterization of short monomeric polyglutamine peptides by replica exchange molecular dynamics simulation.

PubMed

Nakano, Miki; Watanabe, Hirofumi; Rothstein, Stuart M; Tanaka, Shigenori

2010-05-27

Polyglutamine (polyQ) diseases are caused by an abnormal expansion of CAG repeats. While their detailed structure remains unclear, polyQ peptides assume beta-sheet structures when they aggregate. To investigate the conformational ensemble of short, monomeric polyQ peptides, which consist of 15 glutamine residues (Q(15)), we performed replica exchange molecular dynamics (REMD) simulations. We found that Q(15) can assume multiple configurations due to all of the residues affecting the formation of side-chain hydrogen bonds. Analysis of the free energy landscape reveals that Q(15) has a basin for random-coil structures and another for alpha-helix or beta-turn structures. To investigate properties of aggregated polyQ peptides, we performed multiple molecular dynamics (MMD) simulations for monomeric and oligomeric Q(15). MMD revealed that the formation of oligomers stabilizes the beta-turn structure by increasing the number of hydrogen bonds between the main chains.

Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein.

PubMed

Zou, Yu; Sun, Yunxiang; Zhu, Yuzhen; Ma, Buyong; Nussinov, Ruth; Zhang, Qingwen

2016-03-16

The aggregation of the copper-zinc superoxide dismutase (SOD1) protein is linked to familial amyotrophic lateral sclerosis, a progressive neurodegenerative disease. A recent experimental study has shown that the (147)GVIGIAQ(153) SOD1 C-terminal segment not only forms amyloid fibrils in isolation but also accelerates the aggregation of full-length SOD1, while substitution of isoleucine at site 149 by proline blocks its fibril formation. Amyloid formation is a nucleation-polymerization process. In this study, we investigated the oligomerization and the nucleus structure of this heptapeptide. By performing extensive replica-exchange molecular dynamics (REMD) simulations and conventional MD simulations, we found that the GVIGIAQ hexamers can adopt highly ordered bilayer β-sheets and β-barrels. In contrast, substitution of I149 by proline significantly reduces the β-sheet probability and results in the disappearance of bilayer β-sheet structures and the increase of disordered hexamers. We identified mixed parallel-antiparallel bilayer β-sheets in both REMD and conventional MD simulations and provided the conformational transition from the experimentally observed parallel bilayer sheets to the mixed parallel-antiparallel bilayer β-sheets. Our simulations suggest that the critical nucleus consists of six peptide chains and two additional peptide chains strongly stabilize this critical nucleus. The stabilized octamer is able to recruit additional random peptides into the β-sheet. Therefore, our simulations provide insights into the critical nucleus formation and the smallest stable nucleus of the (147)GVIGIAQ(153) peptide.

Efficiency reduction and pseudo-convergence in replica exchange sampling of peptide folding unfolding equilibria

NASA Astrophysics Data System (ADS)

Denschlag, Robert; Lingenheil, Martin; Tavan, Paul

2008-06-01

Replica exchange (RE) molecular dynamics (MD) simulations are frequently applied to sample the folding-unfolding equilibria of β-hairpin peptides in solution, because efficiency gains are expected from this technique. Using a three-state Markov model featuring key aspects of β-hairpin folding we show that RE simulations can be less efficient than conventional techniques. Furthermore we demonstrate that one is easily seduced to erroneously assign convergence to the RE sampling, because RE ensembles can rapidly reach long-lived stationary states. We conclude that typical REMD simulations covering a few tens of nanoseconds are by far too short for sufficient sampling of β-hairpin folding-unfolding equilibria.

Effects of intensity on muscle-specific voluntary electromechanical delay and relaxation electromechanical delay.

PubMed

Smith, Cory M; Housh, Terry J; Hill, Ethan C; Keller, Josh L; Johnson, Glen O; Schmidt, Richard J

2018-06-01

The purposes of this study were to examine: 1) the potential muscle-specific differences in voluntary electromechanical delay (EMD) and relaxation electromechanical delay (R-EMD), and 2) the effects of intensity on EMD and R-EMD during step incremental isometric muscle actions from 10 to 100% maximal voluntary isometric contraction (MVIC). EMD and R-EMD measures were calculated from the simultaneous assessments of electromyography, mechanomyography, and force production from the vastus lateralis (VL), vastus medialis (VM), and rectus femoris (RF) during step isometric muscle actions. There were no differences between the VL, VM, and RF for the voluntary EMD E-M (onsets of the electromyographic to mechanomyographic signals), EMD M-F (onsets the mechanomyographic to force production), or EMD E-F (onsets of the electromyographic signal to force production) as well as R-EMD E-M (cessation of electromyographic to mechanomyographic signal), R-EMD M-F (cessation of mechanomyographic signal to force cessation), or R-EMD E-F (cessation of electromyorgraphic signal to force cessation) at any intensity. There were decreases in all EMD and R-EMD measures with increases in intensity. The relative contributions from EMD E-M and EMD M-F to EMD E-F as well as R-EMD E-M and R-EMD M-F to R-EMD E-F remained similar across all intensities. The superficial muscles of the quadriceps femoris shared similar EMD and R-EMD measurements.

Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics.

PubMed

Galvelis, Raimondas; Re, Suyong; Sugita, Yuji

2017-05-09

Molecular dynamics (MD) simulation of a N-glycan in solution is challenging because of high-energy barriers of the glycosidic linkages, functional group rotational barriers, and numerous intra- and intermolecular hydrogen bonds. In this study, we apply different enhanced conformational sampling approaches, namely, metadynamics (MTD), the replica-exchange MD (REMD), and the recently proposed replica state exchange MTD (RSE-MTD), to a N-glycan in solution and compare the conformational sampling efficiencies of the approaches. MTD helps to cross the high-energy barrier along the ω angle by utilizing a bias potential, but it cannot enhance sampling of the other degrees of freedom. REMD ensures moderate-energy barrier crossings by exchanging temperatures between replicas, while it hardly crosses the barriers along ω. In contrast, RSE-MTD succeeds to cross the high-energy barrier along ω as well as to enhance sampling of the other degrees of freedom. We tested two RSE-MTD schemes: in one scheme, 64 replicas were simulated with the bias potential along ω at different temperatures, while simulations of four replicas were performed with the bias potentials for different CVs at 300 K. In both schemes, one unbiased replica at 300 K was included to compute conformational properties of the glycan. The conformational sampling of the former is better than the other enhanced sampling methods, while the latter shows reasonable performance without spending large computational resources. The latter scheme is likely to be useful when a N-glycan-attached protein is simulated.

Effect of bisecting GlcNAc and core fucosylation on conformational properties of biantennary complex-type N-glycans in solution.

PubMed

Nishima, Wataru; Miyashita, Naoyuki; Yamaguchi, Yoshiki; Sugita, Yuji; Re, Suyong

2012-07-26

The introduction of bisecting GlcNAc and core fucosylation in N-glycans is essential for fine functional regulation of glycoproteins. In this paper, the effect of these modifications on the conformational properties of N-glycans is examined at the atomic level by performing replica-exchange molecular dynamics (REMD) simulations. We simulate four biantennary complex-type N-glycans, namely, unmodified, two single-substituted with either bisecting GlcNAc or core fucose, and disubstituted forms. By using REMD as an enhanced sampling technique, five distinct conformers in solution, each of which is characterized by its local orientation of the Manα1-6Man glycosidic linkage, are observed for all four N-glycans. The chemical modifications significantly change their conformational equilibria. The number of major conformers is reduced from five to two and from five to four upon the introduction of bisecting GlcNAc and core fucosylation, respectively. The population change is attributed to specific inter-residue hydrogen bonds, including water-mediated ones. The experimental NMR data, including nuclear Overhauser enhancement and scalar J-coupling constants, are well reproduced taking the multiple conformers into account. Our structural model supports the concept of "conformer selection", which emphasizes the conformational flexibility of N-glycans in protein-glycan interactions.

Efficiency of Adaptive Temperature-Based Replica Exchange for Sampling Large-Scale Protein Conformational Transitions.

PubMed

Zhang, Weihong; Chen, Jianhan

2013-06-11

Temperature-based replica exchange (RE) is now considered a principal technique for enhanced sampling of protein conformations. It is also recognized that existence of sharp cooperative transitions (such as protein folding/unfolding) can lead to temperature exchange bottlenecks and significantly reduce the sampling efficiency. Here, we revisit two adaptive temperature-based RE protocols, namely, exchange equalization (EE) and current maximization (CM), that were previously examined using atomistic simulations (Lee and Olson, J. Chem. Physics2011, 134, 24111). Both protocols aim to overcome exchange bottlenecks by adaptively adjusting the simulation temperatures, either to achieve uniform exchange rates (in EE) or to maximize temperature diffusion (CM). By designing a realistic yet computationally tractable coarse-grained protein model, one can sample many reversible folding/unfolding transitions using conventional constant temperature molecular dynamics (MD), standard REMD, EE-REMD, and CM-REMD. This allows rigorous evaluation of the sampling efficiency, by directly comparing the rates of folding/unfolding transitions and convergence of various thermodynamic properties of interest. The results demonstrate that both EE and CM can indeed enhance temperature diffusion compared to standard RE, by ∼3- and over 10-fold, respectively. Surprisingly, the rates of reversible folding/unfolding transitions are similar in all three RE protocols. The convergence rates of several key thermodynamic properties, including the folding stability and various 1D and 2D free energy surfaces, are also similar. Therefore, the efficiency of RE protocols does not appear to be limited by temperature diffusion, but by the inherent rates of spontaneous large-scale conformational rearrangements. This is particularly true considering that virtually all RE simulations of proteins in practice involve exchange attempt frequencies (∼ps(-1)) that are several orders of magnitude faster than the slowest protein motions (∼μs(-1)). Our results also suggest that the efficiency of RE will not likely be improved by other protocols that aim to accelerate exchange or temperature diffusion. Instead, protocols with some types of guided tempering will likely be necessary to drive faster large-scale conformational transitions.

Propafenone effects on the stable structures of Aβ16-22 system

NASA Astrophysics Data System (ADS)

Tran, Linh; Ngo, Son Tung; Nguyen, Minh Tho

2018-03-01

An extensive replica exchange molecular dynamics (REMD) simulation was performed to investigate the progress patterns of the molecular interactions of propafenone and Aβ16-22 system. Distinct conformational equilibrium of Aβ16-22 system with and without propafenone was analyzed in detail. Propafenone can act to prevent the Alzheimer's disease (AD) by significantly inhibiting Aβ oligomerization. Our calculated results provide insights into the inhibition mechanism of propafenone on the oligomerization process to form Aβ16-22 peptide aggregation. These findings are valuable for the development of therapeutic drugs in the AD early stage.

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

PubMed

Ostermeir, Katja; Zacharias, Martin

2014-12-01

Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations. © 2014 Wiley Periodicals, Inc.

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.

PubMed

Czaplewski, Cezary; Kalinowski, Sebastian; Liwo, Adam; Scheraga, Harold A

2009-03-10

The replica exchange (RE) method is increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. Recently, we implemented the united-residue UNRES force field for mesoscopic MD. Initial results from UNRES MD simulations show that we are able to simulate folding events that take place in a microsecond or even a millisecond time scale. To speed up the search further, we applied the multiplexing replica exchange molecular dynamics (MREMD) method. The multiplexed variant (MREMD) of the RE method, developed by Rhee and Pande, differs from the original RE method in that several trajectories are run at a given temperature. Each set of trajectories run at a different temperature constitutes a layer. Exchanges are attempted not only within a single layer but also between layers. The code has been parallelized and scales up to 4000 processors. We present a comparison of canonical MD, REMD, and MREMD simulations of protein folding with the UNRES force-field. We demonstrate that the multiplexed procedure increases the power of replica exchange MD considerably and convergence of the thermodynamic quantities is achieved much faster.

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins

PubMed Central

Czaplewski, Cezary; Kalinowski, Sebastian; Liwo, Adam; Scheraga, Harold A.

2009-01-01

The replica exchange (RE) method is increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. Recently, we implemented the united-residue UNRES force field for mesoscopic MD. Initial results from UNRES MD simulations show that we are able to simulate folding events that take place in a microsecond or even a millisecond time scale. To speed up the search further, we applied the multiplexing replica exchange molecular dynamics (MREMD) method. The multiplexed variant (MREMD) of the RE method, developed by Rhee and Pande, differs from the original RE method in that several trajectories are run at a given temperature. Each set of trajectories run at a different temperature constitutes a layer. Exchanges are attempted not only within a single layer but also between layers. The code has been parallelized and scales up to 4000 processors. We present a comparison of canonical MD, REMD, and MREMD simulations of protein folding with the UNRES force-field. We demonstrate that the multiplexed procedure increases the power of replica exchange MD considerably and convergence of the thermodynamic quantities is achieved much faster. PMID:20161452

Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations

PubMed Central

Zheng, Weihua; Gallicchio, Emilio; Deng, Nanjie; Andrec, Michael; Levy, Ronald M.

2011-01-01

We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, Transition Path Theory (TPT) for constructing folding pathways and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270K and 566K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the Weighted-Histogram-Analysis Method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (Pfold) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding “tubes”, a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature, however, the folding transition is dominated by only a few localized pathways. PMID:21254767

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

PubMed

Zheng, Weihua; Gallicchio, Emilio; Deng, Nanjie; Andrec, Michael; Levy, Ronald M

2011-02-17

We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, transition path theory (TPT) for constructing folding pathways, and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270 and 566 K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the weighted-histogram-analysis method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (P(fold)) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding "tubes", a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network, and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature, however, the folding transition is dominated by only a few localized pathways.

Rare diseases in clinical endocrinology: a taxonomic classification system.

PubMed

Marcucci, G; Cianferotti, L; Beck-Peccoz, P; Capezzone, M; Cetani, F; Colao, A; Davì, M V; degli Uberti, E; Del Prato, S; Elisei, R; Faggiano, A; Ferone, D; Foresta, C; Fugazzola, L; Ghigo, E; Giacchetti, G; Giorgino, F; Lenzi, A; Malandrino, P; Mannelli, M; Marcocci, C; Masi, L; Pacini, F; Opocher, G; Radicioni, A; Tonacchera, M; Vigneri, R; Zatelli, M C; Brandi, M L

2015-02-01

Rare endocrine-metabolic diseases (REMD) represent an important area in the field of medicine and pharmacology. The rare diseases of interest to endocrinologists involve all fields of endocrinology, including rare diseases of the pituitary, thyroid and adrenal glands, paraganglia, ovary and testis, disorders of bone and mineral metabolism, energy and lipid metabolism, water metabolism, and syndromes with possible involvement of multiple endocrine glands, and neuroendocrine tumors. Taking advantage of the constitution of a study group on REMD within the Italian Society of Endocrinology, consisting of basic and clinical scientists, a document on the taxonomy of REMD has been produced. This document has been designed to include mainly REMD manifesting or persisting into adulthood. The taxonomy of REMD of the adult comprises a total of 166 main disorders, 338 including all variants and subtypes, described into 11 tables. This report provides a complete taxonomy to classify REMD of the adult. In the future, the creation of registries of rare endocrine diseases to collect data on cohorts of patients and the development of common and standardized diagnostic and therapeutic pathways for each rare endocrine disease is advisable. This will help planning and performing intervention studies in larger groups of patients to prove the efficacy, effectiveness, and safety of a specific treatment.

Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces.

PubMed

Levine, Zachary A; Rapp, Michael V; Wei, Wei; Mullen, Ryan Gotchy; Wu, Chun; Zerze, Gül H; Mittal, Jeetain; Waite, J Herbert; Israelachvili, Jacob N; Shea, Joan-Emma

2016-04-19

Translating sticky biological molecules-such as mussel foot proteins (MFPs)-into synthetic, cost-effective underwater adhesives with adjustable nano- and macroscale characteristics requires an intimate understanding of the glue's molecular interactions. To help facilitate the next generation of aqueous adhesives, we performed a combination of surface forces apparatus (SFA) measurements and replica-exchange molecular dynamics (REMD) simulations on a synthetic, easy to prepare, Dopa-containing peptide (MFP-3s peptide), which adheres to organic surfaces just as effectively as its wild-type protein analog. Experiments and simulations both show significant differences in peptide adsorption on CH3-terminated (hydrophobic) and OH-terminated (hydrophilic) self-assembled monolayers (SAMs), where adsorption is strongest on hydrophobic SAMs because of orientationally specific interactions with Dopa. Additional umbrella-sampling simulations yield free-energy profiles that quantitatively agree with SFA measurements and are used to extract the adhesive properties of individual amino acids within the context of MFP-3s peptide adhesion, revealing a delicate balance between van der Waals, hydrophobic, and electrostatic forces.

A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides

NASA Astrophysics Data System (ADS)

Gao, Ya; Zhang, Chaomin; Wang, Xianwei; Zhu, Tong

2017-07-01

We tested the ability of some current AMBER force fields, namely, AMBER03, AMBER99SB, AMBER99SB-ildn, AMBER99SB-nmr, AMBER12SB, AMBER14SB, and AMBER14ipq, with implicit solvent model in reproducing the folding behavior of two peptides by REMD simulations. AMBER99SB-nmr force field provides the most reliable performance. After a novel polarized hydrogen bond charge model is considered, the α-helix successfully folded to its native state, while the further folding of the β-hairpin is not observed. This study strongly suggests that polarization effect and correct torsional term are important to investigate dynamic and conformational properties of peptides with different secondary structures.

Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation

PubMed Central

Yan, Chunli; Pattani, Varun; Tunnell, James W.; Ren, Pengyu

2010-01-01

Thermal disruption of protein structure and function is a potentially powerful therapeutic vehicle. With the emerging nanoparticle-targeting and femtosecond laser technology, it is possible to deliver heating locally to specific molecules. It is therefore important to understand how fast a protein can unfold or lose its function at high temperatures, such as near the water boiling point. In this study, the thermal damage of EGF was investigated by combining the replica exchange (136 replicas) and conventional molecular dynamics simulations. The REMD simulation was employed to rigorously explore the free energy landscape of EGF unfolding. Interestingly, besides the native and unfolded states, we also observed a distinct molten globule (MG) state that retained substantial amount of native contacts. Based on the understanding that which the unfolding of EGF is a three-state process, we have examined the unfolding kinetics of EGF (N→ MG→h multiple 20-ns conventional MD simulations. The Arrhenius prefactors and activation energy barriers determined from the simulation are within the range of previously studied proteins. In contrast to the thermal damage of cells and tissues which take place on the time scale of seconds to hours at relatively low temperatures, the denaturation of proteins occur in nanoseconds when the temperature of heat bath approaches the boiling point. PMID:20466569

The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier

NASA Astrophysics Data System (ADS)

Lei, Hongxing; Deng, Xiaojian; Wang, Zhixiang; Duan, Yong

2008-10-01

The LYS24/29NLE double mutant of villin headpiece subdomain (HP35) is the fastest folding protein known so far with a folding time constant of 0.6μs. In this work, the folding mechanism of the mutant has been investigated by both conventional and replica exchange molecular dynamics (CMD and REMD) simulations with AMBER FF03 force field and a generalized-Born solvation model. Direct comparison to the ab initio folding of the wild type HP35 enabled a close examination on the mutational effect on the folding process. The mutant folded to the native state, as demonstrated by the 0.50Å Cα-root mean square deviation (RMSD) sampled in both CMD and REMD simulations and the high population of the folded conformation compared with the denatured conformations. Consistent with experiments, the significantly reduced primary folding free energy barrier makes the mutant closer to a downhill folder than the wild type HP35 that directly leads to the faster transition and higher melting temperature. However, unlike the proposed downhill folding which envisages a smooth shift between unfolded and folded states without transition barrier, we observed a well-defined folding transition that was consistent with experiments. Further examination of the secondary structures revealed that the two mutated residues have higher intrinsic helical preference that facilitated the formation of both helix III and the intermediate state which contains the folded segment helix II/III. Other factors contributing to the faster folding include the more favorable electrostatic interactions in the transition state with the removal of the charged NH3+ groups from LYS. In addition, both transition state ensemble and denatured state ensemble are shifted in the mutant.

Probing the interaction between cHAVc3 peptide and the EC1 domain of E-cadherin using NMR and molecular dynamics simulations.

PubMed

Alaofi, Ahmed; Farokhi, Elinaz; Prasasty, Vivitri D; Anbanandam, Asokan; Kuczera, Krzysztof; Siahaan, Teruna J

2017-01-01

The goal of this work is to probe the interaction between cyclic cHAVc3 peptide and the EC1 domain of human E-cadherin protein. Cyclic cHAVc3 peptide (cyclo(1,6)Ac-CSHAVC-NH 2 ) binds to the EC1 domain as shown by chemical shift perturbations in the 2D 1 H,- 15 N-HSQC NMR spectrum. The molecular dynamics (MD) simulations of the EC1 domain showed folding of the C-terminal tail region into the main head region of the EC1 domain. For cHAVc3 peptide, replica exchange molecular dynamics (REMD) simulations generated five structural clusters of cHAVc3 peptide. Representative structures of cHAVc3 and the EC1 structure from MD simulations were used in molecular docking experiments with NMR constraints to determine the binding site of the peptide on EC1. The results suggest that cHAVc3 binds to EC1 around residues Y36, S37, I38, I53, F77, S78, H79, and I94. The dissociation constants (K d values) of cHAVc3 peptide to EC1 were estimated using the NMR chemical shifts data and the estimated K d s are in the range of .5 × 10 -5 -7.0 × 10 -5  M.

Replica-exchange molecular dynamics simulation of basic fibroblast growth factor adsorption on hydroxyapatite.

PubMed

Liao, Chenyi; Zhou, Jian

2014-06-05

The adsorption of basic fibroblast growth factor (bFGF) on the hydroxyapatite (001) surface was investigated by a combination of replica-exchange molecular dynamics (REMD) and conventional molecular dynamics (CMD) methods. In CMD, the protein cannot readily cross the surface water layer, whereas in REMD, the protein can cross the adsorption barrier from the surface water layer and go through weak, medium, then strong adsorption states with three energetically preferred configurations: heparin-binding-up (HP-up), heparin-binding-middle (HP-middle), and heparin-binding-down (HP-down). The HP-middle orientation, with the strongest adsorption energy (-1149 ± 40 kJ·mol(-1)), has the largest adsorption population (52.1-52.6%) and exhibits the largest conformational charge (RMSD of 0.26 ± 0.01 nm) among the three orientations. The HP-down and HP-up orientations, with smaller adsorption energies of -1022 ± 55 and -894 ± 70 kJ·mol(-1), respectively, have smaller adsorption populations of 27.4-27.7% and 19.7-20.5% and present smaller RMSD values of 0.21 ± 0.01 and 0.19 ± 0.01 nm, respectively. The convergent distribution indicates that nearly half of the population (in the HP-middle orientation) will support both FGF/FGFR and DGR-integrin signaling and another half (in the HP-up and HP-down orientations) will support DGR-integrin signaling. The major population (~80%) has the protein dipole directed outward. In the strong adsorption state, there are usually 2 to 3 basic residues that form the anchoring interactions of 210-332 kJ·mol(-1) per residue or that are accompanied by an acidic residue with an adsorption energy of ~207 kJ·mol(-1). Together, the major bound residues form a triangle or a quadrilateral on the surface and stabilize the adsorption geometrically, which indicates topologic matching between the protein and HAP surfaces.

Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations.

PubMed

Dissanayake, Thakshila; Swails, Jason M; Harris, Michael E; Roitberg, Adrian E; York, Darrin M

2015-02-17

The measurement of reaction rate as a function of pH provides essential information about mechanism. These rates are sensitive to the pK(a) values of amino acids directly involved in catalysis that are often shifted by the enzyme active site environment. Experimentally observed pH-rate profiles are usually interpreted using simple kinetic models that allow estimation of "apparent pK(a)" values of presumed general acid and base catalysts. One of the underlying assumptions in these models is that the protonation states are uncorrelated. In this work, we introduce the use of constant pH molecular dynamics simulations in explicit solvent (CpHMD) with replica exchange in the pH-dimension (pH-REMD) as a tool to aid in the interpretation of pH-activity data of enzymes and to test the validity of different kinetic models. We apply the methods to RNase A, a prototype acid-base catalyst, to predict the macroscopic and microscopic pK(a) values, as well as the shape of the pH-rate profile. Results for apo and cCMP-bound RNase A agree well with available experimental data and suggest that deprotonation of the general acid and protonation of the general base are not strongly coupled in transphosphorylation and hydrolysis steps. Stronger coupling, however, is predicted for the Lys41 and His119 protonation states in apo RNase A, leading to the requirement for a microscopic kinetic model. This type of analysis may be important for other catalytic systems where the active forms of the implicated general acid and base are oppositely charged and more highly correlated. These results suggest a new way for CpHMD/pH-REMD simulations to bridge the gap with experiments to provide a molecular-level interpretation of pH-activity data in studies of enzyme mechanisms.

Interpretation of pH-activity Profiles for Acid-Base Catalysis from Molecular Simulations

PubMed Central

Dissanayake, Thakshila; Swails, Jason; Harris, Michael E.; Roitberg, Adrian E.; York, Darrin M.

2015-01-01

The measurement of reaction rate as a function of pH provides essential information about mechanism. These rates are sensitive to the pKa values of amino acids directly involved in catalysis that are often shifted by the enzyme active site environment. Experimentally observed pH-rate profiles are usually interpreted using simple kinetic models that allow estimation of “apparent pKa” values of presumed general acid and base catalysts. One of the underlying assumptions in these models is that the protonation states are uncorrelated. In the present work, we introduce the use of constant pH molecular dynamics simulations in explicit solvent (CpHMD) with replica exchange in the pH-dimension (pH-REMD) as a tool to aid in the interpretation of pH-activity data of enzymes, and test the validity of different kinetic models. We apply the methods to RNase A, a prototype acid/base catalyst, to predict the macroscopic and microscopic pKa values, as well as the shape of the pH-rate profile. Results for apo and cCMP-bound RNase A agree well with available experimental data, and suggest that deprotonation of the general acid and protonation of the general base are not strongly coupled in transphosphorylation and hydrolysis steps. Stronger coupling, however, is predicted for the Lys41 and His119 protonation states in apo RNase A, leading to the requirement for a microscopic kinetic model. This type of analysis may be important for other catalytic systems where the active forms of implicated general acid and base are oppositely charged and more highly correlated. These results suggest a new way for CpHMD/pH-REMD simulations to bridge the gap with experiments to provide a molecular-level interpretation of pH-activity data in studies of enzyme mechanisms. PMID:25615525

Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces

PubMed Central

Levine, Zachary A.; Rapp, Michael V.; Wei, Wei; Mullen, Ryan Gotchy; Wu, Chun; Zerze, Gül H.; Mittal, Jeetain; Waite, J. Herbert; Israelachvili, Jacob N.; Shea, Joan-Emma

2016-01-01

Translating sticky biological molecules—such as mussel foot proteins (MFPs)—into synthetic, cost-effective underwater adhesives with adjustable nano- and macroscale characteristics requires an intimate understanding of the glue’s molecular interactions. To help facilitate the next generation of aqueous adhesives, we performed a combination of surface forces apparatus (SFA) measurements and replica-exchange molecular dynamics (REMD) simulations on a synthetic, easy to prepare, Dopa-containing peptide (MFP-3s peptide), which adheres to organic surfaces just as effectively as its wild-type protein analog. Experiments and simulations both show significant differences in peptide adsorption on CH3-terminated (hydrophobic) and OH-terminated (hydrophilic) self-assembled monolayers (SAMs), where adsorption is strongest on hydrophobic SAMs because of orientationally specific interactions with Dopa. Additional umbrella-sampling simulations yield free-energy profiles that quantitatively agree with SFA measurements and are used to extract the adhesive properties of individual amino acids within the context of MFP-3s peptide adhesion, revealing a delicate balance between van der Waals, hydrophobic, and electrostatic forces. PMID:27036002

Insights into the Folding and Unfolding Processes of Wild-Type and Mutated SH3 Domain by Molecular Dynamics and Replica Exchange Molecular Dynamics Simulations

PubMed Central

Chu, Wen-Ting; Zhang, Ji-Long; Zheng, Qing-Chuan; Chen, Lin; Zhang, Hong-Xing

2013-01-01

Src-homology regions 3 (SH3) domain is essential for the down-regulation of tyrosine kinase activity. Mutation A39V/N53P/V55L of SH3 is found to be relative to the urgent misfolding diseases. To gain insight, the human and gallus SH3 domains (PDB ID: 1NYG and 2LP5), including 58 amino acids in each protein, were selected for MD simulations (Amber11, ff99SB force field) and cluster analysis to investigate the influence of mutations on the spatial structure of the SH3 domain. It is found that the large conformational change of mutations mainly exists in three areas in the vicinity of protein core: RT loop, N-src loop, distal β-hairpin to 310 helix. The C-terminus of the mutated gallus SH3 is disordered after simulation, which represents the intermediate state of aggregation. The disappeared strong Hbond net in the mutated human and gallus systems will make these mutated proteins looser than the wild-type proteins. Additionally, by performing the REMD simulations on the gallus SH3 domain, the mutated domain is found to have an obvious effect on the unfolding process. These studies will be helpful for further aggregation mechanisms investigations on SH3 family. PMID:23734224

Insights into the folding and unfolding processes of wild-type and mutated SH3 domain by molecular dynamics and replica exchange molecular dynamics simulations.

PubMed

Chu, Wen-Ting; Zhang, Ji-Long; Zheng, Qing-Chuan; Chen, Lin; Zhang, Hong-Xing

2013-01-01

Src-homology regions 3 (SH3) domain is essential for the down-regulation of tyrosine kinase activity. Mutation A39V/N53P/V55L of SH3 is found to be relative to the urgent misfolding diseases. To gain insight, the human and gallus SH3 domains (PDB ID: 1NYG and 2LP5), including 58 amino acids in each protein, were selected for MD simulations (Amber11, ff99SB force field) and cluster analysis to investigate the influence of mutations on the spatial structure of the SH3 domain. It is found that the large conformational change of mutations mainly exists in three areas in the vicinity of protein core: RT loop, N-src loop, distal β-hairpin to 310 helix. The C-terminus of the mutated gallus SH3 is disordered after simulation, which represents the intermediate state of aggregation. The disappeared strong Hbond net in the mutated human and gallus systems will make these mutated proteins looser than the wild-type proteins. Additionally, by performing the REMD simulations on the gallus SH3 domain, the mutated domain is found to have an obvious effect on the unfolding process. These studies will be helpful for further aggregation mechanisms investigations on SH3 family.

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains

PubMed Central

Han, Wei; Schulten, Klaus

2012-01-01

PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 – 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 – 30 μs simulations, to its native states (Cα RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins. PMID:23204949

A Probabilistic Framework for Constructing Temporal Relations in Replica Exchange Molecular Trajectories.

PubMed

Chattopadhyay, Aditya; Zheng, Min; Waller, Mark Paul; Priyakumar, U Deva

2018-05-23

Knowledge of the structure and dynamics of biomolecules is essential for elucidating the underlying mechanisms of biological processes. Given the stochastic nature of many biological processes, like protein unfolding, it's almost impossible that two independent simulations will generate the exact same sequence of events, which makes direct analysis of simulations difficult. Statistical models like Markov Chains, transition networks etc. help in shedding some light on the mechanistic nature of such processes by predicting long-time dynamics of these systems from short simulations. However, such methods fall short in analyzing trajectories with partial or no temporal information, for example, replica exchange molecular dynamics or Monte Carlo simulations. In this work we propose a probabilistic algorithm, borrowing concepts from graph theory and machine learning, to extract reactive pathways from molecular trajectories in the absence of temporal data. A suitable vector representation was chosen to represent each frame in the macromolecular trajectory (as a series of interaction and conformational energies) and dimensionality reduction was performed using principal component analysis (PCA). The trajectory was then clustered using a density-based clustering algorithm, where each cluster represents a metastable state on the potential energy surface (PES) of the biomolecule under study. A graph was created with these clusters as nodes with the edges learnt using an iterative expectation maximization algorithm. The most reactive path is conceived as the widest path along this graph. We have tested our method on RNA hairpin unfolding trajectory in aqueous urea solution. Our method makes the understanding of the mechanism of unfolding in RNA hairpin molecule more tractable. As this method doesn't rely on temporal data it can be used to analyze trajectories from Monte Carlo sampling techniques and replica exchange molecular dynamics (REMD).

Role of sleep for encoding of emotional memory.

PubMed

Kaida, Kosuke; Niki, Kazuhisa; Born, Jan

2015-05-01

Total sleep deprivation (TSD) has been consistently found to impair encoding of information during ensuing wakefulness, probably through suppressing NonREM (non-rapid eye movement) sleep. However, a possible contribution of missing REM sleep to this encoding impairment after TSD has so far not been systematically examined in humans, although such contribution might be suspected in particular for emotional information. Here, in two separate experiments in young healthy men, we compared effects of TSD and of selective REM sleep deprivation (REMD), relative to respective control conditions of undisturbed sleep, on the subsequent encoding of neutral and emotional pictures. The pictures were presented in conjunction with colored frames to also assess related source memory. REMD was achieved by tones presented contingently upon initial signs of REM sleep. Encoding capabilities were examined in the evening (18:00h) after the experimental nights, by a picture recognition test right after encoding. TSD significantly decreased both the rate of correctly recognized pictures and of recalled frames associated with the pictures. The TSD effect was robust and translated into an impaired long term memory formation, as it was likewise observed on a second recognition testing one week after the encoding phase. Contrary to our expectation, REMD did not affect encoding in general, or particularly of emotional pictures. Also, REMD did not affect valence ratings of the encoded pictures. However, like TSD, REMD distinctly impaired vigilance at the time of encoding. Altogether, these findings indicate an importance of NonREM rather than REM sleep for the encoding of information that is independent of the emotionality of the materials. Copyright © 2015 Elsevier Inc. All rights reserved.

Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering

PubMed Central

2015-01-01

The lateral heterogeneity of cellular membranes plays an important role in many biological functions such as signaling and regulating membrane proteins. This heterogeneity can result from preferential interactions between membrane components or interactions with membrane proteins. One major difficulty in molecular dynamics simulations aimed at studying the membrane heterogeneity is that lipids diffuse slowly and collectively in bilayers, and therefore, it is difficult to reach equilibrium in lateral organization in bilayer mixtures. Here, we propose the use of the replica exchange with solute tempering (REST) approach to accelerate lateral relaxation in heterogeneous bilayers. REST is based on the replica exchange method but tempers only the solute, leaving the temperature of the solvent fixed. Since the number of replicas in REST scales approximately only with the degrees of freedom in the solute, REST enables us to enhance the configuration sampling of lipid bilayers with fewer replicas, in comparison with the temperature replica exchange molecular dynamics simulation (T-REMD) where the number of replicas scales with the degrees of freedom of the entire system. We apply the REST method to a cholesterol and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer mixture and find that the lateral distribution functions of all molecular pair types converge much faster than in the standard MD simulation. The relative diffusion rate between molecules in REST is, on average, an order of magnitude faster than in the standard MD simulation. Although REST was initially proposed to study protein folding and its efficiency in protein folding is still under debate, we find a unique application of REST to accelerate lateral equilibration in mixed lipid membranes and suggest a promising way to probe membrane lateral heterogeneity through molecular dynamics simulation. PMID:25328493

Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering.

PubMed

Huang, Kun; García, Angel E

2014-10-14

The lateral heterogeneity of cellular membranes plays an important role in many biological functions such as signaling and regulating membrane proteins. This heterogeneity can result from preferential interactions between membrane components or interactions with membrane proteins. One major difficulty in molecular dynamics simulations aimed at studying the membrane heterogeneity is that lipids diffuse slowly and collectively in bilayers, and therefore, it is difficult to reach equilibrium in lateral organization in bilayer mixtures. Here, we propose the use of the replica exchange with solute tempering (REST) approach to accelerate lateral relaxation in heterogeneous bilayers. REST is based on the replica exchange method but tempers only the solute, leaving the temperature of the solvent fixed. Since the number of replicas in REST scales approximately only with the degrees of freedom in the solute, REST enables us to enhance the configuration sampling of lipid bilayers with fewer replicas, in comparison with the temperature replica exchange molecular dynamics simulation (T-REMD) where the number of replicas scales with the degrees of freedom of the entire system. We apply the REST method to a cholesterol and 1,2-dipalmitoyl- sn -glycero-3-phosphocholine (DPPC) bilayer mixture and find that the lateral distribution functions of all molecular pair types converge much faster than in the standard MD simulation. The relative diffusion rate between molecules in REST is, on average, an order of magnitude faster than in the standard MD simulation. Although REST was initially proposed to study protein folding and its efficiency in protein folding is still under debate, we find a unique application of REST to accelerate lateral equilibration in mixed lipid membranes and suggest a promising way to probe membrane lateral heterogeneity through molecular dynamics simulation.

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage mini protein

PubMed Central

Day, Ryan; Paschek, Dietmar; Garcia, Angel E.

2012-01-01

We study the unbiased folding/unfolding thermodynamics of the Trp-cage miniprotein using detailed molecular dynamics simulations of an all-atom model of the protein in explicit solvent, using the Amberff99SB force field. Replica-exchange molecular dynamics (REMD) simulations are used to sample the protein ensembles over a broad range of temperatures covering the folded and unfolded states, and at two densities. The obtained ensembles are shown to reach equilibrium in the 1 μs per replica timescale. The total simulation time employed in the calculations exceeds 100 μs. Ensemble averages of the fraction folded, pressure, and energy differences between the folded and unfolded states as a function of temperature are used to model the free energy of the folding transition, ΔG(P,T), over the whole region of temperature and pressures sampled in the simulations. The ΔG(P,T) diagram describes an ellipse over the range of temperatures and pressures sampled, predicting that the system can undergo pressure induced unfolding and cold denaturation at low temperatures and high pressures, and unfolding at low pressures and high temperatures. The calculated free energy function exhibits remarkably good agreement with the experimental folding transition temperature (Tf = 321 K), free energy and specific heat changes. However, changes in enthalpy and entropy are significantly different than the experimental values. We speculate that these differences may be due to the simplicity of the semi-empirical force field used in the simulations and that more elaborate force fields may be required to describe appropriately the thermodynamics of proteins. PMID:20408169

Influences of conformations of peptides on stereoinversions and/or isomerizations of aspartic acid residues.

PubMed

Oda, Akifumi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Takahashi, Ohgi

2018-07-01

Recently, non-enzymatic stereoinversions of aspartic acid (Asp) residues in proteins and peptides have been reported. Here, we performed replica exchange molecular dynamics (REMD) simulations of model peptides (exon 6, 26A-1, and 26A-2) extracted from elastin to investigate their structural features, thereby revealing the factor that influences stereoinversions. For REMD trajectories, we calculated distances between carboxyl carbon in Asp and amide nitrogen in the (n + 1) residue (CN distances). Because bond formation between carbon and nitrogen is indispensable to the formation of a succinimide intermediate the distance between them seems to play an important role in stereoinversion. Moreover, we calculated polar surface areas (PSAs) for the trajectories, finding that CN distances and PSA were different for each peptide, with the longest CN distance and smallest PSA observed for exon 6 peptide, where stereoinversion of Asp is the slowest. Although the average CN distance was shorter for exon 26A-1 peptide than for exon 26A-2 peptide, the number of conformations with CN distances <3.0 Å was greater for exon 26A-2 peptide than for exon 26A-1 peptide. Furthermore, PSA for amide nitrogen of the (n + 1) residue was larger for exon 26A-2 peptide than for exon 26A-1 peptide. These results indicated that the flexibility of Asp and (n + 1) residues and hydrophilicity of peptides, especially in the (n + 1) residue, play important roles in the stereoinversion of Asp. This article is part of a Special Issue entitled: D-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca. Copyright © 2018 Elsevier B.V. All rights reserved.

Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions.

PubMed

Shao, Qiang

2016-10-26

Large-scale conformational changes in proteins are important for their functions. Tracking the conformational change in real time at the level of a single protein molecule, however, remains a great challenge. In this article, we present a novel in silico approach with the combination of normal mode analysis and integrated-tempering-sampling molecular simulation (NMA-ITS) to give quantitative data for exploring the conformational transition pathway in multi-dimensional energy landscapes starting only from the knowledge of the two endpoint structures of the protein. The open-to-closed transitions of three proteins, including nCaM, AdK, and HIV-1 PR, were investigated using NMA-ITS simulations. The three proteins have varied structural flexibilities and domain communications in their respective conformational changes. The transition state structure in the conformational change of nCaM and the associated free-energy barrier are in agreement with those measured in a standard explicit-solvent REMD simulation. The experimentally measured transition intermediate structures of the intrinsically flexible AdK are captured by the conformational transition pathway measured here. The dominant transition pathways between the closed and fully open states of HIV-1 PR are very similar to those observed in recent REMD simulations. Finally, the evaluated relaxation times of the conformational transitions of three proteins are roughly at the same level as reported experimental data. Therefore, the NMA-ITS method is applicable for a variety of cases, providing both qualitative and quantitative insights into the conformational changes associated with the real functions of proteins.

Early stages of carbonate mineralization revealed from molecular simulations: Implications for biomineral formation

NASA Astrophysics Data System (ADS)

Wallace, A. F.; DeYoreo, J.; Banfield, J. F.

2011-12-01

The carbonate mineral constituents of many biomineralized products, formed both in and ex vivo, grow by a multi-stage crystallization process that involves the nucleation and structural reorganization of transient amorphous phases. The existence of transient phases and cluster species has significant implications for carbonate nucleation and growth in natural and engineered environments, both modern and ancient. The structure of these intermediate phases remains elusive, as does the nature of the disorder to order transition, however, these process details may strongly influence the interpretation of elemental and isotopic climate proxy data obtained from authigenic and biogenic carbonates. While molecular simulations have been applied to certain aspects of crystal growth, studies of metal carbonate nucleation are strongly inhibited by the presence of kinetic traps that prevent adequate sampling of the potential landscape upon which the growing clusters reside within timescales accessible by simulation. This research addresses this challenge by marrying the recent Kawska-Zahn (KZ) approach to simulation of crystal nucleation and growth from solution with replica-exchange molecular dynamics (REMD) techniques. REMD has been used previously to enhance sampling of protein conformations that occupy energy wells that are separated by sizable thermodynamic and kinetic barriers, and is used here to probe the initial formation and onset of order within hydrated calcium and iron carbonate cluster species during nucleation. Results to date suggest that growing clusters initiate as short linear ion chains that evolve into two- and three-dimensional structures with continued growth. The planar structures exhibit an obvious 2d lattice, while establishment of a 3d lattice is hindered by incomplete ion desolvation. The formation of a dehydrated core consisting of a single carbonate ion is observed when the clusters are ~0.75 nm. At the same size a distorted, but discernible calcite-type lattice is also apparent. Continued growth results in expansion of the dehydrated core, however, complete desolvation and incorporation of cations into the growing carbonate phase is not achieved until the cluster grows to ~1.2 nm. Exploration of the system free energy along the crystallization path reveals "special" cluster sizes that correlate with ion desolvation milestones. The formation of these species comprise critical bottlenecks on the energy landscape and for the establishment of order within the growing clusters.

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

PubMed

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

2015-12-01

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

Modeling the onset and offset of dental pain relief by ibuprofen.

PubMed

Li, Hanbin; Mandema, Jaap; Wada, Russell; Jayawardena, Shyamalie; Desjardins, Paul; Doyle, Geraldine; Kellstein, David

2012-01-01

Onset and offset of dental pain relief by ibuprofen following third molar extraction were modeled in a randomized, double-blind, placebo-controlled, parallel-group, 8-hour study of patients receiving either a novel effervescent ibuprofen tablet (400 mg; N = 30), standard ibuprofen tablets (Nurofen(®) 2 × 200 mg; N = 22), or placebo (N = 37). An Emax model was fit to pain relief scores. Linear hazard models were used to analyze the time to first perceptible relief (TFPR), the time to meaningful pain relief (TMPR), and time to remedication (REMD). Nomograms were created to correlate TFPR, TMPR, and REMD with different ibuprofen pharmacokinetic profiles. Effervescent ibuprofen was absorbed rapidly with 95% completion within 15 minutes. Maximum pain relief score by ibuprofen was 1.8 units greater than placebo, with an EC50 (effect-site) for ibuprofen concentration of 10.2 µg·mL(-1). The likelihood to achieve TFPR and TMPR was doubled for every 10 µg·mL(-1) increase in ibuprofen plasma concentration. REMD risk decreased 40-fold as the categorical pain relief score increased from 0 to 3. Rapid absorption of ibuprofen effervescent resulted in an earlier TFPR and TMPR, and a lower REMD rate than standard ibuprofen. The nomograms may be useful in predicting the onset and offset of new faster acting ibuprofen formulations, based on pharmacokinetic profiles.

Amyloidogenesis abolished by proline substitutions but enhanced by lipid binding.

PubMed

Jiang, Ping; Xu, Weixin; Mu, Yuguang

2009-04-01

The influence of lipid molecules on the aggregation of a highly amyloidogenic segment of human islet amyloid polypeptide, hIAPP20-29, and the corresponding sequence from rat has been studied by all-atom replica exchange molecular dynamics (REMD) simulations with explicit solvent model. hIAPP20-29 fragments aggregate into partially ordered beta-sheet oligomers and then undergo large conformational reorganization and convert into parallel/antiparallel beta-sheet oligomers in mixed in-register and out-of-register patterns. The hydrophobic interaction between lipid tails and residues at positions 23-25 is found to stabilize the ordered beta-sheet structure, indicating a catalysis role of lipid molecules in hIAPP20-29 self-assembly. The rat IAPP variants with three proline residues maintain unstructured micelle-like oligomers, which is consistent with non-amyloidogenic behavior observed in experimental studies. Our study provides the atomic resolution descriptions of the catalytic function of lipid molecules on the aggregation of IAPP peptides.

Amyloidogenesis Abolished by Proline Substitutions but Enhanced by Lipid Binding

PubMed Central

Jiang, Ping; Xu, Weixin; Mu, Yuguang

2009-01-01

The influence of lipid molecules on the aggregation of a highly amyloidogenic segment of human islet amyloid polypeptide, hIAPP20–29, and the corresponding sequence from rat has been studied by all-atom replica exchange molecular dynamics (REMD) simulations with explicit solvent model. hIAPP20–29 fragments aggregate into partially ordered β-sheet oligomers and then undergo large conformational reorganization and convert into parallel/antiparallel β-sheet oligomers in mixed in-register and out-of-register patterns. The hydrophobic interaction between lipid tails and residues at positions 23–25 is found to stabilize the ordered β-sheet structure, indicating a catalysis role of lipid molecules in hIAPP20–29 self-assembly. The rat IAPP variants with three proline residues maintain unstructured micelle-like oligomers, which is consistent with non-amyloidogenic behavior observed in experimental studies. Our study provides the atomic resolution descriptions of the catalytic function of lipid molecules on the aggregation of IAPP peptides. PMID:19360098

Exploiting molecular dynamics in Nested Sampling simulations of small peptides

NASA Astrophysics Data System (ADS)

Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor

2016-04-01

Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.

Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity

PubMed Central

Alsamarah, Abdelaziz; LaCuran, Alecander E.; Oelschlaeger, Peter; Hao, Jijun; Luo, Yun

2015-01-01

Abnormal alteration of bone morphogenetic protein (BMP) signaling is implicated in many types of diseases including cancer and heterotopic ossifications. Hence, small molecules targeting BMP type I receptors (BMPRI) to interrupt BMP signaling are believed to be an effective approach to treat these diseases. However, lack of understanding of the molecular determinants responsible for the binding selectivity of current BMP inhibitors has been a big hindrance to the development of BMP inhibitors for clinical use. To address this issue, we carried out in silico experiments to test whether computational methods can reproduce and explain the high selectivity of a small molecule BMP inhibitor DMH1 on BMPRI kinase ALK2 vs. the closely related TGF-β type I receptor kinase ALK5 and vascular endothelial growth factor receptor type 2 (VEGFR2) tyrosine kinase. We found that, while the rigid docking method used here gave nearly identical binding affinity scores among the three kinases; free energy perturbation coupled with Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) simulations reproduced the absolute binding free energies in excellent agreement with experimental data. Furthermore, the binding poses identified by FEP/H-REMD led to a quantitative analysis of physical/chemical determinants governing DMH1 selectivity. The current work illustrates that small changes in the binding site residue type (e.g. pre-hinge region in ALK2 vs. ALK5) or side chain orientation (e.g. Tyr219 in caALK2 vs. wtALK2), as well as a subtle structural modification on the ligand (e.g. DMH1 vs. LDN193189) will cause distinct binding profiles and selectivity among BMP inhibitors. Therefore, the current computational approach represents a new way of investigating BMP inhibitors. Our results provide critical information for designing exclusively selective BMP inhibitors for the development of effective pharmacotherapy for diseases caused by aberrant BMP signaling. PMID:26133550

Enhanced emotional reactivity after selective REM sleep deprivation in humans: an fMRI study

PubMed Central

Rosales-Lagarde, Alejandra; Armony, Jorge L.; del Río-Portilla, Yolanda; Trejo-Martínez, David; Conde, Ruben; Corsi-Cabrera, Maria

2012-01-01

Converging evidence from animal and human studies suggest that rapid eye movement (REM) sleep modulates emotional processing. The aim of the present study was to explore the effects of selective REM sleep deprivation (REM-D) on emotional responses to threatening visual stimuli and their brain correlates using functional magnetic resonance imaging (fMRI). Twenty healthy subjects were randomly assigned to two groups: selective REM-D, by awakening them at each REM sleep onset, or non-rapid eye movement sleep interruptions (NREM-I) as control for potential non-specific effects of awakenings and lack of sleep. In a within-subject design, a visual emotional reactivity task was performed in the scanner before and 24 h after sleep manipulation. Behaviorally, emotional reactivity was enhanced relative to baseline (BL) in the REM deprived group only. In terms of fMRI signal, there was, as expected, an overall decrease in activity in the NREM-I group when subjects performed the task the second time, particularly in regions involved in emotional processing, such as occipital and temporal areas, as well as in the ventrolateral prefrontal cortex, involved in top-down emotion regulation. In contrast, activity in these areas remained the same level or even increased in the REM-D group, compared to their BL level. Taken together, these results suggest that lack of REM sleep in humans is associated with enhanced emotional reactivity, both at behavioral and neural levels, and thus highlight the specific role of REM sleep in regulating the neural substrates for emotional responsiveness. PMID:22719723

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.

PubMed

Kührová, Petra; Best, Robert B; Bottaro, Sandro; Bussi, Giovanni; Šponer, Jiří; Otyepka, Michal; Banáš, Pavel

2016-09-13

The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interactions. Although state-of-the-art Molecular Dynamics (MD) force fields correctly describe the native state of these tetraloops as a stable free-energy basin on the microsecond time scale, enhanced sampling techniques reveal that the native state is not the global free energy minimum, suggesting yet unidentified significant imbalances in the force fields. Here, we tested our ability to fold the RNA tetraloops in various force fields and simulation settings. We employed three different enhanced sampling techniques, namely, temperature replica exchange MD (T-REMD), replica exchange with solute tempering (REST2), and well-tempered metadynamics (WT-MetaD). We aimed to separate problems caused by limited sampling from those due to force-field inaccuracies. We found that none of the contemporary force fields is able to correctly describe folding of the 5'-GAGA-3' tetraloop over a range of simulation conditions. We thus aimed to identify which terms of the force field are responsible for this poor description of TL folding. We showed that at least two different imbalances contribute to this behavior, namely, overstabilization of base-phosphate and/or sugar-phosphate interactions and underestimated stability of the hydrogen bonding interaction in base pairing. The first artifact stabilizes the unfolded ensemble, while the second one destabilizes the folded state. The former problem might be partially alleviated by reparametrization of the van der Waals parameters of the phosphate oxygens suggested by Case et al., while in order to overcome the latter effect we suggest local potentials to better capture hydrogen bonding interactions.

Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant.

PubMed

Lei, Jiangtao; Qi, Ruxi; Wei, Guanghong; Nussinov, Ruth; Ma, Buyong

2016-03-21

Recent studies suggested that p53 aggregation can lead to loss-of-function (LoF), dominant-negative (DN) and gain-of-function (GoF) effects, with adverse cancer consequences. The p53 aggregation-nucleating (251)ILTIITL(257) fragment is a key segment in wild-type p53 aggregation; however, an I254R mutation can prevent it. It was suggested that self-assembly of wild-type p53 and its cross-interaction with mutants differ from the classical amyloid nucleation-growth mechanism. Here, using replica exchange molecular dynamics (REMD) simulations, we studied the cross-interactions of this p53 core fragment and its aggregation rescue I254R mutant. We found that the core fragment displays strong aggregation propensity, whereas the gatekeeper I254R mutant tends to be disordered, consistent with experiments. Our cross-interaction results reveal that the wild-type p53 fragment promotes β-sheet formation of the I254R mutant by shifting the disordered mutant peptides into aggregating states. As a result, the system has similar oligomeric structures, inter-peptide interactions and free energy landscape as the wild type fragment does, revealing a prion-like process. We also found that in the cross-interaction system, the wild-type species has higher tendency to interact with the mutant than with itself. This phenomenon illustrates synergistic effects between the p53 (251)ILTIITL(257) fragment and the mutant resembling prion cross-species propagation, cautioning against exploiting it in drug discovery.

Importance of many-body dispersion and temperature effects on gas-phase gold cluster (meta)stability

NASA Astrophysics Data System (ADS)

Goldsmith, Bryan R.; Gruene, Philipp; Lyon, Jonathan T.; Rayner, David M.; Fielicke, André; Scheffler, Matthias; Ghiringhelli, Luca M.

Gold clusters in the gas phase exhibit many structural isomers that are shown to intercovert frequently, even at room temperature. We performed ab initio replica-exchange molecular dynamics (REMD) calculations on gold clusters (of sizes 5-14 atoms) to identify metastable states and their relative populations at finite temperature, as well as to examine the importance of temperature and van der Waals (vdW) on their isomer energetic ordering. Free energies of the gold cluster isomers are optimally estimated using the Multistate Bennett Acceptance Ratio. The distribution of bond coordination numbers and radius of gyration are used to address the challenge of discriminating isomers along their dynamical trajectories. Dispersion effects are important for stabilizing three-dimensional structures relative to planar structures and brings isomer energetic predictions to closer quantitative agreement compared with RPA@PBE calculations. We find that higher temperatures typically stabilize metastable three-dimensional structures relative to planar/quasiplanar structures. Computed IR spectra of low free energy Au9, Au10, and Au12 isomers are in agreement with experimental spectra obtained by far-IR multiple photon dissociation in a molecular beam at 100 K.

Sequence Dependent Interactions Between DNA and Single-Walled Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Roxbury, Daniel

It is known that single-stranded DNA adopts a helical wrap around a single-walled carbon nanotube (SWCNT), forming a water-dispersible hybrid molecule. The ability to sort mixtures of SWCNTs based on chirality (electronic species) has recently been demonstrated using special short DNA sequences that recognize certain matching SWCNTs of specific chirality. This thesis investigates the intricacies of DNA-SWCNT sequence-specific interactions through both experimental and molecular simulation studies. The DNA-SWCNT binding strengths were experimentally quantified by studying the kinetics of DNA replacement by a surfactant on the surface of particular SWCNTs. Recognition ability was found to correlate strongly with measured binding strength, e.g. DNA sequence (TAT)4 was found to bind 20 times stronger to the (6,5)-SWCNT than sequence (TAT)4T. Next, using replica exchange molecular dynamics (REMD) simulations, equilibrium structures formed by (a) single-strands and (b) multiple-strands of 12-mer oligonucleotides adsorbed on various SWCNTs were explored. A number of structural motifs were discovered in which the DNA strand wraps around the SWCNT and 'stitches' to itself via hydrogen bonding. Great variability among equilibrium structures was observed and shown to be directly influenced by DNA sequence and SWCNT type. For example, the (6,5)-SWCNT DNA recognition sequence, (TAT)4, was found to wrap in a tight single-stranded right-handed helical conformation. In contrast, DNA sequence T12 forms a beta-barrel left-handed structure on the same SWCNT. These are the first theoretical indications that DNA-based SWCNT selectivity can arise on a molecular level. In a biomedical collaboration with the Mayo Clinic, pathways for DNA-SWCNT internalization into healthy human endothelial cells were explored. Through absorbance spectroscopy, TEM imaging, and confocal fluorescence microscopy, we showed that intracellular concentrations of SWCNTs far exceeded those of the incubation solution, which suggested an energy-dependent pathway. Additionally, by means of pharmacological inhibition and vector-induced gene knockout studies, the DNA-SWCNTs were shown to enter the cells via Rac1-mediated macropinocytosis.

How Kinetics within the Unfolded State Affects Protein Folding: an Analysis Based on Markov State Models and an Ultra-Long MD Trajectory

PubMed Central

Deng, Nan-jie; Dai, Wei

2013-01-01

Understanding how kinetics in the unfolded state affects protein folding is a fundamentally important yet less well-understood issue. Here we employ three different models to analyze the unfolded landscape and folding kinetics of the miniprotein Trp-cage. The first is a 208 μs explicit solvent molecular dynamics (MD) simulation from D. E. Shaw Research containing tens of folding events. The second is a Markov state model (MSM-MD) constructed from the same ultra-long MD simulation; MSM-MD can be used to generate thousands of folding events. The third is a Markov state model built from temperature replica exchange MD simulations in implicit solvent (MSM-REMD). All the models exhibit multiple folding pathways, and there is a good correspondence between the folding pathways from direct MD and those computed from the MSMs. The unfolded populations interconvert rapidly between extended and collapsed conformations on time scales ≤ 40 ns, compared with the folding time of ≈ 5 μs. The folding rates are independent of where the folding is initiated from within the unfolded ensemble. About 90 % of the unfolded states are sampled within the first 40 μs of the ultra-long MD trajectory, which on average explores ~27 % of the unfolded state ensemble between consecutive folding events. We clustered the folding pathways according to structural similarity into “tubes”, and kinetically partitioned the unfolded state into populations that fold along different tubes. From our analysis of the simulations and a simple kinetic model, we find that when the mixing within the unfolded state is comparable to or faster than folding, the folding waiting times for all the folding tubes are similar and the folding kinetics is essentially single exponential despite the presence of heterogeneous folding paths with non-uniform barriers. When the mixing is much slower than folding, different unfolded populations fold independently leading to non-exponential kinetics. A kinetic partition of the Trp-cage unfolded state is constructed which reveals that different unfolded populations have almost the same probability to fold along any of the multiple folding paths. We are investigating whether the results for the kinetics in the unfolded state of the twenty-residue Trp-cage is representative of larger single domain proteins. PMID:23705683

Characterization of Aβ Monomers through the Convergence of Ensemble Properties among Simulations with Multiple Force Fields

DOE PAGES

Rosenman, David J.; Wang, Chunyu; García, Angel E.

2016-01-12

We found that amyloid β (Aβ) monomers represent a base state in the pathways of aggregation that result in the fibrils and oligomers implicated in the pathogenesis of Alzheimer’s disease (AD). The structural properties of these intrinsically disordered peptides remain unclear despite extensive experimental and computational investigations. Further, there are mutations within Aβ that change the way the peptide aggregates and are known to cause familial AD (FAD). Here, we analyze the ensembles of different isoforms (Aβ42 and Aβ40) and mutants (E22Δ, D23N, E22K, E22G, and A2T in Aβ40) of Aβ generated with all-atom replica exchange molecular dynamics (REMD) simulationsmore » on the μs/replica time scale. These were run using three different force field/water model combinations: OPLS-AA/L and TIP3P (“OPLS”), AMBER99sb-ILDN and TIP4P-Ew (“ILDN”), as well as CHARMM22* and TIP3SP (“CHARMM”). Despite fundamental changes in simulation parameters, we find that the resulting ensembles demonstrate a strong convergence in structural properties. In particular, antiparallel contacts between L17–A21 and A30–L34 are prevalent in ensembles of Aβ40, directly forming β sheets in the OPLS and ILDN combinations. A21–A30 commonly forms an interceding region that rarely interacts with the rest of the peptide. Further, Aβ42 contributes new β hairpin motifs involving V40–I41 in both OPLS and ILDN. However, the structural flexibility of the central region and the electrostatic interactions that characterize it are notably different between the different conditions. Further, for OPLS, each of the FAD mutations disrupts central bend character and increases the polymorphism of antiparallel contacts across the central region. However, the studied mutations in the ILDN set primarily encourage more global contacts involving the N-terminus and the central region, and promote the formation of new β topologies that may seed different aggregates involved in disease phenotypes. Furthermore, these differences aside, the large degree of agreement between simulation sets across multiple force fields provides a generalizable characterization of Aβ that is also consistent with experimental data and models.« less

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

Rosenman, David J.; Wang, Chunyu; García, Angel E.

We found that amyloid β (Aβ) monomers represent a base state in the pathways of aggregation that result in the fibrils and oligomers implicated in the pathogenesis of Alzheimer’s disease (AD). The structural properties of these intrinsically disordered peptides remain unclear despite extensive experimental and computational investigations. Further, there are mutations within Aβ that change the way the peptide aggregates and are known to cause familial AD (FAD). Here, we analyze the ensembles of different isoforms (Aβ42 and Aβ40) and mutants (E22Δ, D23N, E22K, E22G, and A2T in Aβ40) of Aβ generated with all-atom replica exchange molecular dynamics (REMD) simulationsmore » on the μs/replica time scale. These were run using three different force field/water model combinations: OPLS-AA/L and TIP3P (“OPLS”), AMBER99sb-ILDN and TIP4P-Ew (“ILDN”), as well as CHARMM22* and TIP3SP (“CHARMM”). Despite fundamental changes in simulation parameters, we find that the resulting ensembles demonstrate a strong convergence in structural properties. In particular, antiparallel contacts between L17–A21 and A30–L34 are prevalent in ensembles of Aβ40, directly forming β sheets in the OPLS and ILDN combinations. A21–A30 commonly forms an interceding region that rarely interacts with the rest of the peptide. Further, Aβ42 contributes new β hairpin motifs involving V40–I41 in both OPLS and ILDN. However, the structural flexibility of the central region and the electrostatic interactions that characterize it are notably different between the different conditions. Further, for OPLS, each of the FAD mutations disrupts central bend character and increases the polymorphism of antiparallel contacts across the central region. However, the studied mutations in the ILDN set primarily encourage more global contacts involving the N-terminus and the central region, and promote the formation of new β topologies that may seed different aggregates involved in disease phenotypes. Furthermore, these differences aside, the large degree of agreement between simulation sets across multiple force fields provides a generalizable characterization of Aβ that is also consistent with experimental data and models.« less

Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model

NASA Astrophysics Data System (ADS)

Zhang, Dawei; Lazim, Raudah; Mun Yip, Yew

2017-09-01

We conducted an all-atom ab initio folding of FSD-EY, a protein with a ββα configuration using non-polarizable (AMBER) and polarizable force fields (PHB designed by Gao et al.) in implicit solvent. The effect of reducing the polarization effect integrated into the force field by the PHB model, termed the PHB0.7 was also examined in the folding of FSD-EY. This model incorporates into the force field 70% of the original polarization effect to minimize the likelihood of over-stabilizing the backbone hydrogen bonds. Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure obtained in explicit water.

Sequence-structure correlations in silk: Poly-Ala repeat of N. clavipes MaSp1 is naturally optimized at a critical length scale.

PubMed

Bratzel, Graham; Buehler, Markus J

2012-03-01

Spider silk is a self-assembling biopolymer that outperforms many known materials in terms of its mechanical performance despite being constructed from simple and inferior building blocks. While experimental studies have shown that the molecular structure of silk has a direct influence on the stiffness, toughness, and failure strength of silk, few molecular-level analyses of the nanostructure of silk assemblies in particular under variations of genetic sequences have been reported. Here we report atomistic-level structures of the MaSp1 protein from the Nephila Clavipes spider dragline silk sequence, obtained using an in silico approach based on replica exchange molecular dynamics (REMD) and explicit water molecular dynamics. We apply this method to study the effects of a systematic variation of the poly-alanine repeat lengths, a parameter controlled by the genetic makeup of silk, on the resulting molecular structure of silk at the nanoscale. Confirming earlier experimental and computational work, a structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly β-sheet crystal domains while disorderly regions are formed by glycine-rich repeats that consist of 3(10)-helix type structures and β-turns. Our predictions are directly validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots combined with an analysis of the secondary structure content. The key result of our study is our finding of a strong dependence of the resulting silk nanostructure depending on the poly-alanine length. We observe that the wildtype poly-alanine repeat length of six residues defines a critical minimum length that consistently results in clearly defined β-sheet nanocrystals. For poly-alanine lengths below six, the β-sheet nanocrystals are not well-defined or not visible at all, while for poly-alanine lengths at and above six, the characteristic nanocomposite structure of silk emerges with no significant improvement of the quality of the β-sheet nanocrystal geometry. We present a simple biophysical model that explains these computational observations based on the mechanistic insight gained from the molecular simulations. Our findings set the stage for understanding how variations in the spidroin sequence can be used to engineer the structure and thereby functional properties of this biological superfiber, and present a design strategy for the genetic optimization of spidroins for enhanced mechanical properties. The approach used here may also find application in the design of other self-assembled molecular structures and fibers and in particular biologically inspired or completely synthetic systems. Copyright © 2011 Elsevier Ltd. All rights reserved.

Effects of a mutation on the folding mechanism of a beta-hairpin.

PubMed

Juraszek, Jarek; Bolhuis, Peter G

2009-12-17

The folding mechanism of a protein is determined by its primary sequence. Yet, how the mechanism is changed by a mutation is still poorly understood, even for basic secondary structures such as beta-hairpins. We perform an extensive simulation study of the effects of mutating the GB1 beta-hairpin into Trpzip4 (Y5W, F12W, V14W) on the folding mechanism. While Trpzip4 has a much more stable native state due to very strong hydrophobic interactions of the side chains, its folding rate does not differ significantly from the wild type beta-hairpin. We sample the free-energy landscapes of both hairpins with Replica Exchange Molecular Dynamics (REMD) and identify the four (meta)stable states (U, H, F, and N). Using Transition Path Sampling (TPS), we then harvest ensembles of unbiased pathways between the H and F states and between the F and N states to investigate the unbiased folding mechanisms. In both hairpins, the hydrophobic collapse (U-H) is followed by the middle hydrogen bond formation (H-F), and finally a closing of the strands in a zipper-like fashion (F-N). For the Trpzip4, the path ensembles indicate that the final F-N step is much more difficult than for GB1 and involves partial unfolding, rezipping of hydrogen bonds, and rearrangement of the Trp-14 side chain. For the rate-limiting (H-F) step, the path ensembles show that in GB1 desolvation and strand closure go hand in hand, while in Trpzip4 desolvation is decoupled from strand closure. Nevertheless, likelihood maximization shows that the reaction coordinate for both hairpins remains the interstrand distance. We conclude that the folding mechanism of both hairpins is a combination of hydrophobic collapse and zipping of hydrogen bonds but that the zipper mechanism is more visible in Trpzip4. A major difference between the two hairpins is that in the transition state of the rate-limiting step for Trpzip4 one tryptophan is exposed to the solvent due to steric hindrance, making the folding mechanism more complex and leading to an increased F-N barrier. Thus, our results show in atomistic detail how a mutation leads to a different folding mechanism and results in a more frustrated folding free-energy landscape.

COLLABORATIVE RESEARCH AND DEVELOPMENT (CR&D) Delivery Order 0059: Molecular Dynamics Modeling Support

DTIC Science & Technology

2008-03-01

Molecular Dynamics Simulations 5 Theory: Equilibrium Molecular Dynamics Simulations 6 Theory: Non...Equilibrium Molecular Dynamics Simulations 8 Carbon Nanotube Simulations : Approach and results from equilibrium and non-equilibrium molecular dynamics ...touched from the perspective of molecular dynamics simulations . However, ordered systems such as “Carbon Nanotubes” have been investigated in terms

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.

A data-driven dynamics simulation framework for railway vehicles

NASA Astrophysics Data System (ADS)

Nie, Yinyu; Tang, Zhao; Liu, Fengjia; Chang, Jian; Zhang, Jianjun

2018-03-01

The finite element (FE) method is essential for simulating vehicle dynamics with fine details, especially for train crash simulations. However, factors such as the complexity of meshes and the distortion involved in a large deformation would undermine its calculation efficiency. An alternative method, the multi-body (MB) dynamics simulation provides satisfying time efficiency but limited accuracy when highly nonlinear dynamic process is involved. To maintain the advantages of both methods, this paper proposes a data-driven simulation framework for dynamics simulation of railway vehicles. This framework uses machine learning techniques to extract nonlinear features from training data generated by FE simulations so that specific mesh structures can be formulated by a surrogate element (or surrogate elements) to replace the original mechanical elements, and the dynamics simulation can be implemented by co-simulation with the surrogate element(s) embedded into a MB model. This framework consists of a series of techniques including data collection, feature extraction, training data sampling, surrogate element building, and model evaluation and selection. To verify the feasibility of this framework, we present two case studies, a vertical dynamics simulation and a longitudinal dynamics simulation, based on co-simulation with MATLAB/Simulink and Simpack, and a further comparison with a popular data-driven model (the Kriging model) is provided. The simulation result shows that using the legendre polynomial regression model in building surrogate elements can largely cut down the simulation time without sacrifice in accuracy.

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange

DTIC Science & Technology

2010-01-01

formulations of molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage...ad hoc force term in the SGLD model. Introduction Molecular dynamics (MD) simulations of small proteins provide insight into the mechanisms and... molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage mini-protein. All

Multiscale molecular dynamics simulations of rotary motor proteins.

PubMed

Ekimoto, Toru; Ikeguchi, Mitsunori

2018-04-01

Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

Look-ahead Dynamic Simulation

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

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.

Molecular Dynamics Simulations of Folding and Insertion of the Ebola Virus Fusion Peptide into a Membrane Bilayer

DTIC Science & Technology

2008-07-01

Molecular Dynamics Simulations of Folding and Insertion of the Ebola Virus Fusion Peptide into a Membrane Bilayer Mark A. Olson1, In...presents replica-exchange molecular dynamics simulations of the folding and insertion of a 16- residue Ebola virus fusion peptide into a membrane...separate calculated structures into conformational basins. 2.1 Simulation models Molecular dynamics simulations were performed using the all-atom

Quasi-Dynamic Versus Fully-Dynamic Simulations of Slip Accumulation on Faults with Enhanced Dynamic Weakening

NASA Astrophysics Data System (ADS)

Lapusta, N.; Thomas, M.; Noda, H.; Avouac, J.

2012-12-01

Long-term simulations that incorporate both seismic events and aseismic slip are quite important for studies of earthquake physics but challenging computationally. To study long deformation histories, most simulation methods do not incorporate full inertial effects (wave propagation) during simulated earthquakes, using quasi-dynamic approximations instead. Here we compare the results of quasi-dynamic simulations to the fully dynamic ones for a range of problems to determine the applicability of the quasi-dynamic approach. Intuitively, the quasi-dynamic approach should do relatively well in problems where wave-mediated effects are relatively simple but should have substantially different (and hence wrong) response when the wave-mediated stress transfers dominate the character of the seismic events. This is exactly what we observe in our simulations. We consider a 2D model of a rate-and-state fault with a seismogenic (steady-state velocity-weakening) zone surrounded by creeping (steady-state velocity-strengthening) areas. If the seismogenic zone is described by the standard Dieterich-Ruina rate-and-state friction, the resulting earthquake sequences consist of relatively simple crack-like ruptures, and the inclusion of true wave-propagation effects mostly serves to concentrate stress more efficiently at the rupture front. Hence, in such models, rupture speeds and slip rates are significantly (several times) lower in the quasi-dynamic simulations compared to the fully dynamic ones, but the total slip, the crack-like nature of seismic events, and the overall pattern of earthquake sequences is comparable, consistently with prior studies. Such behavior can be classified as qualitatively similar but quantitatively different, and it motivates the popularity of the quasi-dynamic methods in simulations. However, the comparison changes dramatically once we consider a model with enhanced dynamic weakening in the seismogenic zone in the form of flash heating. In this case, the fully dynamic simulations produce seismic ruptures in the form of short-duration slip pulses, where the pulses form due to a combination of enhanced weakening and wave effects. The quasi-dynamic simulations in the same model produce completely different results, with large crack-like ruptures, different total slips, different rupture patterns, and different prestress state before large, model-spanning events. Such qualitative differences between the quasi-dynamic and fully-dynamic simulation should result in any model where inertial effects lead to qualitative differences, such as cases with supershear transition or fault with different materials on the two sides. We will present results on our current work on how the quasi-dynamic and fully dynamic simulations compare for the cases with heterogeneous fault properties.

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 proteins. PMID:23663843

Mapping conformational dynamics of proteins using torsional dynamics simulations.

PubMed

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

2013-05-07

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 proteins. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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.

Rotational Brownian Dynamics simulations of clathrin cage formation

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

Ilie, Ioana M.; Briels, Wim J.; MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede

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 algorithmmore » 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.« less

Molecular dynamics simulations of large macromolecular complexes.

PubMed

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

2015-04-01

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

NASA Astrophysics Data System (ADS)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).

PubMed

Galindo-Murillo, Rodrigo; Roe, Daniel R; Cheatham, Thomas E

2015-05-01

The structure and dynamics of DNA are critically related to its function. Molecular dynamics simulations augment experiment by providing detailed information about the atomic motions. However, to date the simulations have not been long enough for convergence of the dynamics and structural properties of DNA. Molecular dynamics simulations performed with AMBER using the ff99SB force field with the parmbsc0 modifications, including ensembles of independent simulations, were compared to long timescale molecular dynamics performed with the specialized Anton MD engine on the B-DNA structure d(GCACGAACGAACGAACGC). To assess convergence, the decay of the average RMSD values over longer and longer time intervals was evaluated in addition to assessing convergence of the dynamics via the Kullback-Leibler divergence of principal component projection histograms. These molecular dynamics simulations-including one of the longest simulations of DNA published to date at ~44μs-surprisingly suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the ~1-5μs timescale. We can now reproducibly converge the structure and dynamics of B-DNA helices, omitting the terminal base pairs, on the μs time scale with both the AMBER and CHARMM C36 nucleic acid force fields. Results from independent ensembles of simulations starting from different initial conditions, when aggregated, match the results from long timescale simulations on the specialized Anton MD engine. With access to large-scale GPU resources or the specialized MD engine "Anton" it is possible for a variety of molecular systems to reproducibly and reliably converge the conformational ensemble of sampled structures. This article is part of a Special Issue entitled: Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

Faster than Real-Time Dynamic Simulation for Large-Size Power System with Detailed Dynamic Models using High-Performance Computing Platform

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

Huang, Renke; Jin, Shuangshuang; Chen, Yousu

This paper presents a faster-than-real-time dynamic simulation software package that is designed for large-size power system dynamic simulation. It was developed on the GridPACKTM high-performance computing (HPC) framework. The key features of the developed software package include (1) faster-than-real-time dynamic simulation for a WECC system (17,000 buses) with different types of detailed generator, controller, and relay dynamic models, (2) a decoupled parallel dynamic simulation algorithm with optimized computation architecture to better leverage HPC resources and technologies, (3) options for HPC-based linear and iterative solvers, (4) hidden HPC details, such as data communication and distribution, to enable development centered on mathematicalmore » models and algorithms rather than on computational details for power system researchers, and (5) easy integration of new dynamic models and related algorithms into the software package.« less

Swarm Counter-Asymmetric-Threat (CAT) 6-DOF Dynamics Simulation

DTIC Science & Technology

2005-07-01

NAWCWD TP 8593 Swarm Counter-Asymmetric-Threat ( CAT ) 6-DOF Dynamics Simulation by James Bobinchak Weapons and Energetics...mathematical models used in the swarm counter- asymmetric-threat ( CAT ) simulation and the results of extensive Monte Carlo simulations. The swarm CAT ...Asymmetric-Threat ( CAT ) 6-DOF Dynamics Simulation (U) 6. AUTHOR(S) James Bobinchak and Gary Hewer 7. PERFORMING ORGANIZATION NAME(S) AND

Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations

DTIC Science & Technology

2008-07-17

Membrane insertion profiles of peptides probed by molecular dynamics simulations In-Chul Yeh,* Mark A. Olson,# Michael S. Lee,*#§ and Anders...a methodology based on molecular dynamics simulation techniques to probe the insertion profiles of small peptides across the membrane interface. The...profiles of peptides probed by molecular dynamics simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d

Validation of the train energy and dynamics simulator (TEDS).

DOT National Transportation Integrated Search

2015-01-01

FRA has developed Train Energy and Dynamics Simulator (TEDS) based upon a longitudinal train dynamics and operations : simulation model which allows users to conduct safety and risk evaluations, incident investigations, studies of train operations, :...

Molecular dynamics simulations of thermally activated edge dislocation unpinning from voids in α -Fe

NASA Astrophysics Data System (ADS)

Byggmästar, J.; Granberg, F.; Nordlund, K.

2017-10-01

In this study, thermal unpinning of edge dislocations from voids in α -Fe is investigated by means of molecular dynamics simulations. The activation energy as a function of shear stress and temperature is systematically determined. Simulations with a constant applied stress are compared with dynamic simulations with a constant strain rate. We found that a constant applied stress results in a temperature-dependent activation energy. The temperature dependence is attributed to the elastic softening of iron. If the stress is normalized with the softening of the specific shear modulus, the activation energy is shown to be temperature-independent. From the dynamic simulations, the activation energy as a function of critical shear stress was determined using previously developed methods. The results from the dynamic simulations are in good agreement with the constant stress simulations, after the normalization. This indicates that the computationally more efficient dynamic method can be used to obtain the activation energy as a function of stress and temperature. The obtained relation between stress, temperature, and activation energy can be used to introduce a stochastic unpinning event in larger-scale simulation methods, such as discrete dislocation dynamics.

MCC level C formulation requirements. Shuttle TAEM guidance and flight control, STS-1 baseline

NASA Technical Reports Server (NTRS)

Carman, G. L.; Montez, M. N.

1980-01-01

The TAEM guidance and body rotational dynamics models required for the MCC simulation of the TAEM mission phase are defined. This simulation begins at the end of the entry phase and terminates at TAEM autoland interface. The logic presented is the required configuration for the first shuttle orbital flight (STS-1). The TAEM guidance is simulated in detail. The rotational dynamics simulation is a simplified model that assumes that the commanded rotational rates can be achieved in the integration interval. Thus, the rotational dynamics simulation is essentially a simulation of the autopilot commanded rates and integration of these rates to determine orbiter attitude. The rotational dynamics simulation also includes a simulation of the speedbrake deflection. The body flap and elevon deflections are computed in the orbiter aerodynamic simulation.

Experimental verification of dynamic simulation

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

[Brownian dynamics simulations of protein-protein interactions in photosynthetic electron transport chain].

PubMed

Khruschev, S S; Abaturova, A M; Diakonova, A N; Fedorov, V A; Ustinin, D M; Kovalenko, I B; Riznichenko, G Yu; Rubin, A B

2015-01-01

The application of Brownian dynamics for simulation of transient protein-protein interactions is reviewed. The review focuses on theoretical basics of Brownian dynamics method, its particular implementations, advantages and drawbacks of the method. The outlook for future development of Brownian dynamics-based simulation techniques is discussed. Special attention is given to analysis of Brownian dynamics trajectories. The second part of the review is dedicated to the role of Brownian dynamics simulations in studying photosynthetic electron transport. Interactions of mobile electron carriers (plastocyanin, cytochrome c6, and ferredoxin) with their reaction partners (cytochrome b6f complex, photosystem I, ferredoxin:NADP-reductase, and hydrogenase) are considered.

Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments

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

Jin, Shuangshuang; Chen, Yousu; Wu, Di

2015-12-09

Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Messagemore » Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.« less

Toll-Like Receptor-9-Mediated Invasion in Breast Cancer

DTIC Science & Technology

2011-07-01

Molecular Dynamics Simulations. Theoretical structural models were obtained from molecular dynamics simulations using explicit solvation by...with AMBER by MARDIGRAS. The solution structure was then derived by coupling the resulting NMR distance restraints with a molecular dynamic ...Overlay of NMR restrained structure (red) with theoretical molecular dynamic simulated annealing structure (blue). Energetic stability of the 9-mer

Simulating Open Quantum Systems with Hamiltonian Ensembles and the Nonclassicality of the Dynamics

NASA Astrophysics Data System (ADS)

Chen, Hong-Bin; Gneiting, Clemens; Lo, Ping-Yuan; Chen, Yueh-Nan; Nori, Franco

2018-01-01

The incoherent dynamical properties of open quantum systems are generically attributed to an ongoing correlation between the system and its environment. Here, we propose a novel way to assess the nature of these system-environment correlations by examining the system dynamics alone. Our approach is based on the possibility or impossibility to simulate open-system dynamics with Hamiltonian ensembles. As we show, such (im)possibility to simulate is closely linked to the system-environment correlations. We thus define the nonclassicality of open-system dynamics in terms of the nonexistence of a Hamiltonian-ensemble simulation. This classifies any nonunital open-system dynamics as nonclassical. We give examples for open-system dynamics that are unital and classical, as well as unital and nonclassical.

Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

PubMed

van der Vaart, Arjan

2015-05-01

Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

Selecting a dynamic simulation modeling method for health care delivery research-part 2: report of the ISPOR Dynamic Simulation Modeling Emerging Good Practices Task Force.

PubMed

Marshall, Deborah A; Burgos-Liz, Lina; IJzerman, Maarten J; Crown, William; Padula, William V; Wong, Peter K; Pasupathy, Kalyan S; Higashi, Mitchell K; Osgood, Nathaniel D

2015-03-01

In a previous report, the ISPOR Task Force on Dynamic Simulation Modeling Applications in Health Care Delivery Research Emerging Good Practices introduced the fundamentals of dynamic simulation modeling and identified the types of health care delivery problems for which dynamic simulation modeling can be used more effectively than other modeling methods. The hierarchical relationship between the health care delivery system, providers, patients, and other stakeholders exhibits a level of complexity that ought to be captured using dynamic simulation modeling methods. As a tool to help researchers decide whether dynamic simulation modeling is an appropriate method for modeling the effects of an intervention on a health care system, we presented the System, Interactions, Multilevel, Understanding, Loops, Agents, Time, Emergence (SIMULATE) checklist consisting of eight elements. This report builds on the previous work, systematically comparing each of the three most commonly used dynamic simulation modeling methods-system dynamics, discrete-event simulation, and agent-based modeling. We review criteria for selecting the most suitable method depending on 1) the purpose-type of problem and research questions being investigated, 2) the object-scope of the model, and 3) the method to model the object to achieve the purpose. Finally, we provide guidance for emerging good practices for dynamic simulation modeling in the health sector, covering all aspects, from the engagement of decision makers in the model design through model maintenance and upkeep. We conclude by providing some recommendations about the application of these methods to add value to informed decision making, with an emphasis on stakeholder engagement, starting with the problem definition. Finally, we identify areas in which further methodological development will likely occur given the growing "volume, velocity and variety" and availability of "big data" to provide empirical evidence and techniques such as machine learning for parameter estimation in dynamic simulation models. Upon reviewing this report in addition to using the SIMULATE checklist, the readers should be able to identify whether dynamic simulation modeling methods are appropriate to address the problem at hand and to recognize the differences of these methods from those of other, more traditional modeling approaches such as Markov models and decision trees. This report provides an overview of these modeling methods and examples of health care system problems in which such methods have been useful. The primary aim of the report was to aid decisions as to whether these simulation methods are appropriate to address specific health systems problems. The report directs readers to other resources for further education on these individual modeling methods for system interventions in the emerging field of health care delivery science and implementation. Copyright © 2015. Published by Elsevier Inc.

A simple dynamic engine model for use in a real-time aircraft simulation with thrust vectoring

NASA Technical Reports Server (NTRS)

Johnson, Steven A.

1990-01-01

A simple dynamic engine model was developed at the NASA Ames Research Center, Dryden Flight Research Facility, for use in thrust vectoring control law development and real-time aircraft simulation. The simple dynamic engine model of the F404-GE-400 engine (General Electric, Lynn, Massachusetts) operates within the aircraft simulator. It was developed using tabular data generated from a complete nonlinear dynamic engine model supplied by the manufacturer. Engine dynamics were simulated using a throttle rate limiter and low-pass filter. Included is a description of a method to account for axial thrust loss resulting from thrust vectoring. In addition, the development of the simple dynamic engine model and its incorporation into the F-18 high alpha research vehicle (HARV) thrust vectoring simulation. The simple dynamic engine model was evaluated at Mach 0.2, 35,000 ft altitude and at Mach 0.7, 35,000 ft altitude. The simple dynamic engine model is within 3 percent of the steady state response, and within 25 percent of the transient response of the complete nonlinear dynamic engine model.

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

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

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.

Generalized Green's function molecular dynamics for canonical ensemble simulations

NASA Astrophysics Data System (ADS)

Coluci, V. R.; Dantas, S. O.; Tewary, V. K.

2018-05-01

The need of small integration time steps (˜1 fs) in conventional molecular dynamics simulations is an important issue that inhibits the study of physical, chemical, and biological systems in real timescales. Additionally, to simulate those systems in contact with a thermal bath, thermostating techniques are usually applied. In this work, we generalize the Green's function molecular dynamics technique to allow simulations within the canonical ensemble. By applying this technique to one-dimensional systems, we were able to correctly describe important thermodynamic properties such as the temperature fluctuations, the temperature distribution, and the velocity autocorrelation function. We show that the proposed technique also allows the use of time steps one order of magnitude larger than those typically used in conventional molecular dynamics simulations. We expect that this technique can be used in long-timescale molecular dynamics simulations.

Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.

PubMed

Erban, Radek

2016-02-01

Molecular dynamics (MD) simulations of ions (K + , Na + , Ca 2+ 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.

Molecular Dynamics Analysis of Lysozyme Protein in Ethanol- Water Mixed Solvent

DTIC Science & Technology

2012-01-01

molecular dynamics simulations of solvent effect on lysozyme protein, using water, ethanol, and different concentrations of water-ethanol mixtures as...understood. This work focuses on detailed molecular dynamics simulations of solvent effect on lysozyme protein, using water, ethanol, and different...using GROMACS molecular dynamics simulation (MD) code. Compared to water environment, the lysozyme structure showed remarkable changes in water

The Distributed Diagonal Force Decomposition Method for Parallelizing Molecular Dynamics Simulations

PubMed Central

Boršnik, Urban; Miller, Benjamin T.; Brooks, Bernard R.; Janežič, Dušanka

2011-01-01

Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used. PMID:21793007

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?

PubMed Central

Siwy, Christopher M.

2017-01-01

By applying REMD simulations we have performed comparative analysis of the conformational ensembles of amino-truncated Aβ10-40 peptide produced with five force fields, which combine four protein parameterizations (CHARMM36, CHARMM22*, CHARMM22/cmap, and OPLS-AA) and two water models (standard and modified TIP3P). Aβ10-40 conformations were analyzed by computing secondary structure, backbone fluctuations, tertiary interactions, and radius of gyration. We have also calculated Aβ10-40 3JHNHα-coupling and RDC constants and compared them with their experimental counterparts obtained for the full-length Aβ1-40 peptide. Our study led us to several conclusions. First, all force fields predict that Aβ adopts unfolded structure dominated by turn and random coil conformations. Second, specific TIP3P water model does not dramatically affect secondary or tertiary Aβ10-40 structure, albeit standard TIP3P model favors slightly more compact states. Third, although the secondary structures observed in CHARMM36 and CHARMM22/cmap simulations are qualitatively similar, their tertiary interactions show little consistency. Fourth, two force fields, OPLS-AA and CHARMM22* have unique features setting them apart from CHARMM36 or CHARMM22/cmap. OPLS-AA reveals moderate β-structure propensity coupled with extensive, but weak long-range tertiary interactions leading to Aβ collapsed conformations. CHARMM22* exhibits moderate helix propensity and generates multiple exceptionally stable long- and short-range interactions. Our investigation suggests that among all force fields CHARMM22* differs the most from CHARMM36. Fifth, the analysis of 3JHNHα-coupling and RDC constants based on CHARMM36 force field with standard TIP3P model led us to an unexpected finding that in silico Aβ10-40 and experimental Aβ1-40 constants are generally in better agreement than these quantities computed and measured for identical peptides, such as Aβ1-40 or Aβ1-42. This observation suggests that the differences in the conformational ensembles of Aβ10-40 and Aβ1-40 are small and the former can be used as proxy of the full-length peptide. Based on this argument, we concluded that CHARMM36 force field with standard TIP3P model produces the most accurate representation of Aβ10-40 conformational ensemble. PMID:28085875

Real-time electron dynamics for massively parallel excited-state simulations

NASA Astrophysics Data System (ADS)

Andrade, Xavier

The simulation of the real-time dynamics of electrons, based on time dependent density functional theory (TDDFT), is a powerful approach to study electronic excited states in molecular and crystalline systems. What makes the method attractive is its flexibility to simulate different kinds of phenomena beyond the linear-response regime, including strongly-perturbed electronic systems and non-adiabatic electron-ion dynamics. Electron-dynamics simulations are also attractive from a computational point of view. They can run efficiently on massively parallel architectures due to the low communication requirements. Our implementations of electron dynamics, based on the codes Octopus (real-space) and Qball (plane-waves), allow us to simulate systems composed of thousands of atoms and to obtain good parallel scaling up to 1.6 million processor cores. Due to the versatility of real-time electron dynamics and its parallel performance, we expect it to become the method of choice to apply the capabilities of exascale supercomputers for the simulation of electronic excited states.

Evaluation of a grid based molecular dynamics approach for polypeptide simulations.

PubMed

Merelli, Ivan; Morra, Giulia; Milanesi, Luciano

2007-09-01

Molecular dynamics is very important for biomedical research because it makes possible simulation of the behavior of a biological macromolecule in silico. However, molecular dynamics is computationally rather expensive: the simulation of some nanoseconds of dynamics for a large macromolecule such as a protein takes very long time, due to the high number of operations that are needed for solving the Newton's equations in the case of a system of thousands of atoms. In order to obtain biologically significant data, it is desirable to use high-performance computation resources to perform these simulations. Recently, a distributed computing approach based on replacing a single long simulation with many independent short trajectories has been introduced, which in many cases provides valuable results. This study concerns the development of an infrastructure to run molecular dynamics simulations on a grid platform in a distributed way. The implemented software allows the parallel submission of different simulations that are singularly short but together bring important biological information. Moreover, each simulation is divided into a chain of jobs to avoid data loss in case of system failure and to contain the dimension of each data transfer from the grid. The results confirm that the distributed approach on grid computing is particularly suitable for molecular dynamics simulations thanks to the elevated scalability.

Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

PubMed

Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F

2017-01-01

Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

Structure and Dynamics of End-to-End Loop Formation of the Penta-Peptide Cys-Ala-Gly-Gln-Trp in Implicit Solvents

DTIC Science & Technology

2009-01-01

implicit solvents on peptide structure and dynamics , we performed extensive molecular dynamics simulations on the penta-peptide Cys-Ala-Gly-Gln-Trp. Two...end-to-end distances and dihedral angles obtained from molecular dynamics simulations with implicit solvent models were in a good agreement with those...to maintain the temperature of the systems. Introduction Molecular dynamics (MD) simulation techniques are widely used to study structure and

Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design

DTIC Science & Technology

2009-11-01

dynamics of the complex predicted by multiple molecular dynamics simulations , and discuss further structural optimization to achieve better in vivo efficacy...complex with BoNTAe and the dynamics of the complex predicted by multiple molecular dynamics simulations (MMDSs). On the basis of the 3D model, we discuss...is unlimited whereas AHP exhibited 54% inhibition under the same conditions (Table 1). Computer Simulation Twenty different molecular dynamics

Investigation of the Dynamic Contact Angle Using a Direct Numerical Simulation Method.

PubMed

Zhu, Guangpu; Yao, Jun; Zhang, Lei; Sun, Hai; Li, Aifen; Shams, Bilal

2016-11-15

A large amount of residual oil, which exists as isolated oil slugs, remains trapped in reservoirs after water flooding. Numerous numerical studies are performed to investigate the fundamental flow mechanism of oil slugs to improve flooding efficiency. Dynamic contact angle models are usually introduced to simulate an accurate contact angle and meniscus displacement of oil slugs under a high capillary number. Nevertheless, in the oil slug flow simulation process, it is unnecessary to introduce the dynamic contact angle model because of a negligible change in the meniscus displacement after using the dynamic contact angle model when the capillary number is small. Therefore, a critical capillary number should be introduced to judge whether the dynamic contact model should be incorporated into simulations. In this study, a direct numerical simulation method is employed to simulate the oil slug flow in a capillary tube at the pore scale. The position of the interface between water and the oil slug is determined using the phase-field method. The capacity and accuracy of the model are validated using a classical benchmark: a dynamic capillary filling process. Then, different dynamic contact angle models and the factors that affect the dynamic contact angle are analyzed. The meniscus displacements of oil slugs with a dynamic contact angle and a static contact angle (SCA) are obtained during simulations, and the relative error between them is calculated automatically. The relative error limit has been defined to be 5%, beyond which the dynamic contact angle model needs to be incorporated into the simulation to approach the realistic displacement. Thus, the desired critical capillary number can be determined. A three-dimensional universal chart of critical capillary number, which functions as static contact angle and viscosity ratio, is given to provide a guideline for oil slug simulation. Also, a fitting formula is presented for ease of use.

A parameters optimization method for planar joint clearance model and its application for dynamics simulation of reciprocating compressor

NASA Astrophysics Data System (ADS)

Hai-yang, Zhao; Min-qiang, Xu; Jin-dong, Wang; Yong-bo, Li

2015-05-01

In order to improve the accuracy of dynamics response simulation for mechanism with joint clearance, a parameter optimization method for planar joint clearance contact force model was presented in this paper, and the optimized parameters were applied to the dynamics response simulation for mechanism with oversized joint clearance fault. By studying the effect of increased clearance on the parameters of joint clearance contact force model, the relation of model parameters between different clearances was concluded. Then the dynamic equation of a two-stage reciprocating compressor with four joint clearances was developed using Lagrange method, and a multi-body dynamic model built in ADAMS software was used to solve this equation. To obtain a simulated dynamic response much closer to that of experimental tests, the parameters of joint clearance model, instead of using the designed values, were optimized by genetic algorithms approach. Finally, the optimized parameters were applied to simulate the dynamics response of model with oversized joint clearance fault according to the concluded parameter relation. The dynamics response of experimental test verified the effectiveness of this application.

Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations.

PubMed

Einert, T R; Sing, C E; Alexander-Katz, A; Netz, R R

2011-12-01

We study the conformational dynamics within homopolymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength ε and the globule size N (G) is observed. We find two distinct dynamical regimes: a liquid-like regime (for ε < ε(s) with fast internal dynamics and a solid-like regime (for ε > ε(s) with slow internal dynamics. The cohesion strength ε(s) of this freezing transition depends on N (G) . Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with ε and scales extensive in N (G) . This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.

Dynamic CFD Simulations of the Supersonic Inflatable Aerodynamic Decelerator (SIAD) Ballistic Range Tests

NASA Technical Reports Server (NTRS)

Brock, Joseph M; Stern, Eric

2016-01-01

Dynamic CFD simulations of the SIAD ballistic test model were performed using US3D flow solver. Motivation for performing these simulations is for the purpose of validation and verification of the US3D flow solver as a viable computational tool for predicting dynamic coefficients.

High performance computing in biology: multimillion atom simulations of nanoscale systems

PubMed Central

Sanbonmatsu, K. Y.; Tung, C.-S.

2007-01-01

Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nanoscale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail. PMID:17187988

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

PubMed Central

Schöneberg, Johannes; Noé, Frank

2013-01-01

We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics. PMID:24040218

Dynamic Mesh CFD Simulations of Orion Parachute Pendulum Motion During Atmospheric Entry

NASA Technical Reports Server (NTRS)

Halstrom, Logan D.; Schwing, Alan M.; Robinson, Stephen K.

2016-01-01

This paper demonstrates the usage of computational fluid dynamics to study the effects of pendulum motion dynamics of the NASAs Orion Multi-Purpose Crew Vehicle parachute system on the stability of the vehicles atmospheric entry and decent. Significant computational fluid dynamics testing has already been performed at NASAs Johnson Space Center, but this study sought to investigate the effect of bulk motion of the parachute, such as pitching, on the induced aerodynamic forces. Simulations were performed with a moving grid geometry oscillating according to the parameters observed in flight tests. As with the previous simulations, OVERFLOW computational fluid dynamics tool is used with the assumption of rigid, non-permeable geometry. Comparison to parachute wind tunnel tests is included for a preliminary validation of the dynamic mesh model. Results show qualitative differences in the flow fields of the static and dynamic simulations and quantitative differences in the induced aerodynamic forces, suggesting that dynamic mesh modeling of the parachute pendulum motion may uncover additional dynamic effects.

High Speed Civil Transport Aircraft Simulation: Reference-H Cycle 1, MATLAB Implementation

NASA Technical Reports Server (NTRS)

Sotack, Robert A.; Chowdhry, Rajiv S.; Buttrill, Carey S.

1999-01-01

The mathematical model and associated code to simulate a high speed civil transport aircraft - the Boeing Reference H configuration - are described. The simulation was constructed in support of advanced control law research. In addition to providing time histories of the dynamic response, the code includes the capabilities for calculating trim solutions and for generating linear models. The simulation relies on the nonlinear, six-degree-of-freedom equations which govern the motion of a rigid aircraft in atmospheric flight. The 1962 Standard Atmosphere Tables are used along with a turbulence model to simulate the Earth atmosphere. The aircraft model has three parts - an aerodynamic model, an engine model, and a mass model. These models use the data from the Boeing Reference H cycle 1 simulation data base. Models for the actuator dynamics, landing gear, and flight control system are not included in this aircraft model. Dynamic responses generated by the nonlinear simulation are presented and compared with results generated from alternate simulations at Boeing Commercial Aircraft Company and NASA Langley Research Center. Also, dynamic responses generated using linear models are presented and compared with dynamic responses generated using the nonlinear simulation.

Coarse-Grained Lattice Model Simulations of Sequence-Structure Fitness of a Ribosome-Inactivating Protein

DTIC Science & Technology

2007-11-05

limits of what is considered practical when applying all-atom molecular - dynamics simulation methods. Lattice models provide computationally robust...of expectation values from the density of states. All-atom molecular - dynamics simulations provide the most rigorous sampling method to generate con... molecular - dynamics simulations of protein folding,6–9 reported studies of computing a heat capacity or other calorimetric observables have been limited to

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

Dynamic system simulation of small satellite projects

NASA Astrophysics Data System (ADS)

Raif, Matthias; Walter, Ulrich; Bouwmeester, Jasper

2010-11-01

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

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.

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.

Tethered satellite system dynamics and control

NASA Technical Reports Server (NTRS)

Musetti, B.; Cibrario, B.; Bussolino, L.; Bodley, C. S.; Flanders, H. A.; Mowery, D. K.; Tomlin, D. D.

1990-01-01

The first tethered satellite system, scheduled for launch in May 1991, is reviewed. The system dynamics, dynamics control, and dynamics simulations are discussed. Particular attention is given to in-plane and out-of-plane librations; tether oscillation modes; orbiter and sub-satellite dynamics; deployer control system; the sub-satellite attitude measurement and control system; the Aeritalia Dynamics Model; the Martin-Marietta and NASA-MSFC Dynamics Model; and simulation results.

Numerical Simulation of Rolling-Airframes Using a Multi-Level Cartesian Method

NASA Technical Reports Server (NTRS)

Murman, Scott M.; Aftosmis, Michael J.; Berger, Marsha J.; Kwak, Dochan (Technical Monitor)

2002-01-01

A supersonic rolling missile with two synchronous canard control surfaces is analyzed using an automated, inviscid, Cartesian method. Sequential-static and time-dependent dynamic simulations of the complete motion are computed for canard dither schedules for level flight, pitch, and yaw maneuver. The dynamic simulations are compared directly against both high-resolution viscous simulations and relevant experimental data, and are also utilized to compute dynamic stability derivatives. The results show that both the body roll rate and canard dither motion influence the roll-averaged forces and moments on the body. At the relatively, low roll rates analyzed in the current work these dynamic effects are modest, however the dynamic computations are effective in predicting the dynamic stability derivatives which can be significant for highly-maneuverable missiles.

Analysis, simulation and visualization of 1D tapping via reduced dynamical models

NASA Astrophysics Data System (ADS)

Blackmore, Denis; Rosato, Anthony; Tricoche, Xavier; Urban, Kevin; Zou, Luo

2014-04-01

A low-dimensional center-of-mass dynamical model is devised as a simplified means of approximately predicting some important aspects of the motion of a vertical column comprised of a large number of particles subjected to gravity and periodic vertical tapping. This model is investigated first as a continuous dynamical system using analytical, simulation and visualization techniques. Then, by employing an approach analogous to that used to approximate the dynamics of a bouncing ball on an oscillating flat plate, it is modeled as a discrete dynamical system and analyzed to determine bifurcations and transitions to chaotic motion along with other properties. The predictions of the analysis are then compared-primarily qualitatively-with visualization and simulation results of the reduced continuous model, and ultimately with simulations of the complete system dynamics.

A CONTINUUM HARD-SPHERE MODEL OF PROTEIN ADSORPTION

PubMed Central

Finch, Craig; Clarke, Thomas; Hickman, James J.

2012-01-01

Protein adsorption plays a significant role in biological phenomena such as cell-surface interactions and the coagulation of blood. Two-dimensional random sequential adsorption (RSA) models are widely used to model the adsorption of proteins on solid surfaces. Continuum equations have been developed so that the results of RSA simulations can be used to predict the kinetics of adsorption. Recently, Brownian dynamics simulations have become popular for modeling protein adsorption. In this work a continuum model was developed to allow the results from a Brownian dynamics simulation to be used as the boundary condition in a computational fluid dynamics (CFD) simulation. Brownian dynamics simulations were used to model the diffusive transport of hard-sphere particles in a liquid and the adsorption of the particles onto a solid surface. The configuration of the adsorbed particles was analyzed to quantify the chemical potential near the surface, which was found to be a function of the distance from the surface and the fractional surface coverage. The near-surface chemical potential was used to derive a continuum model of adsorption that incorporates the results from the Brownian dynamics simulations. The equations of the continuum model were discretized and coupled to a CFD simulation of diffusive transport to the surface. The kinetics of adsorption predicted by the continuum model closely matched the results from the Brownian dynamics simulation. This new model allows the results from mesoscale simulations to be incorporated into micro- or macro-scale CFD transport simulations of protein adsorption in practical devices. PMID:23729843

Advanced Polymer Network Structures

DTIC Science & Technology

2016-02-01

double networks in a single step was identified from coarse-grained molecular dynamics simulations of polymer solvents bearing rigid side chains dissolved...in a polymer network. Coarse-grained molecular dynamics simulations also explored the mechanical behavior of traditional double networks and...DRI), polymer networks, polymer gels, molecular dynamics simulations , double networks 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF

A cable-driven parallel robots application: modelling and simulation of a dynamic cable model in Dymola

NASA Astrophysics Data System (ADS)

Othman, M. F.; Kurniawan, R.; Schramm, D.; Ariffin, A. K.

2018-05-01

Modeling a cable model in multibody dynamics simulation tool which dynamically varies in length, mass and stiffness is a challenging task. Simulation of cable-driven parallel robots (CDPR) for instance requires a cable model that can dynamically change in length for every desired pose of the platform. Thus, in this paper, a detailed procedure for modeling and simulation of a dynamic cable model in Dymola is proposed. The approach is also applicable for other types of Modelica simulation environments. The cable is modeled using standard mechanical elements like mass, spring, damper and joint. The parameters of the cable model are based on the factsheet of the manufacturer and experimental results. Its dynamic ability is tested by applying it on a complete planar CDPR model in which the parameters are based on a prototype named CABLAR, which is developed in Chair of Mechatronics, University of Duisburg-Essen. The prototype has been developed to demonstrate an application of CDPR as a goods storage and retrieval machine. The performance of the cable model during the simulation is analyzed and discussed.

Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

NASA Astrophysics Data System (ADS)

Bolhuis, Peter

Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the 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. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

Real-time dynamics simulation of the Cassini spacecraft using DARTS. Part 1: Functional capabilities and the spatial algebra algorithm

NASA Technical Reports Server (NTRS)

Jain, A.; Man, G. K.

1993-01-01

This paper describes the Dynamics Algorithms for Real-Time Simulation (DARTS) real-time hardware-in-the-loop dynamics simulator for the National Aeronautics and Space Administration's Cassini spacecraft. The spacecraft model consists of a central flexible body with a number of articulated rigid-body appendages. The demanding performance requirements from the spacecraft control system require the use of a high fidelity simulator for control system design and testing. The DARTS algorithm provides a new algorithmic and hardware approach to the solution of this hardware-in-the-loop simulation problem. It is based upon the efficient spatial algebra dynamics for flexible multibody systems. A parallel and vectorized version of this algorithm is implemented on a low-cost, multiprocessor computer to meet the simulation timing requirements.

An AD100 implementation of a real-time STOVL aircraft propulsion system

NASA Technical Reports Server (NTRS)

Ouzts, Peter J.; Drummond, Colin K.

1990-01-01

A real-time dynamic model of the propulsion system for a Short Take-Off and Vertical Landing (STOVL) aircraft was developed for the AD100 simulation environment. The dynamic model was adapted from a FORTRAN based simulation using the dynamic programming capabilities of the AD100 ADSIM simulation language. The dynamic model includes an aerothermal representation of a turbofan jet engine, actuator and sensor models, and a multivariable control system. The AD100 model was tested for agreement with the FORTRAN model and real-time execution performance. The propulsion system model was also linked to an airframe dynamic model to provide an overall STOVL aircraft simulation for the purposes of integrated flight and propulsion control studies. An evaluation of the AD100 system for use as an aircraft simulation environment is included.

CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis.

PubMed

Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki

2014-09-01

Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

Software-Engineering Process Simulation (SEPS) model

NASA Technical Reports Server (NTRS)

Lin, C. Y.; Abdel-Hamid, T.; Sherif, J. S.

1992-01-01

The Software Engineering Process Simulation (SEPS) model is described which was developed at JPL. SEPS is a dynamic simulation model of the software project development process. It uses the feedback principles of system dynamics to simulate the dynamic interactions among various software life cycle development activities and management decision making processes. The model is designed to be a planning tool to examine tradeoffs of cost, schedule, and functionality, and to test the implications of different managerial policies on a project's outcome. Furthermore, SEPS will enable software managers to gain a better understanding of the dynamics of software project development and perform postmodern assessments.

Molecular dynamics simulations of collision-induced absorption: Implementation in LAMMPS

NASA Astrophysics Data System (ADS)

Fakhardji, W.; Gustafsson, M.

2017-02-01

We pursue simulations of collision-induced absorption in a mixture of argon and xenon gas at room temperature by means of classical molecular dynamics. The established theoretical approach (Hartmann et al. 2011 J. Chem. Phys. 134 094316) is implemented with the molecular dynamics package LAMMPS. The bound state features in the absorption spectrum are well reproduced with the molecular dynamics simulation in comparison with a laboratory measurement. The magnitude of the computed absorption, however, is underestimated in a large part of the spectrum. We suggest some aspects of the simulation that could be improved.

Simulating Food Web Dynamics along a Gradient: Quantifying Human Influence

PubMed Central

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 could greatly contribute to understanding various aspects of functional diversity. PMID:22768346

System Simulation by Recursive Feedback: Coupling a Set of Stand-Alone Subsystem Simulations

NASA Technical Reports Server (NTRS)

Nixon, D. D.

2001-01-01

Conventional construction of digital dynamic system simulations often involves collecting differential equations that model each subsystem, arran g them to a standard form, and obtaining their numerical gin solution as a single coupled, total-system simultaneous set. Simulation by numerical coupling of independent stand-alone subsimulations is a fundamentally different approach that is attractive because, among other things, the architecture naturally facilitates high fidelity, broad scope, and discipline independence. Recursive feedback is defined and discussed as a candidate approach to multidiscipline dynamic system simulation by numerical coupling of self-contained, single-discipline subsystem simulations. A satellite motion example containing three subsystems (orbit dynamics, attitude dynamics, and aerodynamics) has been defined and constructed using this approach. Conventional solution methods are used in the subsystem simulations. Distributed and centralized implementations of coupling have been considered. Numerical results are evaluated by direct comparison with a standard total-system, simultaneous-solution approach.

Simulating the flow of entangled polymers.

PubMed

Masubuchi, Yuichi

2014-01-01

To optimize automation for polymer processing, attempts have been made to simulate the flow of entangled polymers. In industry, fluid dynamics simulations with phenomenological constitutive equations have been practically established. However, to account for molecular characteristics, a method to obtain the constitutive relationship from the molecular structure is required. Molecular dynamics simulations with atomic description are not practical for this purpose; accordingly, coarse-grained models with reduced degrees of freedom have been developed. Although the modeling of entanglement is still a challenge, mesoscopic models with a priori settings to reproduce entangled polymer dynamics, such as tube models, have achieved remarkable success. To use the mesoscopic models as staging posts between atomistic and fluid dynamics simulations, studies have been undertaken to establish links from the coarse-grained model to the atomistic and macroscopic simulations. Consequently, integrated simulations from materials chemistry to predict the macroscopic flow in polymer processing are forthcoming.

Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations.

PubMed

Allnér, Olof; Foloppe, Nicolas; Nilsson, Lennart

2015-01-22

Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory data. NMR relaxation is the most widely used experimental method to obtain data on dynamics of proteins, but it is limited to relatively short timescales and to motions of backbone amides or in some cases (13)C-H vectors. By relating the experimental data to the all-atom picture obtained in molecular dynamics simulations, valuable insights on the interpretation of the experiment can be gained. We have estimated the internal dynamics and their timescales by calculating the generalized order parameters (O) for different time windows. We then calculate the quasiharmonic entropy (S) and compare it to the entropy calculated from the NMR-derived generalized order parameter of the amide vectors. Special emphasis is put on characterizing dynamics that are not expressed through the motions of the amide group. The NMR and MD methods suffer from complementary limitations, with NMR being restricted to local vectors and dynamics on a timescale determined by the rotational diffusion of the solute, while in simulations, it may be difficult to obtain sufficient sampling to ensure convergence of the results. We also evaluate the amount of sampling obtained with molecular dynamics simulations and how it is affected by the length of individual simulations, by clustering of the sampled conformations. We find that two structural turns act as hinges, allowing the α helix between them to undergo large, long timescale motions that cannot be detected in the time window of the NMR dipolar relaxation experiments. We also show that the entropy obtained from the amide vector does not account for correlated motions of adjacent residues. Finally, we show that the sampling in a total of 100 ns molecular dynamics simulation can be increased by around 50%, by dividing the trajectory into 10 replicas with different starting velocities.

Dielectric Properties of Poly(ethylene oxide) from Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

Smith, Grant D.

1994-01-01

The order, conformations and dynamics of poly(oxyethylene) (POE) melts have been investigated through molecular dynamics simulations. The potential energy functions were determined from detailed ab initio electronic structure calculations of the conformational energies of the model molecules 1,2-dimethoxyethane (DME) and diethylether. The x-ray structure factor for POE from simulation will be compared to experiment. In terms of conformation, simulations reveal that chains are extended in the melt relative to isolated chains due to the presence of strong intermolecular O...H interactions, which occur at the expense of intramolecular O...H interactions. Conformational dynamics about the C-C bond were found to be significantly faster than in polymethylene, while conformational dynamics about the C-O bond even faster than the C-C dynamics. The faster local dynamics in POE relative to polymethylene is consistent with C-13 NMR spin-lattice relaxation experiments. Conformational transitions showed significant second-neighbor correlation, as was found for polymethylene. This correlation of transitions with C-C neighbors was found to be reduced relative to C-O neighbors. Dielectric relaxation from simulation will also be compared with experiment.

Similarities between principal components of protein dynamics and random diffusion

NASA Astrophysics Data System (ADS)

Hess, Berk

2000-12-01

Principal component analysis, also called essential dynamics, is a powerful tool for finding global, correlated motions in atomic simulations of macromolecules. It has become an established technique for analyzing molecular dynamics simulations of proteins. The first few principal components of simulations of large proteins often resemble cosines. We derive the principal components for high-dimensional random diffusion, which are almost perfect cosines. This resemblance between protein simulations and noise implies that for many proteins the time scales of current simulations are too short to obtain convergence of collective motions.

Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation

NASA Technical Reports Server (NTRS)

Afjeh, Abdollah A.; Reed, John A.

2003-01-01

The following reports are presented on this project:A first year progress report on: Development of a Dynamically Configurable,Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; A second year progress report on: Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; An Extensible, Interchangeable and Sharable Database Model for Improving Multidisciplinary Aircraft Design; Interactive, Secure Web-enabled Aircraft Engine Simulation Using XML Databinding Integration; and Improving the Aircraft Design Process Using Web-based Modeling and Simulation.

Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment

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

Pratihar, Subha; Barnes, George L.; Laskin, Julia

In this Perspective mass spectrometry experiments and chemical dynamics simulations are described which have explored the atomistic dynamics of protonated peptide ions, peptide-H+, colliding with organic surfaces. These studies have investigated surface-induced dissociation (SID) for which peptide-H+ fragments upon collision with the surface, peptide-H+ physisorption on the surface, soft landing (SL), and peptide-H+ reaction with the surface, reactive landing (RL). The simulations include QM+MM and QM/MM direct dynamics. For collisions with self-assembled monolayer (SAM) surfaces there is quite good agreement between experiment and simulation in the efficiency of energy transfer to the peptide-H+ ion’s internal degrees of freedom. Both themore » experiments and simulations show two mechanisms for peptide-H+ fragmentation, i.e. shattering and statistical, RRKM dynamics. Mechanisms for SL are probed in simulations of collisions of protonated dialanine with a perfluorinated SAM surface. RL has been studied experimentally for a number of peptide-H+ + surface systems, and qualitative agreement between simulation and experiment is found for two similar systems.« less

Dynamic computer simulations of electrophoresis: three decades of active research.

PubMed

Thormann, Wolfgang; Caslavska, Jitka; Breadmore, Michael C; Mosher, Richard A

2009-06-01

Dynamic models for electrophoresis are based upon model equations derived from the transport concepts in solution together with user-inputted conditions. They are able to predict theoretically the movement of ions and are as such the most versatile tool to explore the fundamentals of electrokinetic separations. Since its inception three decades ago, the state of dynamic computer simulation software and its use has progressed significantly and Electrophoresis played a pivotal role in that endeavor as a large proportion of the fundamental and application papers were published in this periodical. Software is available that simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. This has been employed to show the detailed mechanisms of many of the fundamental phenomena that occur in electrophoretic separations. Dynamic electrophoretic simulations are relevant for separations on any scale and instrumental format, including free-fluid preparative, gel, capillary and chip electrophoresis. This review includes a historical overview, a survey of current simulators, simulation examples and a discussion of the applications and achievements of dynamic simulation.

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

NASA Astrophysics Data System (ADS)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

Equivalence of Brownian dynamics and dynamic Monte Carlo simulations in multicomponent colloidal suspensions.

PubMed

Cuetos, Alejandro; Patti, Alessandro

2015-08-01

We propose a simple but powerful theoretical framework to quantitatively compare Brownian dynamics (BD) and dynamic Monte Carlo (DMC) simulations of multicomponent colloidal suspensions. By extending our previous study focusing on monodisperse systems of rodlike colloids, here we generalize the formalism described there to multicomponent colloidal mixtures and validate it by investigating the dynamics in isotropic and liquid crystalline phases containing spherical and rodlike particles. In order to investigate the dynamics of multicomponent colloidal systems by DMC simulations, it is key to determine the elementary time step of each species and establish a unique timescale. This is crucial to consistently study the dynamics of colloidal particles with different geometry. By analyzing the mean-square displacement, the orientation autocorrelation functions, and the self part of the van Hove correlation functions, we show that DMC simulation is a very convenient and reliable technique to describe the stochastic dynamics of any multicomponent colloidal system. Our theoretical formalism can be easily extended to any colloidal system containing size and/or shape polydisperse particles.

Flight Dynamic Simulation of Fighter In the Asymmetric External Store Release Process

NASA Astrophysics Data System (ADS)

Safi’i, Imam; Arifianto, Ony; Nurohman, Chandra

2018-04-01

In the fighter design, it is important to evaluate and analyze the flight dynamic of the aircraft earlier in the development process. One of the case is the dynamics of external store release process. A simulation tool can be used to analyze the fighter/external store system’s dynamics in the preliminary design stage. This paper reports the flight dynamics of Jet Fighter Experiment (JF-1 E) in asymmetric Advance Medium Range Air to Air Missile (AMRAAM) release process through simulations. The JF-1 E and AIM 120 AMRAAAM models are built by using Advanced Aircraft Analysis (AAA) and Missile Datcom software. By using these softwares, the aerodynamic stability and control derivatives can be obtained and used to model the dynamic characteristic of the fighter and the external store. The dynamic system is modeled by using MATLAB/Simulink software. By using this software, both the fighter/external store integration and the external store release process is simulated, and the dynamic of the system can be analyzed.

Molecular dynamics simulations of a K+ channel blocker: Tc1 toxin from Tityus cambridgei.

PubMed

Grottesi, Alessandro; Sansom, Mark S P

2003-01-30

Toxins that block voltage-gated potassium (Kv) channels provide a possible template for improved homology models of the Kv pore. In assessing the interactions of Kv channels and their toxins it is important to determine the dynamic flexibility of the toxins. Multiple 10 ns duration molecular dynamics simulations combined with essential dynamics analysis have been used to explore the flexibility of four different Kv channel-blocking toxins. Three toxins (Tc1, AgTx and ChTx) share a common fold. They also share a common pattern of conformational dynamics, as revealed by essential dynamics analysis of the simulation results. This suggests that some aspects of dynamic behaviour are conserved across a single protein fold class. In each of these three toxins, the residue exhibiting minimum flexibility corresponds to a conserved lysine residue that is suggested to interact with the filter domain of the channel. Thus, comparative simulations reveal functionally important conservation of molecular dynamics as well as protein fold across a family of related toxins.

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.

Rob Guglielmetti | NREL

Science.gov Websites

2009. Rob's areas of expertise are daylighting, physically based lighting simulation, the integration of lighting simulation with whole-building energy simulations, and high-dynamic range imaging. He has simulation, and high-dynamic range imaging. Rob is an advisory member of the Illuminating Engineering Society

Characterizing rare-event property distributions via replicate molecular dynamics simulations of proteins.

PubMed

Krishnan, Ranjani; Walton, Emily B; Van Vliet, Krystyn J

2009-11-01

As computational resources increase, molecular dynamics simulations of biomolecules are becoming an increasingly informative complement to experimental studies. In particular, it has now become feasible to use multiple initial molecular configurations to generate an ensemble of replicate production-run simulations that allows for more complete characterization of rare events such as ligand-receptor unbinding. However, there are currently no explicit guidelines for selecting an ensemble of initial configurations for replicate simulations. Here, we use clustering analysis and steered molecular dynamics simulations to demonstrate that the configurational changes accessible in molecular dynamics simulations of biomolecules do not necessarily correlate with observed rare-event properties. This informs selection of a representative set of initial configurations. We also employ statistical analysis to identify the minimum number of replicate simulations required to sufficiently sample a given biomolecular property distribution. Together, these results suggest a general procedure for generating an ensemble of replicate simulations that will maximize accurate characterization of rare-event property distributions in biomolecules.

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.

The influence of fatty acids on the GpA dimer interface by coarse-grained molecular dynamics simulation.

PubMed

Flinner, Nadine; Mirus, Oliver; Schleiff, Enrico

2014-08-15

The hydrophobic thickness of membranes, which is manly defined by fatty acids, influences the packing of transmembrane domains of proteins and thus can modulate the activity of these proteins. We analyzed the dynamics of the dimerization of Glycophorin A (GpA) by molecular dynamics simulations to describe the fatty acid dependence of the transmembrane region assembly. GpA represents a well-established model for dimerization of single transmembrane helices containing a GxxxG motif in vitro and in silico. We performed simulations of the dynamics of the NMR-derived dimer as well as self-assembly simulations of monomers in membranes composed of different fatty acid chains and monitored the formed interfaces and their transitions. The observed dimeric interfaces, which also include the one known from NMR, are highly dynamic and converted into each other. The frequency of interface formation and the preferred transitions between interfaces similar to the interface observed by NMR analysis strongly depend on the fatty acid used to build the membrane. Molecular dynamic simulations after adaptation of the helix topology parameters to better represent NMR derived structures of single transmembrane helices yielded an enhanced occurrence of the interface determined by NMR in molecular dynamics simulations. Taken together we give insights into the influence of fatty acids and helix conformation on the dynamics of the transmembrane domain of GpA.

The Influence of Fatty Acids on the GpA Dimer Interface by Coarse-Grained Molecular Dynamics Simulation

PubMed Central

Flinner, Nadine; Mirus, Oliver; Schleiff, Enrico

2014-01-01

The hydrophobic thickness of membranes, which is manly defined by fatty acids, influences the packing of transmembrane domains of proteins and thus can modulate the activity of these proteins. We analyzed the dynamics of the dimerization of Glycophorin A (GpA) by molecular dynamics simulations to describe the fatty acid dependence of the transmembrane region assembly. GpA represents a well-established model for dimerization of single transmembrane helices containing a GxxxG motif in vitro and in silico. We performed simulations of the dynamics of the NMR-derived dimer as well as self-assembly simulations of monomers in membranes composed of different fatty acid chains and monitored the formed interfaces and their transitions. The observed dimeric interfaces, which also include the one known from NMR, are highly dynamic and converted into each other. The frequency of interface formation and the preferred transitions between interfaces similar to the interface observed by NMR analysis strongly depend on the fatty acid used to build the membrane. Molecular dynamic simulations after adaptation of the helix topology parameters to better represent NMR derived structures of single transmembrane helices yielded an enhanced occurrence of the interface determined by NMR in molecular dynamics simulations. Taken together we give insights into the influence of fatty acids and helix conformation on the dynamics of the transmembrane domain of GpA. PMID:25196522

Dynamic performance of accommodating intraocular lenses in a negative feedback control system: a simulation-based study.

PubMed

Schor, Clifton M; Bharadwaj, Shrikant R; Burns, Christopher D

2007-07-01

A dynamic model of ocular accommodation is used to simulate the stability and dynamic performance of accommodating intraocular lenses (A-IOLs) that replace the hardened natural ocular lens that is unable to change focus. Accommodation simulations of an older eye with A-IOL materials having biomechanical properties of a younger eye illustrate overshoots and oscillations resulting from decreased visco-elasticity of the A-IOL. Stable dynamics of an A-IOL are restored by adaptation of phasic and tonic neural-control properties of accommodation. Simulations indicate that neural control must be recalibrated to avoid unstable dynamic accommodation with A-IOLs. An interactive web-model of A-IOL illustrating these properties is available at http://schorlab.berkeley.edu.

Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.

PubMed

Chavent, Matthieu; Duncan, Anna L; Sansom, Mark Sp

2016-10-01

Molecular dynamics simulations provide a computational tool to probe membrane proteins and systems at length scales ranging from nanometers to close to a micrometer, and on microsecond timescales. All atom and coarse-grained simulations may be used to explore in detail the interactions of membrane proteins and specific lipids, yielding predictions of lipid binding sites in good agreement with available structural data. Building on the success of protein-lipid interaction simulations, larger scale simulations reveal crowding and clustering of proteins, resulting in slow and anomalous diffusional dynamics, within realistic models of cell membranes. Current methods allow near atomic resolution simulations of small membrane organelles, and of enveloped viruses to be performed, revealing key aspects of their structure and functionally important dynamics. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Molecular Dynamics Simulations of Shear Induced Transformations in Nitromethane

NASA Astrophysics Data System (ADS)

Larentzos, James; Steele, Brad

2017-06-01

Recent experiments demonstrate that NM undergoes explosive chemical initiation under compressive shear stress. The atomistic dynamics of the shear response of single-crystalline and bi-crystalline nitromethane (NM) are simulated using molecular dynamics simulations under high pressure conditions to aid in interpreting these experiments. The atomic interactions are described using a recently re-optimized ReaxFF-lg potential trained specifically for NM under pressure. The simulations demonstrate that the NM crystal transforms into a disordered state upon sufficient application of shear stress; its maximum value, shear angle, and atomic-scale dynamics being highly dependent on crystallographic orientation of the applied shear. Shear simulations in bi-crystalline NM show more complex behavior resulting in the appearance of the disordered state at the grain boundary.

Molecular Dynamics Simulations of Shear Induced Transformations in Nitromethane

NASA Astrophysics Data System (ADS)

Larentzos, James; Steele, Brad

Recent experiments demonstrate that NM undergoes explosive chemical initiation under compressive shear stress. The atomistic dynamics of the shear response of single-crystalline and bi-crystalline nitromethane (NM) are simulated using molecular dynamics simulations under high pressure conditions to aid in interpreting these experiments. The atomic interactions are described using a recently re-optimized ReaxFF-lg potential trained specifically for NM under pressure. The simulations demonstrate that the NM crystal transforms into a disordered state upon sufficient application of shear stress; its maximum value, shear angle, and atomic-scale dynamics being highly dependent on crystallographic orientation of the applied shear. Shear simulations in bi-crystalline NM show more complex behavior resulting in the appearance of the disordered state at the grain boundary.

Near real-time traffic routing

NASA Technical Reports Server (NTRS)

Yang, Chaowei (Inventor); Xie, Jibo (Inventor); Zhou, Bin (Inventor); Cao, Ying (Inventor)

2012-01-01

A near real-time physical transportation network routing system comprising: a traffic simulation computing grid and a dynamic traffic routing service computing grid. The traffic simulator produces traffic network travel time predictions for a physical transportation network using a traffic simulation model and common input data. The physical transportation network is divided into a multiple sections. Each section has a primary zone and a buffer zone. The traffic simulation computing grid includes multiple of traffic simulation computing nodes. The common input data includes static network characteristics, an origin-destination data table, dynamic traffic information data and historical traffic data. The dynamic traffic routing service computing grid includes multiple dynamic traffic routing computing nodes and generates traffic route(s) using the traffic network travel time predictions.

Compression Behavior and Energy Absorption of Aluminum Alloy AA6061 Tubes with Multiple Holes

NASA Astrophysics Data System (ADS)

Simhachalam, Bade; Lakshmana Rao, C.; Srinivas, Krishna

2014-05-01

In this article, compression behavior and energy absorption of aluminum alloy AA6061 tubes are investigated both experimentally and numerically. Static and dynamic simulations are done using LS-Dyna Software for AA6061 tubes. True stress-plastic strain curves from the tensile test are used in the static and dynamic simulations of AA6061 tubes. The energy absorption values between experimental compression results and numeral simulation are found to be in good agreement. Dynamic simulations are done with drop velocity of up to 10 m/s to understand the inertia effects on energy absorption. The deformed modes from the numerical simulation are compared between tubes with and without holes in static and dynamic conditions.

Code Samples Used for Complexity and Control

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir G.; Reid, Darryn J.

2015-11-01

The following sections are included: * MathematicaⓇ Code * Generic Chaotic Simulator * Vector Differential Operators * NLS Explorer * 2C++ Code * C++ Lambda Functions for Real Calculus * Accelerometer Data Processor * Simple Predictor-Corrector Integrator * Solving the BVP with the Shooting Method * Linear Hyperbolic PDE Solver * Linear Elliptic PDE Solver * Method of Lines for a Set of the NLS Equations * C# Code * Iterative Equation Solver * Simulated Annealing: A Function Minimum * Simple Nonlinear Dynamics * Nonlinear Pendulum Simulator * Lagrangian Dynamics Simulator * Complex-Valued Crowd Attractor Dynamics * Freeform Fortran Code * Lorenz Attractor Simulator * Complex Lorenz Attractor * Simple SGE Soliton * Complex Signal Presentation * Gaussian Wave Packet * Hermitian Matrices * Euclidean L2-Norm * Vector/Matrix Operations * Plain C-Code: Levenberg-Marquardt Optimizer * Free Basic Code: 2D Crowd Dynamics with 3000 Agents

Liquid li structure and dynamics: A comparison between OFDFT and second nearest-neighbor embedded-atom method

DOE PAGES

Chen, Mohan; Vella, Joseph R.; Panagiotopoulos, Athanassios Z.; ...

2015-04-08

The structure and dynamics of liquid lithium are studied using two simulation methods: orbital-free (OF) first-principles molecular dynamics (MD), which employs OF density functional theory (DFT), and classical MD utilizing a second nearest-neighbor embedded-atom method potential. The properties we studied include the dynamic structure factor, the self-diffusion coefficient, the dispersion relation, the viscosity, and the bond angle distribution function. Our simulation results were compared to available experimental data when possible. Each method has distinct advantages and disadvantages. For example, OFDFT gives better agreement with experimental dynamic structure factors, yet is more computationally demanding than classical simulations. Classical simulations can accessmore » a broader temperature range and longer time scales. The combination of first-principles and classical simulations is a powerful tool for studying properties of liquid lithium.« less

Advanced Simulation of Coupled Earthquake and Tsunami Events

NASA Astrophysics Data System (ADS)

Behrens, Joern

2013-04-01

Tsunami-Earthquakes represent natural catastrophes threatening lives and well-being of societies in a solitary and unexpected extreme event as tragically demonstrated in Sumatra (2004), Samoa (2009), Chile (2010), or Japan (2011). Both phenomena are consequences of the complex system of interactions of tectonic stress, fracture mechanics, rock friction, rupture dynamics, fault geometry, ocean bathymetry, and coastline geometry. The ASCETE project forms an interdisciplinary research consortium that couples the most advanced simulation technologies for earthquake rupture dynamics and tsunami propagation to understand the fundamental conditions of tsunami generation. We report on the latest research results in physics-based dynamic rupture and tsunami wave propagation simulation, using unstructured and adaptive meshes with continuous and discontinuous Galerkin discretization approaches. Coupling both simulation tools - the physics-based dynamic rupture simulation and the hydrodynamic tsunami wave propagation - will give us the possibility to conduct highly realistic studies of the interaction of rupture dynamics and tsunami impact characteristics.

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules

NASA Astrophysics Data System (ADS)

Hamelberg, Donald; Mongan, John; McCammon, J. Andrew

2004-06-01

Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution.

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.

Peptide crystal simulations reveal hidden dynamics

PubMed Central

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

2013-01-01

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

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

PubMed Central

Galindo-Murillo, Rodrigo; Roe, Daniel R.; Cheatham, Thomas E.

2014-01-01

Background The structure and dynamics of DNA are critically related to its function. Molecular dynamics (MD) simulations augment experiment by providing detailed information about the atomic motions. However, to date the simulations have not been long enough for convergence of the dynamics and structural properties of DNA. Methods MD simulations performed with AMBER using the ff99SB force field with the parmbsc0 modifications, including ensembles of independent simulations, were compared to long timescale MD performed with the specialized Anton MD engine on the B-DNA structure d(GCACGAACGAACGAACGC). To assess convergence, the decay of the average RMSD values over longer and longer time intervals was evaluated in addition to assessing convergence of the dynamics via the Kullback-Leibler divergence of principal component projection histograms. Results These MD simulations —including one of the longest simulations of DNA published to date at ~44 μs—surprisingly suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the ~1–5 μs timescale. Conclusions We can now reproducibly converge the structure and dynamics of B-DNA helices, omitting the terminal base pairs, on the μs time scale with both the AMBER and CHARMM C36 nucleic acid force fields. Results from independent ensembles of simulations starting from different initial conditions, when aggregated, match the results from long timescale simulations on the specialized Anton MD engine. General Significance With access to large-scale GPU resources or the specialized MD engine “Anton” it is possibly for a variety of molecular systems to reproducibly and reliably converge the conformational ensemble of sampled structures. PMID:25219455

A Quantitative Dynamic Simulation of Bremia lactucae Airborne Conidia Concentration above a Lettuce Canopy.

PubMed

Fall, Mamadou Lamine; Van der Heyden, Hervé; Carisse, Odile

2016-01-01

Lettuce downy mildew, caused by the oomycete Bremia lactucae Regel, is a major threat to lettuce production worldwide. Lettuce downy mildew is a polycyclic disease driven by airborne spores. A weather-based dynamic simulation model for B. lactucae airborne spores was developed to simulate the aerobiological characteristics of the pathogen. The model was built using the STELLA platform by following the system dynamics methodology. The model was developed using published equations describing disease subprocesses (e.g., sporulation) and assembled knowledge of the interactions among pathogen, host, and weather. The model was evaluated with four years of independent data by comparing model simulations with observations of hourly and daily airborne spore concentrations. The results show an accurate simulation of the trend and shape of B. lactucae temporal dynamics of airborne spore concentration. The model simulated hourly and daily peaks in airborne spore concentrations. More than 95% of the simulation runs, the daily-simulated airborne conidia concentration was 0 when airborne conidia were not observed. Also, the relationship between the simulated and the observed airborne spores was linear. In more than 94% of the simulation runs, the proportion of the linear variation in the hourly-observed values explained by the variation in the hourly-simulated values was greater than 0.7 in all years except one. Most of the errors came from the deviation from the 1:1 line, and the proportion of errors due to the model bias was low. This model is the only dynamic model developed to mimic the dynamics of airborne inoculum and represents an initial step towards improved lettuce downy mildew understanding, forecasting and management.

A Quantitative Dynamic Simulation of Bremia lactucae Airborne Conidia Concentration above a Lettuce Canopy

PubMed Central

Fall, Mamadou Lamine; Van der Heyden, Hervé; Carisse, Odile

2016-01-01

Lettuce downy mildew, caused by the oomycete Bremia lactucae Regel, is a major threat to lettuce production worldwide. Lettuce downy mildew is a polycyclic disease driven by airborne spores. A weather-based dynamic simulation model for B. lactucae airborne spores was developed to simulate the aerobiological characteristics of the pathogen. The model was built using the STELLA platform by following the system dynamics methodology. The model was developed using published equations describing disease subprocesses (e.g., sporulation) and assembled knowledge of the interactions among pathogen, host, and weather. The model was evaluated with four years of independent data by comparing model simulations with observations of hourly and daily airborne spore concentrations. The results show an accurate simulation of the trend and shape of B. lactucae temporal dynamics of airborne spore concentration. The model simulated hourly and daily peaks in airborne spore concentrations. More than 95% of the simulation runs, the daily-simulated airborne conidia concentration was 0 when airborne conidia were not observed. Also, the relationship between the simulated and the observed airborne spores was linear. In more than 94% of the simulation runs, the proportion of the linear variation in the hourly-observed values explained by the variation in the hourly-simulated values was greater than 0.7 in all years except one. Most of the errors came from the deviation from the 1:1 line, and the proportion of errors due to the model bias was low. This model is the only dynamic model developed to mimic the dynamics of airborne inoculum and represents an initial step towards improved lettuce downy mildew understanding, forecasting and management. PMID:26953691

SS-mPMG and SS-GA: tools for finding pathways and dynamic simulation of metabolic networks.

PubMed

Katsuragi, Tetsuo; Ono, Naoaki; Yasumoto, Keiichi; Altaf-Ul-Amin, Md; Hirai, Masami Y; Sriyudthsak, Kansuporn; Sawada, Yuji; Yamashita, Yui; Chiba, Yukako; Onouchi, Hitoshi; Fujiwara, Toru; Naito, Satoshi; Shiraishi, Fumihide; Kanaya, Shigehiko

2013-05-01

Metabolomics analysis tools can provide quantitative information on the concentration of metabolites in an organism. In this paper, we propose the minimum pathway model generator tool for simulating the dynamics of metabolite concentrations (SS-mPMG) and a tool for parameter estimation by genetic algorithm (SS-GA). SS-mPMG can extract a subsystem of the metabolic network from the genome-scale pathway maps to reduce the complexity of the simulation model and automatically construct a dynamic simulator to evaluate the experimentally observed behavior of metabolites. Using this tool, we show that stochastic simulation can reproduce experimentally observed dynamics of amino acid biosynthesis in Arabidopsis thaliana. In this simulation, SS-mPMG extracts the metabolic network subsystem from published databases. The parameters needed for the simulation are determined using a genetic algorithm to fit the simulation results to the experimental data. We expect that SS-mPMG and SS-GA will help researchers to create relevant metabolic networks and carry out simulations of metabolic reactions derived from metabolomics data.

Complex double-mass dynamic model of rotor on thrust foil gas dynamic bearings

NASA Astrophysics Data System (ADS)

Sytin, A.; Babin, A.; Vasin, S.

2017-08-01

The present paper considers simulation of a rotor’s dynamics behaviour on thrust foil gas dynamic bearings based on simultaneous solution of gas dynamics differential equations, equations of theory of elasticity, motion equations and some additional equations. A double-mass dynamic system was considered during the rotor’s motion simulation which allows not only evaluation of rotor’s dynamic behaviour, but also to evaluate the influence of operational and load parameters on the dynamics of the rotor-bearing system.

Experimental simulation of decoherence in photonics qudits

PubMed Central

Marques, B.; Matoso, A. A.; Pimenta, W. M.; Gutiérrez-Esparza, A. J.; Santos, M. F.; Pádua, S.

2015-01-01

We experimentally perform the simulation of open quantum dynamics in single-qudit systems. Using a spatial light modulator as a dissipative optical device, we implement dissipative-dynamical maps onto qudits encoded in the transverse momentum of spontaneous parametric down-converted photon pairs. We show a well-controlled technique to prepare entangled qudits states as well as to implement dissipative local measurements; the latter realize two specific dynamics: dephasing and amplitude damping. Our work represents a new analogy-dynamical experiment for simulating an open quantum system. PMID:26527330

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.

Brownian dynamics simulation of protein diffusion in crowded environments

NASA Astrophysics Data System (ADS)

Mereghetti, Paolo; Wade, Rebecca C.

2013-02-01

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. We first describe the development of a Brownian dynamics simulation methodology to investigate the dynamic and structural properties of protein solutions using atomic-detail protein structures. We then discuss insights obtained from applying this approach to simulation of solutions of a range of types of proteins.

Digital Quantum Simulation of Z2 Lattice Gauge Theories with Dynamical Fermionic Matter

NASA Astrophysics Data System (ADS)

Zohar, Erez; Farace, Alessandro; Reznik, Benni; Cirac, J. Ignacio

2017-02-01

We propose a scheme for digital quantum simulation of lattice gauge theories with dynamical fermions. Using a layered optical lattice with ancilla atoms that can move and interact with the other atoms (simulating the physical degrees of freedom), we obtain a stroboscopic dynamics which yields the four-body plaquette interactions, arising in models with (2 +1 ) and higher dimensions, without the use of perturbation theory. As an example we show how to simulate a Z2 model in (2 +1 ) dimensions.

Robust state preparation in quantum simulations of Dirac dynamics

NASA Astrophysics Data System (ADS)

Song, Xue-Ke; Deng, Fu-Guo; Lamata, Lucas; Muga, J. G.

2017-02-01

A nonrelativistic system such as an ultracold trapped ion may perform a quantum simulation of a Dirac equation dynamics under specific conditions. The resulting Hamiltonian and dynamics are highly controllable, but the coupling between momentum and internal levels poses some difficulties to manipulate the internal states accurately in wave packets. We use invariants of motion to inverse engineer robust population inversion processes with a homogeneous, time-dependent simulated electric field. This exemplifies the usefulness of inverse-engineering techniques to improve the performance of quantum simulation protocols.

Dynamic Simulation of AN Helium Refrigerator

NASA Astrophysics Data System (ADS)

Deschildre, C.; Barraud, A.; Bonnay, P.; Briend, P.; Girard, A.; Poncet, J. M.; Roussel, P.; Sequeira, S. E.

2008-03-01

A dynamic simulation of a large scale existing refrigerator has been performed using the software Aspen Hysys®. The model comprises the typical equipments of a cryogenic system: heat exchangers, expanders, helium phase separators and cold compressors. It represents the 400 W @ 1.8 K Test Facility located at CEA—Grenoble. This paper describes the model development and shows the possibilities and limitations of the dynamic module of Aspen Hysys®. Then, comparison between simulation results and experimental data are presented; the simulation of cooldown process was also performed.

Digital Quantum Simulation of Z_{2} Lattice Gauge Theories with Dynamical Fermionic Matter.

PubMed

Zohar, Erez; Farace, Alessandro; Reznik, Benni; Cirac, J Ignacio

2017-02-17

We propose a scheme for digital quantum simulation of lattice gauge theories with dynamical fermions. Using a layered optical lattice with ancilla atoms that can move and interact with the other atoms (simulating the physical degrees of freedom), we obtain a stroboscopic dynamics which yields the four-body plaquette interactions, arising in models with (2+1) and higher dimensions, without the use of perturbation theory. As an example we show how to simulate a Z_{2} model in (2+1) dimensions.

A Low Cost Microcomputer System for Process Dynamics and Control Simulations.

ERIC Educational Resources Information Center

Crowl, D. A.; Durisin, M. J.

1983-01-01

Discusses a video simulator microcomputer system used to provide real-time demonstrations to strengthen students' understanding of process dynamics and control. Also discusses hardware/software and simulations developed using the system. The four simulations model various configurations of a process liquid level tank system. (JN)

System Simulation by Recursive Feedback: Coupling A Set of Stand-Alone Subsystem Simulations

NASA Technical Reports Server (NTRS)

Nixon, Douglas D.; Hanson, John M. (Technical Monitor)

2002-01-01

Recursive feedback is defined and discussed as a framework for development of specific algorithms and procedures that propagate the time-domain solution for a dynamical system simulation consisting of multiple numerically coupled self-contained stand-alone subsystem simulations. A satellite motion example containing three subsystems (other dynamics, attitude dynamics, and aerodynamics) has been defined and constructed using this approach. Conventional solution methods are used in the subsystem simulations. Centralized and distributed versions of coupling structure have been addressed. Numerical results are evaluated by direct comparison with a standard total-system simultaneous-solution approach.

Validation of Potential Models for Li2O in Classical Molecular Dynamics Simulation

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

Oda, Takuji; Oya, Yasuhisa; Tanaka, Satoru

2007-08-01

Four Buckingham-type pairwise potential models for Li2O were assessed by molecular static and dynamics simulations. In the static simulation, all models afforded acceptable agreement with experimental values and ab initio calculation results for the crystalline properties. Moreover, the superionic phase transition was realized in the dynamics simulation. However, the Li diffusivity and the lattice expansion were not adequately reproduced at the same time by any model. When using these models in future radiation simulation, these features should be taken into account, in order to reduce the model dependency of the results.

FAST Simulation Tool Containing Methods for Predicting the Dynamic Response of Wind Turbines

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

Jonkman, Jason

2015-08-12

FAST is a simulation tool (computer software) for modeling tlie dynamic response of horizontal-axis wind turbines. FAST employs a combined modal and multibody structural-dynamics formulation in the time domain.

Molecular dynamics simulation of low-energy recoil events in titanate pyrochlores

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

Dong, Liyuan; Setyawan, Wahyu; Li, Yuhong

2017-01-01

Molecular dynamics simulations of low-energy displacements in titanate pyrochlores have been carried out along three main directions, to determineE dfor A, Ti and O, corresponding defect configurations, and defect formation dynamics.

Explicit symplectic algorithms based on generating functions for relativistic charged particle dynamics in time-dependent electromagnetic field

NASA Astrophysics Data System (ADS)

Zhang, Ruili; Wang, Yulei; He, Yang; Xiao, Jianyuan; Liu, Jian; Qin, Hong; Tang, Yifa

2018-02-01

Relativistic dynamics of a charged particle in time-dependent electromagnetic fields has theoretical significance and a wide range of applications. The numerical simulation of relativistic dynamics is often multi-scale and requires accurate long-term numerical simulations. Therefore, explicit symplectic algorithms are much more preferable than non-symplectic methods and implicit symplectic algorithms. In this paper, we employ the proper time and express the Hamiltonian as the sum of exactly solvable terms and product-separable terms in space-time coordinates. Then, we give the explicit symplectic algorithms based on the generating functions of orders 2 and 3 for relativistic dynamics of a charged particle. The methodology is not new, which has been applied to non-relativistic dynamics of charged particles, but the algorithm for relativistic dynamics has much significance in practical simulations, such as the secular simulation of runaway electrons in tokamaks.

Space station dynamics, attitude control and momentum management

NASA Technical Reports Server (NTRS)

Sunkel, John W.; Singh, Ramen P.; Vengopal, Ravi

1989-01-01

The Space Station Attitude Control System software test-bed provides a rigorous environment for the design, development and functional verification of GN and C algorithms and software. The approach taken for the simulation of the vehicle dynamics and environmental models using a computationally efficient algorithm is discussed. The simulation includes capabilities for docking/berthing dynamics, prescribed motion dynamics associated with the Mobile Remote Manipulator System (MRMS) and microgravity disturbances. The vehicle dynamics module interfaces with the test-bed through the central Communicator facility which is in turn driven by the Station Control Simulator (SCS) Executive. The Communicator addresses issues such as the interface between the discrete flight software and the continuous vehicle dynamics, and multi-programming aspects such as the complex flow of control in real-time programs. Combined with the flight software and redundancy management modules, the facility provides a flexible, user-oriented simulation platform.

Supersonic Flight Dynamics Test 1 - Post-Flight Assessment of Simulation Performance

NASA Technical Reports Server (NTRS)

Dutta, Soumyo; Bowes, Angela L.; Striepe, Scott A.; Davis, Jody L.; Queen, Eric M.; Blood, Eric M.; Ivanov, Mark C.

2015-01-01

NASA's Low Density Supersonic Decelerator (LDSD) project conducted its first Supersonic Flight Dynamics Test (SFDT-1) on June 28, 2014. Program to Optimize Simulated Trajectories II (POST2) was one of the flight dynamics codes used to simulate and predict the flight performance and Monte Carlo analysis was used to characterize the potential flight conditions experienced by the test vehicle. This paper compares the simulation predictions with the reconstructed trajectory of SFDT-1. Additionally, off-nominal conditions seen during flight are modeled in post-flight simulations to find the primary contributors that reconcile the simulation with flight data. The results of these analyses are beneficial for the pre-flight simulation and targeting of the follow-on SFDT flights currently scheduled for summer 2015.

Influence of feedbacks from simulated crop growth on integrated regional hydrologic simulations under climate scenarios

NASA Astrophysics Data System (ADS)

van Walsum, P. E. V.

2011-11-01

Climate change impact modelling of hydrologic responses is hampered by climate-dependent model parameterizations. Reducing this dependency was one of the goals of extending the regional hydrologic modelling system SIMGRO with a two-way coupling to the crop growth simulation model WOFOST. The coupling includes feedbacks to the hydrologic model in terms of the root zone depth, soil cover, leaf area index, interception storage capacity, crop height and crop factor. For investigating whether such feedbacks lead to significantly different simulation results, two versions of the model coupling were set up for a test region: one with exogenous vegetation parameters, the "static" model, and one with endogenous simulation of the crop growth, the "dynamic" model WOFOST. The used parameterization methods of the static/dynamic vegetation models ensure that for the current climate the simulated long-term average of the actual evapotranspiration is the same for both models. Simulations were made for two climate scenarios. Owing to the higher temperatures in combination with a higher CO2-concentration of the atmosphere, a forward time shift of the crop development is simulated in the dynamic model; the used arable land crop, potatoes, also shows a shortening of the growing season. For this crop, a significant reduction of the potential transpiration is simulated compared to the static model, in the example by 15% in a warm, dry year. In consequence, the simulated crop water stress (the unit minus the relative transpiration) is lower when the dynamic model is used; also the simulated increase of crop water stress due to climate change is lower; in the example, the simulated increase is 15 percentage points less (of 55) than when a static model is used. The static/dynamic models also simulate different absolute values of the transpiration. The difference is most pronounced for potatoes at locations with ample moisture supply; this supply can either come from storage release of a good soil or from capillary rise. With good supply of moisture, the dynamic model simulates up to 10% less actual evapotranspiration than the static one in the example. This can lead to cases where the dynamic model predicts a slight increase of the recharge in a climate scenario, where the static model predicts a decrease. The use of a dynamic model also affects the simulated demand for surface water from external sources; especially the timing is affected. The proposed modelling approach uses postulated relationships that require validation with controlled field trials. In the Netherlands there is a lack of experimental facilities for performing such validations.

Man-in-the-control-loop simulation of manipulators

NASA Technical Reports Server (NTRS)

Chang, J. L.; Lin, Tsung-Chieh; Yae, K. Harold

1989-01-01

A method to achieve man-in-the-control-loop simulation is presented. Emerging real-time dynamics simulation suggests a potential for creating an interactive design workstation with a human operator in the control loop. The recursive formulation for multibody dynamics simulation is studied to determine requirements for man-in-the-control-loop simulation. High speed computer graphics techniques provides realistic visual cues for the simulator. Backhoe and robot arm simulations are implemented to demonstrate the capability of man-in-the-control-loop simulation.

Wavelet-based surrogate time series for multiscale simulation of heterogeneous catalysis

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

Savara, Aditya Ashi; Daw, C. Stuart; Xiong, Qingang

We propose a wavelet-based scheme that encodes the essential dynamics of discrete microscale surface reactions in a form that can be coupled with continuum macroscale flow simulations with high computational efficiency. This makes it possible to simulate the dynamic behavior of reactor-scale heterogeneous catalysis without requiring detailed concurrent simulations at both the surface and continuum scales using different models. Our scheme is based on the application of wavelet-based surrogate time series that encodes the essential temporal and/or spatial fine-scale dynamics at the catalyst surface. The encoded dynamics are then used to generate statistically equivalent, randomized surrogate time series, which canmore » be linked to the continuum scale simulation. As a result, we illustrate an application of this approach using two different kinetic Monte Carlo simulations with different characteristic behaviors typical for heterogeneous chemical reactions.« less

Molecular dynamics and dynamic Monte-Carlo simulation of irradiation damage with focused ion beams

NASA Astrophysics Data System (ADS)

Ohya, Kaoru

2017-03-01

The focused ion beam (FIB) has become an important tool for micro- and nanostructuring of samples such as milling, deposition and imaging. However, this leads to damage of the surface on the nanometer scale from implanted projectile ions and recoiled material atoms. It is therefore important to investigate each kind of damage quantitatively. We present a dynamic Monte-Carlo (MC) simulation code to simulate the morphological and compositional changes of a multilayered sample under ion irradiation and a molecular dynamics (MD) simulation code to simulate dose-dependent changes in the backscattering-ion (BSI)/secondary-electron (SE) yields of a crystalline sample. Recent progress in the codes for research to simulate the surface morphology and Mo/Si layers intermixing in an EUV lithography mask irradiated with FIBs, and the crystalline orientation effect on BSI and SE yields relating to the channeling contrast in scanning ion microscopes, is also presented.

Wavelet-based surrogate time series for multiscale simulation of heterogeneous catalysis

DOE PAGES

Savara, Aditya Ashi; Daw, C. Stuart; Xiong, Qingang; ...

2016-01-28

We propose a wavelet-based scheme that encodes the essential dynamics of discrete microscale surface reactions in a form that can be coupled with continuum macroscale flow simulations with high computational efficiency. This makes it possible to simulate the dynamic behavior of reactor-scale heterogeneous catalysis without requiring detailed concurrent simulations at both the surface and continuum scales using different models. Our scheme is based on the application of wavelet-based surrogate time series that encodes the essential temporal and/or spatial fine-scale dynamics at the catalyst surface. The encoded dynamics are then used to generate statistically equivalent, randomized surrogate time series, which canmore » be linked to the continuum scale simulation. As a result, we illustrate an application of this approach using two different kinetic Monte Carlo simulations with different characteristic behaviors typical for heterogeneous chemical reactions.« less

Ultrafast spectroscopy reveals subnanosecond peptide conformational dynamics and validates molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Spörlein, Sebastian; Carstens, Heiko; Satzger, Helmut; Renner, Christian; Behrendt, Raymond; Moroder, Luis; Tavan, Paul; Zinth, Wolfgang; Wachtveitl, Josef

2002-06-01

Femtosecond time-resolved spectroscopy on model peptides with built-in light switches combined with computer simulation of light-triggered motions offers an attractive integrated approach toward the understanding of peptide conformational dynamics. It was applied to monitor the light-induced relaxation dynamics occurring on subnanosecond time scales in a peptide that was backbone-cyclized with an azobenzene derivative as optical switch and spectroscopic probe. The femtosecond spectra permit the clear distinguishing and characterization of the subpicosecond photoisomerization of the chromophore, the subsequent dissipation of vibrational energy, and the subnanosecond conformational relaxation of the peptide. The photochemical cis/trans-isomerization of the chromophore and the resulting peptide relaxations have been simulated with molecular dynamics calculations. The calculated reaction kinetics, as monitored by the energy content of the peptide, were found to match the spectroscopic data. Thus we verify that all-atom molecular dynamics simulations can quantitatively describe the subnanosecond conformational dynamics of peptides, strengthening confidence in corresponding predictions for longer time scales.

Dynamical simulation of E-ELT segmented primary mirror

NASA Astrophysics Data System (ADS)

Sedghi, B.; Muller, M.; Bauvir, B.

2011-09-01

The dynamical behavior of the primary mirror (M1) has an important impact on the control of the segments and the performance of the telescope. Control of large segmented mirrors with a large number of actuators and sensors and multiple control loops in real life is a challenging problem. In virtual life, modeling, simulation and analysis of the M1 bears similar difficulties and challenges. In order to capture the dynamics of the segment subunits (high frequency modes) and the telescope back structure (low frequency modes), high order dynamical models with a very large number of inputs and outputs need to be simulated. In this paper, different approaches for dynamical modeling and simulation of the M1 segmented mirror subject to various perturbations, e.g. sensor noise, wind load, vibrations, earthquake are presented.

Review of Dynamic Modeling and Simulation of Large Scale Belt Conveyor System

NASA Astrophysics Data System (ADS)

He, Qing; Li, Hong

Belt conveyor is one of the most important devices to transport bulk-solid material for long distance. Dynamic analysis is the key to decide whether the design is rational in technique, safe and reliable in running, feasible in economy. It is very important to study dynamic properties, improve efficiency and productivity, guarantee conveyor safe, reliable and stable running. The dynamic researches and applications of large scale belt conveyor are discussed. The main research topics, the state-of-the-art of dynamic researches on belt conveyor are analyzed. The main future works focus on dynamic analysis, modeling and simulation of main components and whole system, nonlinear modeling, simulation and vibration analysis of large scale conveyor system.

Generalized dynamic engine simulation techniques for the digital computer

NASA Technical Reports Server (NTRS)

Sellers, J.; Teren, F.

1974-01-01

Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program, DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design-point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar all-digital programs on future engine simulation philosophy is also discussed.

Generalized dynamic engine simulation techniques for the digital computer

NASA Technical Reports Server (NTRS)

Sellers, J.; Teren, F.

1974-01-01

Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design-point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar all-digital programs on future engine simulation philosophy is also discussed.

Generalized dynamic engine simulation techniques for the digital computers

NASA Technical Reports Server (NTRS)

Sellers, J.; Teren, F.

1975-01-01

Recently advanced simulation techniques have been developed for the digital computer and used as the basis for development of a generalized dynamic engine simulation computer program, called DYNGEN. This computer program can analyze the steady state and dynamic performance of many kinds of aircraft gas turbine engines. Without changes to the basic program, DYNGEN can analyze one- or two-spool turbofan engines. The user must supply appropriate component performance maps and design point information. Examples are presented to illustrate the capabilities of DYNGEN in the steady state and dynamic modes of operation. The analytical techniques used in DYNGEN are briefly discussed, and its accuracy is compared with a comparable simulation using the hybrid computer. The impact of DYNGEN and similar digital programs on future engine simulation philosophy is also discussed.

A high performance system for molecular dynamics simulation of biomolecules using a special-purpose computer.

PubMed

Komeiji, Y; Yokoyama, H; Uebayasi, M; Taiji, M; Fukushige, T; Sugimoto, D; Takata, R; Shimizu, A; Itsukashi, K

1996-01-01

GRAPE (GRavity PipE) processors are special purpose computers for simulation of classical particles. The performance of MD-GRAPE, one of the GRAPEs developed for molecular dynamics, was investigated. The effective speed of MD-GRAPE was equivalent to approximately 6 Gflops. The precision of MD-GRAPE was good judging from the acceptable fluctuation of the total energy. Then a software named PEACH (Program for Energetic Analysis of bioCHemical molecules) was developed for molecular dynamics of biomolecules in combination with MD-GRAPE. Molecular dynamics simulation was performed for several protein-solvent systems with different sizes. Simulation of the largest system investigated (27,000 atoms) took only 5 sec/step. Thus, the PEACH-GRAPE system is expected to be useful in accurate and reliable simulation of large biomolecules.

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors.

PubMed

Glowacki, David R; O'Connor, Michael; Calabró, Gaetano; Price, James; Tew, Philip; Mitchell, Thomas; Hyde, Joseph; Tew, David P; Coughtrie, David J; McIntosh-Smith, Simon

2014-01-01

With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude.

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

Time scale bridging in atomistic simulation of slow dynamics: viscous relaxation and defect activation

NASA Astrophysics Data System (ADS)

Kushima, A.; Eapen, J.; Li, Ju; Yip, S.; Zhu, T.

2011-08-01

Atomistic simulation methods are known for timescale limitations in resolving slow dynamical processes. Two well-known scenarios of slow dynamics are viscous relaxation in supercooled liquids and creep deformation in stressed solids. In both phenomena the challenge to theory and simulation is to sample the transition state pathways efficiently and follow the dynamical processes on long timescales. We present a perspective based on the biased molecular simulation methods such as metadynamics, autonomous basin climbing (ABC), strain-boost and adaptive boost simulations. Such algorithms can enable an atomic-level explanation of the temperature variation of the shear viscosity of glassy liquids, and the relaxation behavior in solids undergoing creep deformation. By discussing the dynamics of slow relaxation in two quite different areas of condensed matter science, we hope to draw attention to other complex problems where anthropological or geological-scale time behavior can be simulated at atomic resolution and understood in terms of micro-scale processes of molecular rearrangements and collective interactions. As examples of a class of phenomena that can be broadly classified as materials ageing, we point to stress corrosion cracking and cement setting as opportunities for atomistic modeling and simulations.

Si amorphization by focused ion beam milling: Point defect model with dynamic BCA simulation and experimental validation.

PubMed

Huang, J; Loeffler, M; Muehle, U; Moeller, W; Mulders, J J L; Kwakman, L F Tz; Van Dorp, W F; Zschech, E

2018-01-01

A Ga focused ion beam (FIB) is often used in transmission electron microscopy (TEM) analysis sample preparation. In case of a crystalline Si sample, an amorphous near-surface layer is formed by the FIB process. In order to optimize the FIB recipe by minimizing the amorphization, it is important to predict the amorphous layer thickness from simulation. Molecular Dynamics (MD) simulation has been used to describe the amorphization, however, it is limited by computational power for a realistic FIB process simulation. On the other hand, Binary Collision Approximation (BCA) simulation is able and has been used to simulate ion-solid interaction process at a realistic scale. In this study, a Point Defect Density approach is introduced to a dynamic BCA simulation, considering dynamic ion-solid interactions. We used this method to predict the c-Si amorphization caused by FIB milling on Si. To validate the method, dedicated TEM studies are performed. It shows that the amorphous layer thickness predicted by the numerical simulation is consistent with the experimental data. In summary, the thickness of the near-surface Si amorphization layer caused by FIB milling can be well predicted using the Point Defect Density approach within the dynamic BCA model. Copyright © 2017 Elsevier B.V. All rights reserved.

Rupture Dynamics and Seismic Radiation on Rough Faults for Simulation-Based PSHA

NASA Astrophysics Data System (ADS)

Mai, P. M.; Galis, M.; Thingbaijam, K. K. S.; Vyas, J. C.; Dunham, E. M.

2017-12-01

Simulation-based ground-motion predictions may augment PSHA studies in data-poor regions or provide additional shaking estimations, incl. seismic waveforms, for critical facilities. Validation and calibration of such simulation approaches, based on observations and GMPE's, is important for engineering applications, while seismologists push to include the precise physics of the earthquake rupture process and seismic wave propagation in 3D heterogeneous Earth. Geological faults comprise both large-scale segmentation and small-scale roughness that determine the dynamics of the earthquake rupture process and its radiated seismic wavefield. We investigate how different parameterizations of fractal fault roughness affect the rupture evolution and resulting near-fault ground motions. Rupture incoherence induced by fault roughness generates realistic ω-2 decay for high-frequency displacement amplitude spectra. Waveform characteristics and GMPE-based comparisons corroborate that these rough-fault rupture simulations generate realistic synthetic seismogram for subsequent engineering application. Since dynamic rupture simulations are computationally expensive, we develop kinematic approximations that emulate the observed dynamics. Simplifying the rough-fault geometry, we find that perturbations in local moment tensor orientation are important, while perturbations in local source location are not. Thus, a planar fault can be assumed if the local strike, dip, and rake are maintained. The dynamic rake angle variations are anti-correlated with local dip angles. Based on a dynamically consistent Yoffe source-time function, we show that the seismic wavefield of the approximated kinematic rupture well reproduces the seismic radiation of the full dynamic source process. Our findings provide an innovative pseudo-dynamic source characterization that captures fault roughness effects on rupture dynamics. Including the correlations between kinematic source parameters, we present a new pseudo-dynamic rupture modeling approach for computing broadband ground-motion time-histories for simulation-based PSHA

Post-Flight Assessment of Low Density Supersonic Decelerator Flight Dynamics Test 2 Simulation

NASA Technical Reports Server (NTRS)

Dutta, Soumyo; Bowes, Angela L.; White, Joseph P.; Striepe, Scott A.; Queen, Eric M.; O'Farrel, Clara; Ivanov, Mark C.

2016-01-01

NASA's Low Density Supersonic Decelerator (LDSD) project conducted its second Supersonic Flight Dynamics Test (SFDT-2) on June 8, 2015. The Program to Optimize Simulated Trajectories II (POST2) was one of the flight dynamics tools used to simulate and predict the flight performance and was a major tool used in the post-flight assessment of the flight trajectory. This paper compares the simulation predictions with the reconstructed trajectory. Additionally, off-nominal conditions seen during flight are modeled in the simulation to reconcile the predictions with flight data. These analyses are beneficial to characterize the results of the flight test and to improve the simulation and targeting of the subsequent LDSD flights.

Novel Breast Cancer Therapeutics Based on Bacterial Cupredoxin

DTIC Science & Technology

2008-09-01

M. and Lim, C. (1999) Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the...crowding has structural effects on the folded ensemble of polypeptides. energy landscape theory excluded volume effect molecular simulations protein... molecular simulations (51). Thermo- dynamic properties such as the radius of gyration (Rg), shape parameters ( and S) (11), and the fraction of native

Improved Pyrolysis Micro reactor Design via Computational Fluid Dynamics Simulations

DTIC Science & Technology

2017-05-23

Dynamics Simulations Ghanshyam L. Vaghjiani Air Force Research Laboratory (AFMC) AFRL/RQRS 1 Ara Drive Edwards AFB, CA 93524-7013 Air Force...Aerospace Systems Directorate Air Force Research Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil IMPROVED...PYROLYSIS MICRO-REACTOR DESIGN VIA COMPUTATIONAL FLUID DYNAMICS SIMULATIONS Ghanshyam L. Vaghjiani* DISTRIBUTION A: Approved for public release

Combat Simulation Using Breach Computer Language

DTIC Science & Technology

1979-09-01

simulation and weapon system analysis computer language Two types of models were constructed: a stochastic duel and a dynamic engagement model The... duel model validates the BREACH approach by comparing results with mathematical solutions. The dynamic model shows the capability of the BREACH...BREACH 2 Background 2 The Language 3 Static Duel 4 Background and Methodology 4 Validation 5 Results 8 Tank Duel Simulation 8 Dynamic Assault Model

Control Performance, Aerodynamic Modeling, and Validation of Coupled Simulation Techniques for Guided Projectile Roll Dynamics

DTIC Science & Technology

2014-11-01

39–44) has been explored in depth in the literature. Of particular interest for this study are investigations into roll control. Isolating the...Control Performance, Aerodynamic Modeling, and Validation of Coupled Simulation Techniques for Guided Projectile Roll Dynamics by Jubaraj...Simulation Techniques for Guided Projectile Roll Dynamics Jubaraj Sahu, Frank Fresconi, and Karen R. Heavey Weapons and Materials Research

Free-Energy Profiles of Membrane Insertion of the M2 Transmembrane Peptide from Influenza A Virus

DTIC Science & Technology

2008-12-01

ABSTRACT The insertion of the M2 transmembrane peptide from influenza A virus into a membrane has been studied with molecular - dynamics simulations ...performed replica-exchange molecular - dynamics simulations with umbrella-sampling techniques to characterize the probability distribution and conformation...atomic- detailed molecular dynamics (MD) simulation techniques represent a valuable complementary methodology to inves- tigate membrane-insertion of

Study of the dynamics of poly(ethylene oxide) by combining molecular dynamic simulations and neutron scattering experiments

NASA Astrophysics Data System (ADS)

Brodeck, M.; Alvarez, F.; Arbe, A.; Juranyi, F.; Unruh, T.; Holderer, O.; Colmenero, J.; Richter, D.

2009-03-01

We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below ≈0.6 Å-1. We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.

Study of the dynamics of poly(ethylene oxide) by combining molecular dynamic simulations and neutron scattering experiments.

PubMed

Brodeck, M; Alvarez, F; Arbe, A; Juranyi, F; Unruh, T; Holderer, O; Colmenero, J; Richter, D

2009-03-07

We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below approximately 0.6 A(-1). We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.

An intercomparison of GCM and RCM dynamical downscaling for characterizing the hydroclimatology of California and Nevada

NASA Astrophysics Data System (ADS)

Xu, Z.; Rhoades, A.; Johansen, H.; Ullrich, P. A.; Collins, W. D.

2017-12-01

Dynamical downscaling is widely used to properly characterize regional surface heterogeneities that shape the local hydroclimatology. However, the factors in dynamical downscaling, including the refinement of model horizontal resolution, large-scale forcing datasets and dynamical cores, have not been fully evaluated. Two cutting-edge global-to-regional downscaling methods are used to assess these, specifically the variable-resolution Community Earth System Model (VR-CESM) and the Weather Research & Forecasting (WRF) regional climate model, under different horizontal resolutions (28, 14, and 7 km). Two groups of WRF simulations are driven by either the NCEP reanalysis dataset (WRF_NCEP) or VR-CESM outputs (WRF_VRCESM) to evaluate the effects of the large-scale forcing datasets. The impacts of dynamical core are assessed by comparing the VR-CESM simulations to the coupled WRF_VRCESM simulations with the same physical parameterizations and similar grid domains. The simulated hydroclimatology (i.e., total precipitation, snow cover, snow water equivalent and surface temperature) are compared with the reference datasets. The large-scale forcing datasets are critical to the WRF simulations in more accurately simulating total precipitation, SWE and snow cover, but not surface temperature. Both the WRF and VR-CESM results highlight that no significant benefit is found in the simulated hydroclimatology by just increasing horizontal resolution refinement from 28 to 7 km. Simulated surface temperature is sensitive to the choice of dynamical core. WRF generally simulates higher temperatures than VR-CESM, alleviates the systematic cold bias of DJF temperatures over the California mountain region, but overestimates the JJA temperature in California's Central Valley.

Modelling and simulation of Space Station Freedom berthing dynamics and control

NASA Technical Reports Server (NTRS)

Cooper, Paul A.; Garrison, James L., Jr.; Montgomery, Raymond C.; Wu, Shih-Chin; Stockwell, Alan E.; Demeo, Martha E.

1994-01-01

A large-angle, flexible, multibody, dynamic modeling capability has been developed to help validate numerical simulations of the dynamic motion and control forces which occur during berthing of Space Station Freedom to the Shuttle Orbiter in the early assembly flights. This paper outlines the dynamics and control of the station, the attached Shuttle Remote Manipulator System, and the orbiter. The simulation tool developed for the analysis is described and the results of two simulations are presented. The first is a simulated maneuver from a gravity-gradient attitude to a torque equilibrium attitude using the station reaction control jets. The second simulation is the berthing of the station to the orbiter with the station control moment gyros actively maintaining an estimated torque equilibrium attitude. The influence of the elastic dynamic behavior of the station and of the Remote Manipulator System on the attitude control of the station/orbiter system during each maneuver was investigated. The flexibility of the station and the arm were found to have only a minor influence on the attitude control of the system during the maneuvers.

Simulating Vibrations in a Complex Loaded Structure

NASA Technical Reports Server (NTRS)

Cao, Tim T.

2005-01-01

The Dynamic Response Computation (DIRECT) computer program simulates vibrations induced in a complex structure by applied dynamic loads. Developed to enable rapid analysis of launch- and landing- induced vibrations and stresses in a space shuttle, DIRECT also can be used to analyze dynamic responses of other structures - for example, the response of a building to an earthquake, or the response of an oil-drilling platform and attached tanks to large ocean waves. For a space-shuttle simulation, the required input to DIRECT includes mathematical models of the space shuttle and its payloads, and a set of forcing functions that simulates launch and landing loads. DIRECT can accommodate multiple levels of payload attachment and substructure as well as nonlinear dynamic responses of structural interfaces. DIRECT combines the shuttle and payload models into a single structural model, to which the forcing functions are then applied. The resulting equations of motion are reduced to an optimum set and decoupled into a unique format for simulating dynamics. During the simulation, maximum vibrations, loads, and stresses are monitored and recorded for subsequent analysis to identify structural deficiencies in the shuttle and/or payloads.

Focused and Corrective Feedback Versus Structured and Supported Debriefing in a Simulation-Based Cardiac Arrest Team Training: A Pilot Randomized Controlled Study.

PubMed

Kim, Ji-Hoon; Kim, Young-Min; Park, Seong Heui; Ju, Eun A; Choi, Se Min; Hong, Tai Yong

2017-06-01

The aim of the study was to compare the educational impact of two postsimulation debriefing methods-focused and corrective feedback (FCF) versus Structured and Supported Debriefing (SSD)-on team dynamics in simulation-based cardiac arrest team training. This was a pilot randomized controlled study conducted at a simulation center. Fourth-year medical students were randomly assigned to the FCF or SSD group, with each team composed of six students and a confederate. Each team participated in two simulations and the assigned debriefing (FCF or SSD) sessions and then underwent a test simulation. Two trained raters blindly assessed all of the recorded simulations using checklists. The primary outcome was the improvement in team dynamics scores between baseline and test simulation. The secondary outcomes were improvements before and after training in team clinical performance scores, self-assessed comprehension of and confidence in cardiac arrest management and team dynamics, as well as evaluations of the postsimulation debriefing intervention. In total, 95 students participated [FCF (8 teams, n = 47) and SSD (8 teams, n = 48)]. The SSD team dynamics score during the test simulation was higher than at baseline [baseline: 74.5 (65.9-80.9), test: 85.0 (71.9-87.6), P = 0.035]. However, there were no differences in the improvement in the team dynamics or team clinical performance scores between the two groups (P = 0.328, respectively). There was no significant difference in improvement in team dynamics scores during the test simulation compared with baseline between the SSD and FCF groups in a simulation-based cardiac arrest team training in fourth-year Korean medical students.

Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

PubMed

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

Troubleshooting Instruction in Vocational-Technical Education Via Dynamic Simulation. Final Report.

ERIC Educational Resources Information Center

Finch, Curtis R.

This study was designed to examine the feasibility of using simulation as a means of teaching vocational-technical students to detect and identify malfunctions in selected electrical and mechanical systems. A dynamic simulator was employed which features interchangeable panels and logic that permits the simulation of electrical or mechanical…

Towards a comprehensive framework for cosimulation of dynamic models with an emphasis on time stepping

NASA Astrophysics Data System (ADS)

Hoepfer, Matthias

Over the last two decades, computer modeling and simulation have evolved as the tools of choice for the design and engineering of dynamic systems. With increased system complexities, modeling and simulation become essential enablers for the design of new systems. Some of the advantages that modeling and simulation-based system design allows for are the replacement of physical tests to ensure product performance, reliability and quality, the shortening of design cycles due to the reduced need for physical prototyping, the design for mission scenarios, the invoking of currently nonexisting technologies, and the reduction of technological and financial risks. Traditionally, dynamic systems are modeled in a monolithic way. Such monolithic models include all the data, relations and equations necessary to represent the underlying system. With increased complexity of these models, the monolithic model approach reaches certain limits regarding for example, model handling and maintenance. Furthermore, while the available computer power has been steadily increasing according to Moore's Law (a doubling in computational power every 10 years), the ever-increasing complexities of new models have negated the increased resources available. Lastly, modern systems and design processes are interdisciplinary, enforcing the necessity to make models more flexible to be able to incorporate different modeling and design approaches. The solution to bypassing the shortcomings of monolithic models is cosimulation. In a very general sense, co-simulation addresses the issue of linking together different dynamic sub-models to a model which represents the overall, integrated dynamic system. It is therefore an important enabler for the design of interdisciplinary, interconnected, highly complex dynamic systems. While a basic co-simulation setup can be very easy, complications can arise when sub-models display behaviors such as algebraic loops, singularities, or constraints. This work frames the co-simulation approach to modeling and simulation. It lays out the general approach to dynamic system co-simulation, and gives a comprehensive overview of what co-simulation is and what it is not. It creates a taxonomy of the requirements and limits of co-simulation, and the issues arising with co-simulating sub-models. Possible solutions towards resolving the stated problems are investigated to a certain depth. A particular focus is given to the issue of time stepping. It will be shown that for dynamic models, the selection of the simulation time step is a crucial issue with respect to computational expense, simulation accuracy, and error control. The reasons for this are discussed in depth, and a time stepping algorithm for co-simulation with unknown dynamic sub-models is proposed. Motivations and suggestions for the further treatment of selected issues are presented.

Microsecond Simulations of DNA and Ion Transport in Nanopores with Novel Ion-Ion and Ion-Nucleotides Effective Potentials

PubMed Central

De Biase, Pablo M.; Markosyan, Suren; Noskov, Sergei

2014-01-01

We developed a novel scheme based on the Grand-Canonical Monte-Carlo/Brownian Dynamics (GCMC/BD) simulations and have extended it to studies of ion currents across three nanopores with the potential for ssDNA sequencing: solid-state nanopore Si3N4, α-hemolysin, and E111N/M113Y/K147N mutant. To describe nucleotide-specific ion dynamics compatible with ssDNA coarse-grained model, we used the Inverse Monte-Carlo protocol, which maps the relevant ion-nucleotide distribution functions from an all-atom MD simulations. Combined with the previously developed simulation platform for Brownian Dynamic (BD) simulations of ion transport, it allows for microsecond- and millisecond-long simulations of ssDNA dynamics in nanopore with a conductance computation accuracy that equals or exceeds that of all-atom MD simulations. In spite of the simplifications, the protocol produces results that agree with the results of previous studies on ion conductance across open channels and provide direct correlations with experimentally measured blockade currents and ion conductances that have been estimated from all-atom MD simulations. PMID:24738152

Model structure identification for wastewater treatment simulation based on computational fluid dynamics.

PubMed

Alex, J; Kolisch, G; Krause, K

2002-01-01

The objective of this presented project is to use the results of an CFD simulation to automatically, systematically and reliably generate an appropriate model structure for simulation of the biological processes using CSTR activated sludge compartments. Models and dynamic simulation have become important tools for research but also increasingly for the design and optimisation of wastewater treatment plants. Besides the biological models several cases are reported about the application of computational fluid dynamics ICFD) to wastewater treatment plants. One aim of the presented method to derive model structures from CFD results is to exclude the influence of empirical structure selection to the result of dynamic simulations studies of WWTPs. The second application of the approach developed is the analysis of badly performing treatment plants where the suspicion arises that bad flow behaviour such as short cut flows is part of the problem. The method suggested requires as the first step the calculation of fluid dynamics of the biological treatment step at different loading situations by use of 3-dimensional CFD simulation. The result of this information is used to generate a suitable model structure for conventional dynamic simulation of the treatment plant by use of a number of CSTR modules with a pattern of exchange flows between the tanks automatically. The method is explained in detail and the application to the WWTP Wuppertal Buchenhofen is presented.

Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins.

PubMed

Pang, Yuan-Ping

2016-09-01

Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2-9 ± 1 Å 2 for Cα and 7.3 ± 0.9-9.6 ± 0.2 Å 2 for Cγ, when the sampling was done for each of these proteins over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations with AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive to a priori prediction of crystallographic B-factors of a folded globular protein.

From laws of inference to protein folding dynamics.

PubMed

Tseng, Chih-Yuan; Yu, Chun-Ping; Lee, H C

2010-08-01

Protein folding dynamics is one of major issues constantly investigated in the study of protein functions. The molecular dynamic (MD) simulation with the replica exchange method (REM) is a common theoretical approach considered. Yet a trade-off in applying the REM is that the dynamics toward the native configuration in the simulations seems lost. In this work, we show that given REM-MD simulation results, protein folding dynamics can be directly derived from laws of inference. The applicability of the resulting approach, the entropic folding dynamics, is illustrated by investigating a well-studied Trp-cage peptide. Our results are qualitatively comparable with those from other studies. The current studies suggest that the incorporation of laws of inference and physics brings in a comprehensive perspective on exploring the protein folding dynamics.

Applying Parallel Adaptive Methods with GeoFEST/PYRAMID to Simulate Earth Surface Crustal Dynamics

NASA Technical Reports Server (NTRS)

Norton, Charles D.; Lyzenga, Greg; Parker, Jay; Glasscoe, Margaret; Donnellan, Andrea; Li, Peggy

2006-01-01

This viewgraph presentation reviews the use Adaptive Mesh Refinement (AMR) in simulating the Crustal Dynamics of Earth's Surface. AMR simultaneously improves solution quality, time to solution, and computer memory requirements when compared to generating/running on a globally fine mesh. The use of AMR in simulating the dynamics of the Earth's Surface is spurred by future proposed NASA missions, such as InSAR for Earth surface deformation and other measurements. These missions will require support for large-scale adaptive numerical methods using AMR to model observations. AMR was chosen because it has been successful in computation fluid dynamics for predictive simulation of complex flows around complex structures.

Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package

NASA Astrophysics Data System (ADS)

Dizkirici, Ayten; Tekpinar, Mustafa

2015-03-01

GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.

Insights from molecular dynamics simulations for computational protein design.

PubMed

Childers, Matthew Carter; Daggett, Valerie

2017-02-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

Insights from molecular dynamics simulations for computational protein design

PubMed Central

Childers, Matthew Carter; Daggett, Valerie

2017-01-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

Virtual Habitat -a dynamic simulation of closed life support systems -human model status

NASA Astrophysics Data System (ADS)

Markus Czupalla, M. Sc.; Zhukov, Anton; Hwang, Su-Au; Schnaitmann, Jonas

In order to optimize Life Support Systems on a system level, stability questions must be in-vestigated. To do so the exploration group of the Technical University of Munich (TUM) is developing the "Virtual Habitat" (V-HAB) dynamic LSS simulation software. V-HAB shall provide the possibility to conduct dynamic simulations of entire mission scenarios for any given LSS configuration. The Virtual Habitat simulation tool consists of four main modules: • Closed Environment Module (CEM) -monitoring of compounds in a closed environment • Crew Module (CM) -dynamic human simulation • P/C Systems Module (PCSM) -dynamic P/C subsystems • Plant Module (PM) -dynamic plant simulation The core module of the simulation is the dynamic and environment sensitive human module. Introduced in its basic version in 2008, the human module has been significantly updated since, increasing its capabilities and maturity significantly. In this paper three newly added human model subsystems (thermal regulation, digestion and schedule controller) are introduced touching also on the human stress subsystem which is cur-rently under development. Upon the introduction of these new subsystems, the integration of these into the overall V-HAB human model is discussed, highlighting the impact on the most important I/F. The overall human model capabilities shall further be summarized and presented based on meaningful test cases. In addition to the presentation of the results, the correlation strategy for the Virtual Habitat human model shall be introduced assessing the models current confidence level and giving an outlook on the future correlation strategy. Last but not least, the remaining V-HAB mod-ules shall be introduced shortly showing how the human model is integrated into the overall simulation.

Parallel Performance of Linear Solvers and Preconditioners

DTIC Science & Technology

2014-01-01

are produced by a discrete dislocation dynamics ( DDD ) simulation and change with each timestep of the DDD simulation as the dislocation structure...evolves. However, the coefficient—or stiffness matrix— remains constant during the DDD simulation and some expensive matrix factorizations only occur once...discrete dislocation dynamics ( DDD ) simulations. This can be achieved by coupling a DDD simulator for bulk material (Arsenlis et al., 2007) to a

Dynamical properties of magnetized two-dimensional one-component plasma

NASA Astrophysics Data System (ADS)

Dubey, Girija S.; Gumbs, Godfrey; Fessatidis, Vassilios

2018-05-01

Molecular dynamics simulation are used to examine the effect of a uniform perpendicular magnetic field on a two-dimensional interacting electron system. In this simulation we include the effect of the magnetic field classically through the Lorentz force. Both the Coulomb and the magnetic forces are included directly in the electron dynamics to study their combined effect on the dynamical properties of the 2D system. Results are presented for the velocity autocorrelation function and the diffusion constants in the presence and absence of an external magnetic field. Our simulation results clearly show that the external magnetic field has an effect on the dynamical properties of the system.

A comparison of East Asian summer monsoon simulations from CAM3.1 with three dynamic cores

NASA Astrophysics Data System (ADS)

Wei, Ting; Wang, Lanning; Dong, Wenjie; Dong, Min; Zhang, Jingyong

2011-12-01

This paper examines the sensitivity of CAM3.1 simulations of East Asian summer monsoon (EASM) to the choice of dynamic cores using three long-term simulations, one with each of the following cores: the Eulerian spectral transform method (EUL), semi-Lagrangian scheme (SLD) and finite volume approach (FV). Our results indicate that the dynamic cores significantly influence the simulated fields not only through dynamics, such as wind, but also through physical processes, such as precipitation. Generally speaking, SLD is superior to EUL and FV in simulating the climatological features of EASM and its interannual variability. The SLD version of the CAM model partially reduces its known deficiency in simulating the climatological features of East Asian summer precipitation. The strength and position of simulated western Pacific subtropical high (WPSH) and its ridge line compare more favourably with observations in SLD and FV than in EUL. They contribute to the intensification of the south-easterly along the south of WPSH and the vertical motion through the troposphere around 30° N, where the subtropical rain belt exists. Additionally, SLD simulates the scope of the westerly jet core over East Asia more realistically than the other two dynamic cores do. Considerable systematic errors of the seasonal migration of monsoon rain belt and water vapour flux exist in all of the three versions of CAM3.1 model, although it captures the broad northward shift of convection, and the simulated results share similarities. The interannual variation of EASM is found to be more accurate in SLD simulation, which reasonably reproduces the leading combined patterns of precipitation and 850-hPa winds in East Asia, as well as the 2.5- and 10-year periods of Li-Zeng EASM index. These results emphasise the importance of dynamic cores for the EASM simulation as distinct from the simulation's sensitivity to the physical parameterisations.

Cluster growth mechanisms in Lennard-Jones fluids: A comparison between molecular dynamics and Brownian dynamics simulations

NASA Astrophysics Data System (ADS)

Jung, Jiyun; Lee, Jumin; Kim, Jun Soo

2015-03-01

We present a simulation study on the mechanisms of a phase separation in dilute fluids of Lennard-Jones (LJ) particles as a model of self-interacting molecules. Molecular dynamics (MD) and Brownian dynamics (BD) simulations of the LJ fluids are employed to model the condensation of a liquid droplet in the vapor phase and the mesoscopic aggregation in the solution phase, respectively. With emphasis on the cluster growth at late times well beyond the nucleation stage, we find that the growth mechanisms can be qualitatively different: cluster diffusion and coalescence in the MD simulations and Ostwald ripening in the BD simulations. We also show that the rates of the cluster growth have distinct scaling behaviors during cluster growth. This work suggests that in the solution phase the random Brownian nature of the solute dynamics may lead to the Ostwald ripening that is qualitatively different from the cluster coalescence in the vapor phase.

Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

PubMed

Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A

2017-01-01

Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

ChainMail based neural dynamics modeling of soft tissue deformation for surgical simulation.

PubMed

Zhang, Jinao; Zhong, Yongmin; Smith, Julian; Gu, Chengfan

2017-07-20

Realistic and real-time modeling and simulation of soft tissue deformation is a fundamental research issue in the field of surgical simulation. In this paper, a novel cellular neural network approach is presented for modeling and simulation of soft tissue deformation by combining neural dynamics of cellular neural network with ChainMail mechanism. The proposed method formulates the problem of elastic deformation into cellular neural network activities to avoid the complex computation of elasticity. The local position adjustments of ChainMail are incorporated into the cellular neural network as the local connectivity of cells, through which the dynamic behaviors of soft tissue deformation are transformed into the neural dynamics of cellular neural network. Experiments demonstrate that the proposed neural network approach is capable of modeling the soft tissues' nonlinear deformation and typical mechanical behaviors. The proposed method not only improves ChainMail's linear deformation with the nonlinear characteristics of neural dynamics but also enables the cellular neural network to follow the principle of continuum mechanics to simulate soft tissue deformation.

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

Noe, F; Diadone, Isabella; Lollmann, Marc

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 observedmore » 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.« less

Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible?

PubMed

Knapp, B; Frantal, S; Cibena, M; Schreiner, W; Bauer, P

2011-08-01

Molecular dynamics is a commonly used technique in computational biology. One key issue of each molecular dynamics simulation is: When does this simulation reach equilibrium state? A widely used way to determine this is the visual and intuitive inspection of root mean square deviation (RMSD) plots of the simulation. Although this technique has been criticized several times, it is still often used. Therefore, we present a study proving that this method is not reliable at all. We conducted a survey with participants from the field in which we illustrated different RMSD plots to scientists in the field of molecular dynamics. These plots were randomized and repeated, using a statistical model and different variants of the plots. We show that there is no mutual consent about the point of equilibrium. The decisions are severely biased by different parameters. Therefore, we conclude that scientists should not discuss the equilibration of a molecular dynamics simulation on the basis of a RMSD plot.

Determination and Control of Optical and X-Ray Wave Fronts

NASA Technical Reports Server (NTRS)

Kim, Young K.

1997-01-01

A successful design of a space-based or ground optical system requires an iterative procedure which includes the kinematics and dynamics of the system in operating environment, control synthesis and verification. To facilitate the task of designing optical wave front control systems being developed at NASA/MSFC, a multi-discipline dynamics and control tool has been developed by utilizing TREETOPS, a multi-body dynamics and control simulation, NASTRAN and MATLAB. Dynamics and control models of STABLE and ARIS were developed for TREETOPS simulation, and their simulation results are documented in this report.

Mesoscopic modelling and simulation of soft matter.

PubMed

Schiller, Ulf D; Krüger, Timm; Henrich, Oliver

2017-12-20

The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We review a number of the most popular simulation methods that have emerged, such as Langevin dynamics, dissipative particle dynamics, multi-particle collision dynamics, sometimes also referred to as stochastic rotation dynamics, and the lattice-Boltzmann method. We conclude this review with a short glance at current compute architectures for high-performance computing and community codes for soft matter simulation.

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

Simulations of Operation Dynamics of Different Type GaN Particle Sensors

PubMed Central

Gaubas, Eugenijus; Ceponis, Tomas; Kalesinskas, Vidas; Pavlov, Jevgenij; Vysniauskas, Juozas

2015-01-01

The operation dynamics of the capacitor-type and PIN diode type detectors based on GaN have been simulated using the dynamic and drift-diffusion models. The drift-diffusion current simulations have been implemented by employing the software package Synopsys TCAD Sentaurus. The monopolar and bipolar drift regimes have been analyzed by using dynamic models based on the Shockley-Ramo theorem. The carrier multiplication processes determined by impact ionization have been considered in order to compensate carrier lifetime reduction due to introduction of radiation defects into GaN detector material. PMID:25751080

Movement Characteristics Analysis and Dynamic Simulation of Collaborative Measuring Robot

NASA Astrophysics Data System (ADS)

guoqing, MA; li, LIU; zhenglin, YU; guohua, CAO; yanbin, ZHENG

2017-03-01

Human-machine collaboration is becoming increasingly more necessary, and so collaborative robot applications are also in high demand. We selected a UR10 robot as our research subject for this study. First, we applied D-H coordinate transformation of the robot to establish a link system, and we then used inverse transformation to solve the robot’s inverse kinematics and find all the joints. Use Lagrange method to analysis UR robot dynamics; use ADAMS multibody dynamics simulation software to dynamic simulation; verifying the correctness of the derived kinetic models.

System Dynamics Modeling for Supply Chain Information Sharing

NASA Astrophysics Data System (ADS)

Feng, Yang

In this paper, we try to use the method of system dynamics to model supply chain information sharing. Firstly, we determine the model boundaries, establish system dynamics model of supply chain before information sharing, analyze the model's simulation results under different changed parameters and suggest improvement proposal. Then, we establish system dynamics model of supply chain information sharing and make comparison and analysis on the two model's simulation results, to show the importance of information sharing in supply chain management. We wish that all these simulations would provide scientific supports for enterprise decision-making.

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...

Dynamic extension of the Simulation Problem Analysis Kernel (SPANK)

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

Sowell, E.F.; Buhl, W.F.

1988-07-15

The Simulation Problem Analysis Kernel (SPANK) is an object-oriented simulation environment for general simulation purposes. Among its unique features is use of the directed graph as the primary data structure, rather than the matrix. This allows straightforward use of graph algorithms for matching variables and equations, and reducing the problem graph for efficient numerical solution. The original prototype implementation demonstrated the principles for systems of algebraic equations, allowing simulation of steady-state, nonlinear systems (Sowell 1986). This paper describes how the same principles can be extended to include dynamic objects, allowing simulation of general dynamic systems. The theory is developed andmore » an implementation is described. An example is taken from the field of building energy system simulation. 2 refs., 9 figs.« less

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

PubMed

Šponer, Jiří; Banáš, Pavel; Jurečka, Petr; Zgarbová, Marie; Kührová, Petra; Havrila, Marek; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, Michal

2014-05-15

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.

Open-source framework for power system transmission and distribution dynamics co-simulation

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

Huang, Renke; Fan, Rui; Daily, Jeff

The promise of the smart grid entails more interactions between the transmission and distribution networks, and there is an immediate need for tools to provide the comprehensive modelling and simulation required to integrate operations at both transmission and distribution levels. Existing electromagnetic transient simulators can perform simulations with integration of transmission and distribution systems, but the computational burden is high for large-scale system analysis. For transient stability analysis, currently there are only separate tools for simulating transient dynamics of the transmission and distribution systems. In this paper, we introduce an open source co-simulation framework “Framework for Network Co-Simulation” (FNCS), togethermore » with the decoupled simulation approach that links existing transmission and distribution dynamic simulators through FNCS. FNCS is a middleware interface and framework that manages the interaction and synchronization of the transmission and distribution simulators. Preliminary testing results show the validity and capability of the proposed open-source co-simulation framework and the decoupled co-simulation methodology.« less

Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.

PubMed

Dalby, Andrew; Shamsir, Mohd Shahir

2015-01-01

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation.

Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.

PubMed Central

Dalby, Andrew; Shamsir, Mohd Shahir

2015-01-01

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation. PMID:26539292

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.

Development of a Computational Assay for the Estrogen Receptor

DTIC Science & Technology

2006-07-01

University Ashley Deline, Senior Thesis in chemistry, " Molecular Dynamic Simulations of a Glycoform and its Constituent Parts Related to Rheumatoid Arthritis...involves running a long molecular dynamics (MD) simulation of the uncoupled receptor in order to sample the protein’s unique conformations. The second...Receptor binding domain. * Performed several long molecular dynamics simulations (800 ps - 3 ns) on the ligand-ER system using ligands with known

New Finite Element/Multibody System Algorithm for Modeling Flexible Tracked Vehicles

DTIC Science & Technology

2011-08-01

U.S. Army RDECOM-TARDEC & 2 University of Illinois at Chicago ABSTRACT The dynamic simulation of multibody tracked vehicles offers engineers a...bodies. Then in a follow-on structural analysis, the loads from the multibody dynamic simulation are input to calculate strains and stresses within the...multibody dynamic simulation environment allowing for an integrated solution. In addition, a new formulation for the interaction between the rigid sprocket

In Silico Analyses of Substrate Interactions with Human Serum Paraoxonase 1

DTIC Science & Technology

2008-01-01

substrate interactions of HuPON1 remains elusive. In this study, we apply homology modeling, docking, and molecular dynamic (MD) simulations to probe the...mod- eling; docking; molecular dynamics simulations ; binding free energy decomposition. 486 PROTEINS Published 2008 WILEY-LISS, INC. yThis article is a...apply homology modeling, docking, and molecular dynamic (MD) simulations to probe the binding interactions of HuPON1 with representative substrates. The

Predictions of Crystal Structures from First Principles

DTIC Science & Technology

2007-06-01

RDX crystal in hoped that the problem could be resolved by the molecular dynamics simulations . The fully ab initio development of density functional... Molecular Dynamics Simulations of RDX i.e., without any use of experimental results (except that Crystal the geometry of monomers was derived from X-ray...applied in molecular dynamics simulations of the RDX system, due to its size, is intractable by any high-level ab crystal. We performed isothermal

A reduced basis method for molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Vincent-Finley, Rachel Elisabeth

In this dissertation, we develop a method for molecular simulation based on principal component analysis (PCA) of a molecular dynamics trajectory and least squares approximation of a potential energy function. Molecular dynamics (MD) simulation is a computational tool used to study molecular systems as they evolve through time. With respect to protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds. To capture motion at all levels, time steps on the order of a femtosecond are employed when solving the equations of motion and simulations must continue long enough to capture the desired large-scale motion. To date, simulations of solvated proteins on the order of nanoseconds have been reported. It is typically the case that simulations of a few nanoseconds do not provide adequate information for the study of large-scale motions. Thus, the development of techniques that allow longer simulation times can advance the study of protein function and dynamics. In this dissertation we use principal component analysis (PCA) to identify the dominant characteristics of an MD trajectory and to represent the coordinates with respect to these characteristics. We augment PCA with an updating scheme based on a reduced representation of a molecule and consider equations of motion with respect to the reduced representation. We apply our method to butane and BPTI and compare the results to standard MD simulations of these molecules. Our results indicate that the molecular activity with respect to our simulation method is analogous to that observed in the standard MD simulation with simulations on the order of picoseconds.

Comparative Implementation of High Performance Computing for Power System Dynamic Simulations

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

Jin, Shuangshuang; Huang, Zhenyu; Diao, Ruisheng

Dynamic simulation for transient stability assessment is one of the most important, but intensive, computations for power system planning and operation. Present commercial software is mainly designed for sequential computation to run a single simulation, which is very time consuming with a single processer. The application of High Performance Computing (HPC) to dynamic simulations is very promising in accelerating the computing process by parallelizing its kernel algorithms while maintaining the same level of computation accuracy. This paper describes the comparative implementation of four parallel dynamic simulation schemes in two state-of-the-art HPC environments: Message Passing Interface (MPI) and Open Multi-Processing (OpenMP).more » These implementations serve to match the application with dedicated multi-processor computing hardware and maximize the utilization and benefits of HPC during the development process.« less

27ps DFT Molecular Dynamics Simulation of a-maltose: A Reduced Basis Set Study.

USDA-ARS?s Scientific Manuscript database

DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as alpha-maltose, requiring up to three or more weeks on a fast 16-processor computer to obtain just 5ps of constant energy dynamics. In a recent publication [1] forces for dynamics were generated from B3LY...

Implicit methods for efficient musculoskeletal simulation and optimal control

PubMed Central

van den Bogert, Antonie J.; Blana, Dimitra; Heinrich, Dieter

2011-01-01

The ordinary differential equations for musculoskeletal dynamics are often numerically stiff and highly nonlinear. Consequently, simulations require small time steps, and optimal control problems are slow to solve and have poor convergence. In this paper, we present an implicit formulation of musculoskeletal dynamics, which leads to new numerical methods for simulation and optimal control, with the expectation that we can mitigate some of these problems. A first order Rosenbrock method was developed for solving forward dynamic problems using the implicit formulation. It was used to perform real-time dynamic simulation of a complex shoulder arm system with extreme dynamic stiffness. Simulations had an RMS error of only 0.11 degrees in joint angles when running at real-time speed. For optimal control of musculoskeletal systems, a direct collocation method was developed for implicitly formulated models. The method was applied to predict gait with a prosthetic foot and ankle. Solutions were obtained in well under one hour of computation time and demonstrated how patients may adapt their gait to compensate for limitations of a specific prosthetic limb design. The optimal control method was also applied to a state estimation problem in sports biomechanics, where forces during skiing were estimated from noisy and incomplete kinematic data. Using a full musculoskeletal dynamics model for state estimation had the additional advantage that forward dynamic simulations, could be done with the same implicitly formulated model to simulate injuries and perturbation responses. While these methods are powerful and allow solution of previously intractable problems, there are still considerable numerical challenges, especially related to the convergence of gradient-based solvers. PMID:22102983

OSS: OSSOS Survey Simulator

NASA Astrophysics Data System (ADS)

Petit, J.-M.; Kavelaars, J. J.; Gladman, B.; Alexandersen, M.

2018-05-01

Comparing properties of discovered trans-Neptunian Objects (TNOs) with dynamical models is impossible due to the observational biases that exist in surveys. The OSSOS Survey Simulator takes an intrinsic orbital model (from, for example, the output of a dynamical Kuiper belt emplacement simulation) and applies the survey biases, so the biased simulated objects can be directly compared with real discoveries.

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…

Exploring travelers' behavior in response to dynamic message signs (DMS) using a driving simulator.

DOT National Transportation Integrated Search

2013-10-01

This research studies the effectiveness of a dynamic message sign (DMS) using a driving : simulator. Over 100 subjects from different socio-economic and age groups were recruited to : drive the simulator under different traffic and driving conditions...

Gamma Ray Observatory (GRO) dynamics simulator requirements and mathematical specifications, revision 1

NASA Technical Reports Server (NTRS)

Harman, R.; Blejer, D.

1990-01-01

The requirements and mathematical specifications for the Gamma Ray Observatory (GRO) Dynamics Simulator are presented. The complete simulator system, which consists of the profie subsystem, simulation control and input/output subsystem, truth model subsystem, onboard computer model subsystem, and postprocessor, is described. The simulator will be used to evaluate and test the attitude determination and control models to be used on board GRO under conditions that simulate the expected in-flight environment.

High Fidelity, “Faster than Real-Time” Simulator for Predicting Power System Dynamic Behavior - Final Technical Report

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

Flueck, Alex

The “High Fidelity, Faster than Real­Time Simulator for Predicting Power System Dynamic Behavior” was designed and developed by Illinois Institute of Technology with critical contributions from Electrocon International, Argonne National Laboratory, Alstom Grid and McCoy Energy. Also essential to the project were our two utility partners: Commonwealth Edison and AltaLink. The project was a success due to several major breakthroughs in the area of large­scale power system dynamics simulation, including (1) a validated faster than real­ time simulation of both stable and unstable transient dynamics in a large­scale positive sequence transmission grid model, (2) a three­phase unbalanced simulation platform formore » modeling new grid devices, such as independently controlled single­phase static var compensators (SVCs), (3) the world’s first high fidelity three­phase unbalanced dynamics and protection simulator based on Electrocon’s CAPE program, and (4) a first­of­its­ kind implementation of a single­phase induction motor model with stall capability. The simulator results will aid power grid operators in their true time of need, when there is a significant risk of cascading outages. The simulator will accelerate performance and enhance accuracy of dynamics simulations, enabling operators to maintain reliability and steer clear of blackouts. In the long­term, the simulator will form the backbone of the newly conceived hybrid real­time protection and control architecture that will coordinate local controls, wide­area measurements, wide­area controls and advanced real­time prediction capabilities. The nation’s citizens will benefit in several ways, including (1) less down time from power outages due to the faster­than­real­time simulator’s predictive capability, (2) higher levels of reliability due to the detailed dynamics plus protection simulation capability, and (3) more resiliency due to the three­ phase unbalanced simulator’s ability to model three­phase and single­ phase networks and devices.« less

Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator.

PubMed

Dequidt, Alain; Devémy, Julien; Pádua, Agílio A H

2016-01-25

LAMMPS is a very customizable molecular dynamics simulation software, which can be used to simulate a large diversity of systems. We introduce a new package for simulation of polarizable systems with LAMMPS using thermalized Drude oscillators. The implemented functionalities are described and are illustrated by examples. The implementation was validated by comparing simulation results with published data and using a reference software. Computational performance is also analyzed.

Computational Fluid Dynamics Demonstration of Rigid Bodies in Motion

NASA Technical Reports Server (NTRS)

Camarena, Ernesto; Vu, Bruce T.

2011-01-01

The Design Analysis Branch (NE-Ml) at the Kennedy Space Center has not had the ability to accurately couple Rigid Body Dynamics (RBD) and Computational Fluid Dynamics (CFD). OVERFLOW-D is a flow solver that has been developed by NASA to have the capability to analyze and simulate dynamic motions with up to six Degrees of Freedom (6-DOF). Two simulations were prepared over the course of the internship to demonstrate 6DOF motion of rigid bodies under aerodynamic loading. The geometries in the simulations were based on a conceptual Space Launch System (SLS). The first simulation that was prepared and computed was the motion of a Solid Rocket Booster (SRB) as it separates from its core stage. To reduce computational time during the development of the simulation, only half of the physical domain with respect to the symmetry plane was simulated. Then a full solution was prepared and computed. The second simulation was a model of the SLS as it departs from a launch pad under a 20 knot crosswind. This simulation was reduced to Two Dimensions (2D) to reduce both preparation and computation time. By allowing 2-DOF for translations and 1-DOF for rotation, the simulation predicted unrealistic rotation. The simulation was then constrained to only allow translations.

Use of dynamical downscaling to improve the simulation of Central U.S. warm season precipitation in CMIP5 models

NASA Astrophysics Data System (ADS)

Harding, Keith J.; Snyder, Peter K.; Liess, Stefan

2013-11-01

supporting exceptionally productive agricultural lands, the Central U.S. is susceptible to severe droughts and floods. Such precipitation extremes are expected to worsen with climate change. However, future projections are highly uncertain as global climate models (GCMs) generally fail to resolve precipitation extremes. In this study, we assess how well models from the Coupled Model Intercomparison Project Phase 5 (CMIP5) simulate summer means, variability, extremes, and the diurnal cycle of Central U.S. summer rainfall. Output from a subset of historical CMIP5 simulations are used to drive the Weather Research and Forecasting model to determine whether dynamical downscaling improves the representation of Central U.S. rainfall. We investigate which boundary conditions influence dynamically downscaled precipitation estimates and identify GCMs that can reasonably simulate precipitation when downscaled. The CMIP5 models simulate the seasonal mean and variability of summer rainfall reasonably well but fail to resolve extremes, the diurnal cycle, and the dynamic forcing of precipitation. Downscaling to 30 km improves these characteristics of precipitation, with the greatest improvement in the representation of extremes. Additionally, sizeable diurnal cycle improvements occur with higher (10 km) resolution and convective parameterization disabled, as the daily rainfall peak shifts 4 h closer to observations than 30 km resolution simulations. This lends greater confidence that the mechanisms responsible for producing rainfall are better simulated. Because dynamical downscaling can more accurately simulate these aspects of Central U.S. summer rainfall, policymakers can have added confidence in dynamically downscaled rainfall projections, allowing for more targeted adaptation and mitigation.

Molecular Dynamics Simulations to Determine the Structure and Dynamics of Hepatitis B Virus Capsid Bound to a Novel Anti-viral Drug.

PubMed

Watanabe, Go; Sato, Shunsuke; Iwadate, Mitsuo; Umeyama, Hideaki; Hayakawa, Michiyo; Murakami, Yoshiki; Yoneda, Shigetaka

2016-01-01

Hepatitis B virus (HBV) chronically infects millions of people worldwide and is a major cause of serious liver diseases, including liver cirrhosis and liver cancer. In our previous study, in silico screening was used to isolate new anti-viral compounds predicted to bind to the HBV capsid. Four of the isolated compounds have been reported to suppress the cellular multiplication of HBV experimentally. In the present study, molecular dynamics simulations of the HBV capsid were performed under rotational symmetry boundary conditions, to clarify how the structure and dynamics of the capsid are affected at the atomic level by the binding of one of the isolated compounds, C13. Two simulations of the free HBV capsid, two further simulations of the capsid-C13 complex, and one simulation of the capsid-AT-130 complex were performed. For statistical confidence, each set of simulations was repeated by five times, changing the simulation conditions. C13 continued to bind at the predicted binding site during the simulations, supporting the hypothesis that C13 is a capsid-binding compound. The structure and dynamics of the HBV capsid were greatly influenced by the binding and release of C13, and these effects were essentially identical to those seen for AT-130, indicating that C13 likely inhibits the function of the HBV capsid.

Faster protein folding using enhanced conformational sampling of molecular dynamics simulation.

PubMed

Kamberaj, Hiqmet

2018-05-01

In this study, we applied swarm particle-like molecular dynamics (SPMD) approach to enhance conformational sampling of replica exchange simulations. In particular, the approach showed significant improvement in sampling efficiency of conformational phase space when combined with replica exchange method (REM) in computer simulation of peptide/protein folding. First we introduce the augmented dynamical system of equations, and demonstrate the stability of the algorithm. Then, we illustrate the approach by using different fully atomistic and coarse-grained model systems, comparing them with the standard replica exchange method. In addition, we applied SPMD simulation to calculate the time correlation functions of the transitions in a two dimensional surface to demonstrate the enhancement of transition path sampling. Our results showed that folded structure can be obtained in a shorter simulation time using the new method when compared with non-augmented dynamical system. Typically, in less than 0.5 ns using replica exchange runs assuming that native folded structure is known and within simulation time scale of 40 ns in the case of blind structure prediction. Furthermore, the root mean square deviations from the reference structures were less than 2Å. To demonstrate the performance of new method, we also implemented three simulation protocols using CHARMM software. Comparisons are also performed with standard targeted molecular dynamics simulation method. Copyright © 2018 Elsevier Inc. All rights reserved.

SIMULATION OF SUMMER-TIME DIURNAL BACTERIAL DYNAMICS IN THE ATMOSPHERIC SURFACE LAYER

EPA Science Inventory

A model was prepared to simulate the observed concentration dynamics of culturable bacteria in the diurnal summer atmosphere at a Willamette River Valley, Oregon location. The meteorological and bacterial mechanisms included in a dynamic null-dimensional model with one-second tim...

A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes.

PubMed

Xu, Rosalind J; Blasiak, Bartosz; Cho, Minhaeng; Layfield, Joshua P; Londergan, Casey H

2018-05-17

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.

Potential-based dynamical reweighting for Markov state models of protein dynamics.

PubMed

Weber, Jeffrey K; Pande, Vijay S

2015-06-09

As simulators attempt to replicate the dynamics of large cellular components in silico, problems related to sampling slow, glassy degrees of freedom in molecular systems will be amplified manyfold. It is tempting to augment simulation techniques with external biases to overcome such barriers with ease; biased simulations, however, offer little utility unless equilibrium properties of interest (both kinetic and thermodynamic) can be recovered from the data generated. In this Article, we present a general scheme that harnesses the power of Markov state models (MSMs) to extract equilibrium kinetic properties from molecular dynamics trajectories collected on biased potential energy surfaces. We first validate our reweighting protocol on a simple two-well potential, and we proceed to test our method on potential-biased simulations of the Trp-cage miniprotein. In both cases, we find that equilibrium populations, time scales, and dynamical processes are reliably reproduced as compared to gold standard, unbiased data sets. We go on to discuss the limitations of our dynamical reweighting approach, and we suggest auspicious target systems for further application.

Concerted Dynamic Motions of an FABP4 Model and Its Ligands Revealed by Microsecond Molecular Dynamics Simulations

PubMed Central

2015-01-01

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

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

PubMed

Li, Yan; Li, Xiang; Dong, Zigang

2014-10-14

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

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.

PubMed

Caulfield, Thomas R; Devkota, Batsal; Rollins, Geoffrey C

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

Non-monotonic dynamics of water in its binary mixture with 1,2-dimethoxy ethane: A combined THz spectroscopic and MD simulation study.

PubMed

Das Mahanta, Debasish; Patra, Animesh; Samanta, Nirnay; Luong, Trung Quan; Mukherjee, Biswaroop; Mitra, Rajib Kumar

2016-10-28

A combined experimental (mid- and far-infrared FTIR spectroscopy and THz time domain spectroscopy (TTDS) (0.3-1.6 THz)) and molecular dynamics (MD) simulation technique are used to understand the evolution of the structure and dynamics of water in its binary mixture with 1,2-dimethoxy ethane (DME) over the entire concentration range. The cooperative hydrogen bond dynamics of water obtained from Debye relaxation of TTDS data reveals a non-monotonous behaviour in which the collective dynamics is much faster in the low X w region (where X w is the mole fraction of water in the mixture), whereas in X w ∼ 0.8 region, the dynamics gets slower than that of pure water. The concentration dependence of the reorientation times of water, calculated from the MD simulations, also captures this non-monotonous character. The MD simulation trajectories reveal presence of large amplitude angular jumps, which dominate the orientational relaxation. We rationalize the non-monotonous, concentration dependent orientational dynamics by identifying two different physical mechanisms which operate at high and low water concentration regimes.

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.

Temperature for a dynamic spin ensemble

NASA Astrophysics Data System (ADS)

Ma, Pui-Wai; Dudarev, S. L.; Semenov, A. A.; Woo, C. H.

2010-09-01

In molecular dynamics simulations, temperature is evaluated, via the equipartition principle, by computing the mean kinetic energy of atoms. There is no similar recipe yet for evaluating temperature of a dynamic system of interacting spins. By solving semiclassical Langevin spin-dynamics equations, and applying the fluctuation-dissipation theorem, we derive an equation for the temperature of a spin ensemble, expressed in terms of dynamic spin variables. The fact that definitions for the kinetic and spin temperatures are fully consistent is illustrated using large-scale spin dynamics and spin-lattice dynamics simulations.

A fast recursive algorithm for molecular dynamics simulation

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

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.

Exploring travelers' behavior in response to dynamic message signs (DMS) using a driving simulator : final report.

DOT National Transportation Integrated Search

2013-10-01

This research studies the effectiveness of a dynamic message sign (DMS) using a driving : simulator. Over 100 subjects from different socio-economic and age groups were recruited to : drive the simulator under different traffic and driving conditions...

Buffer Management Simulation in ATM Networks

NASA Technical Reports Server (NTRS)

Yaprak, E.; Xiao, Y.; Chronopoulos, A.; Chow, E.; Anneberg, L.

1998-01-01

This paper presents a simulation of a new dynamic buffer allocation management scheme in ATM networks. To achieve this objective, an algorithm that detects congestion and updates the dynamic buffer allocation scheme was developed for the OPNET simulation package via the creation of a new ATM module.

MD Simulations of P-Type ATPases in a Lipid Bilayer System.

PubMed

Autzen, Henriette Elisabeth; Musgaard, Maria

2016-01-01

Molecular dynamics (MD) simulation is a computational method which provides insight on protein dynamics with high resolution in both space and time, in contrast to many experimental techniques. MD simulations can be used as a stand-alone method to study P-type ATPases as well as a complementary method aiding experimental studies. In particular, MD simulations have proved valuable in generating and confirming hypotheses relating to the structure and function of P-type ATPases. In the following, we describe a detailed practical procedure on how to set up and run a MD simulation of a P-type ATPase embedded in a lipid bilayer using software free of use for academics. We emphasize general considerations and problems typically encountered when setting up simulations. While full coverage of all possible procedures is beyond the scope of this chapter, we have chosen to illustrate the MD procedure with the Nanoscale Molecular Dynamics (NAMD) and the Visual Molecular Dynamics (VMD) software suites.

Simulation of FRET dyes allows quantitative comparison against experimental data

NASA Astrophysics Data System (ADS)

Reinartz, Ines; Sinner, Claude; Nettels, Daniel; Stucki-Buchli, Brigitte; Stockmar, Florian; Panek, Pawel T.; Jacob, Christoph R.; Nienhaus, Gerd Ulrich; Schuler, Benjamin; Schug, Alexander

2018-03-01

Fully understanding biomolecular function requires detailed insight into the systems' structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function.

OpenSim: open-source software to create and analyze dynamic simulations of movement.

PubMed

Delp, Scott L; Anderson, Frank C; Arnold, Allison S; Loan, Peter; Habib, Ayman; John, Chand T; Guendelman, Eran; Thelen, Darryl G

2007-11-01

Dynamic simulations of movement allow one to study neuromuscular coordination, analyze athletic performance, and estimate internal loading of the musculoskeletal system. Simulations can also be used to identify the sources of pathological movement and establish a scientific basis for treatment planning. We have developed a freely available, open-source software system (OpenSim) that lets users develop models of musculoskeletal structures and create dynamic simulations of a wide variety of movements. We are using this system to simulate the dynamics of individuals with pathological gait and to explore the biomechanical effects of treatments. OpenSim provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through a multi-institutional collaboration. Developing software that enables a concerted effort from many investigators poses technical and sociological challenges. Meeting those challenges will accelerate the discovery of principles that govern movement control and improve treatments for individuals with movement pathologies.

Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins.

PubMed

Li, Min; Zhang, John Z H

2017-03-08

The development of polarizable water models at coarse-grained (CG) levels is of much importance to CG molecular dynamics simulations of large biomolecular systems. In this work, we combined the newly developed two-bead multipole force field (TMFF) for proteins with the two-bead polarizable water models to carry out CG molecular dynamics simulations for benchmark proteins. In our simulations, two different two-bead polarizable water models are employed, the RTPW model representing five water molecules by Riniker et al. and the LTPW model representing four water molecules. The LTPW model is developed in this study based on the Martini three-bead polarizable water model. Our simulation results showed that the combination of TMFF with the LTPW model significantly stabilizes the protein's native structure in CG simulations, while the use of the RTPW model gives better agreement with all-atom simulations in predicting the residue-level fluctuation dynamics. Overall, the TMFF coupled with the two-bead polarizable water models enables one to perform an efficient and reliable CG dynamics study of the structural and functional properties of large biomolecules.

Multiscale modeling of dislocation-precipitate interactions in Fe: From molecular dynamics to discrete dislocations.

PubMed

Lehtinen, Arttu; Granberg, Fredric; Laurson, Lasse; Nordlund, Kai; Alava, Mikko J

2016-01-01

The stress-driven motion of dislocations in crystalline solids, and thus the ensuing plastic deformation process, is greatly influenced by the presence or absence of various pointlike defects such as precipitates or solute atoms. These defects act as obstacles for dislocation motion and hence affect the mechanical properties of the material. Here we combine molecular dynamics studies with three-dimensional discrete dislocation dynamics simulations in order to model the interaction between different kinds of precipitates and a 1/2〈111〉{110} edge dislocation in BCC iron. We have implemented immobile spherical precipitates into the ParaDis discrete dislocation dynamics code, with the dislocations interacting with the precipitates via a Gaussian potential, generating a normal force acting on the dislocation segments. The parameters used in the discrete dislocation dynamics simulations for the precipitate potential, the dislocation mobility, shear modulus, and dislocation core energy are obtained from molecular dynamics simulations. We compare the critical stresses needed to unpin the dislocation from the precipitate in molecular dynamics and discrete dislocation dynamics simulations in order to fit the two methods together and discuss the variety of the relevant pinning and depinning mechanisms.

Recent research and applications of numerical simulation for dynamic response of long-span bridges subjected to multiple loads.

PubMed

Chen, Zhiwei; Chen, Bo

2014-01-01

Many long-span bridges have been built throughout the world in recent years but they are often subject to multiple types of dynamic loads, especially those located in wind-prone regions and carrying both trains and road vehicles. To ensure the safety and functionality of these bridges, dynamic responses of long-span bridges are often required for bridge assessment. Given that there are several limitations for the assessment based on field measurement of dynamic responses, a promising approach is based on numerical simulation technologies. This paper provides a detailed review of key issues involved in dynamic response analysis of long-span multiload bridges based on numerical simulation technologies, including dynamic interactions between running trains and bridge, between running road vehicles and bridge, and between wind and bridge, and in the wind-vehicle-bridge coupled system. Then a comprehensive review is conducted for engineering applications of newly developed numerical simulation technologies to safety assessment of long-span bridges, such as assessment of fatigue damage and assessment under extreme events. Finally, the existing problems and promising research efforts for the numerical simulation technologies and their applications to assessment of long-span multiload bridges are explored.

Recent Research and Applications of Numerical Simulation for Dynamic Response of Long-Span Bridges Subjected to Multiple Loads

PubMed Central

Chen, Zhiwei; Chen, Bo

2014-01-01

Many long-span bridges have been built throughout the world in recent years but they are often subject to multiple types of dynamic loads, especially those located in wind-prone regions and carrying both trains and road vehicles. To ensure the safety and functionality of these bridges, dynamic responses of long-span bridges are often required for bridge assessment. Given that there are several limitations for the assessment based on field measurement of dynamic responses, a promising approach is based on numerical simulation technologies. This paper provides a detailed review of key issues involved in dynamic response analysis of long-span multiload bridges based on numerical simulation technologies, including dynamic interactions between running trains and bridge, between running road vehicles and bridge, and between wind and bridge, and in the wind-vehicle-bridge coupled system. Then a comprehensive review is conducted for engineering applications of newly developed numerical simulation technologies to safety assessment of long-span bridges, such as assessment of fatigue damage and assessment under extreme events. Finally, the existing problems and promising research efforts for the numerical simulation technologies and their applications to assessment of long-span multiload bridges are explored. PMID:25006597

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

NASA Astrophysics Data System (ADS)

Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

2018-04-01

The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

Application of principal component analysis in protein unfolding: an all-atom molecular dynamics simulation study.

PubMed

Das, Atanu; Mukhopadhyay, Chaitali

2007-10-28

We have performed molecular dynamics (MD) simulation of the thermal denaturation of one protein and one peptide-ubiquitin and melittin. To identify the correlation in dynamics among various secondary structural fragments and also the individual contribution of different residues towards thermal unfolding, principal component analysis method was applied in order to give a new insight to protein dynamics by analyzing the contribution of coefficients of principal components. The cross-correlation matrix obtained from MD simulation trajectory provided important information regarding the anisotropy of backbone dynamics that leads to unfolding. Unfolding of ubiquitin was found to be a three-state process, while that of melittin, though smaller and mostly helical, is more complicated.

Application of principal component analysis in protein unfolding: An all-atom molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Das, Atanu; Mukhopadhyay, Chaitali

2007-10-01

We have performed molecular dynamics (MD) simulation of the thermal denaturation of one protein and one peptide—ubiquitin and melittin. To identify the correlation in dynamics among various secondary structural fragments and also the individual contribution of different residues towards thermal unfolding, principal component analysis method was applied in order to give a new insight to protein dynamics by analyzing the contribution of coefficients of principal components. The cross-correlation matrix obtained from MD simulation trajectory provided important information regarding the anisotropy of backbone dynamics that leads to unfolding. Unfolding of ubiquitin was found to be a three-state process, while that of melittin, though smaller and mostly helical, is more complicated.

Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations.

PubMed

Kortkhonjia, Ekaterine; Brandman, Relly; Zhou, Joe Zhongxiang; Voelz, Vincent A; Chorny, Ilya; Kabakoff, Bruce; Patapoff, Thomas W; Dill, Ken A; Swartz, Trevor E

2013-01-01

The solution dynamics of antibodies are critical to antibody function. We explore the internal solution dynamics of antibody molecules through the combination of time-resolved fluorescence anisotropy experiments on IgG1 with more than two microseconds of all-atom molecular dynamics (MD) simulations in explicit water, an order of magnitude more than in previous simulations. We analyze the correlated motions with a mutual information entropy quantity, and examine state transition rates in a Markov-state model, to give coarse-grained descriptors of the motions. Our MD simulations show that while there are many strongly correlated motions, antibodies are highly flexible, with F(ab) and F(c) domains constantly forming and breaking contacts, both polar and non-polar. We find that salt bridges break and reform, and not always with the same partners. While the MD simulations in explicit water give the right time scales for the motions, the simulated motions are about 3-fold faster than the experiments. Overall, the picture that emerges is that antibodies do not simply fluctuate around a single state of atomic contacts. Rather, in these large molecules, different atoms come in contact during different motions.

OSSOS: X. How to use a Survey Simulator: Statistical Testing of Dynamical Models Against the Real Kuiper Belt

NASA Astrophysics Data System (ADS)

Lawler, Samantha M.; Kavelaars, J. J.; Alexandersen, Mike; Bannister, Michele T.; Gladman, Brett; Petit, Jean-Marc; Shankman, Cory

2018-05-01

All surveys include observational biases, which makes it impossible to directly compare properties of discovered trans-Neptunian Objects (TNOs) with dynamical models. However, by carefully keeping track of survey pointings on the sky, detection limits, tracking fractions, and rate cuts, the biases from a survey can be modelled in Survey Simulator software. A Survey Simulator takes an intrinsic orbital model (from, for example, the output of a dynamical Kuiper belt emplacement simulation) and applies the survey biases, so that the biased simulated objects can be directly compared with real discoveries. This methodology has been used with great success in the Outer Solar System Origins Survey (OSSOS) and its predecessor surveys. In this chapter, we give four examples of ways to use the OSSOS Survey Simulator to gain knowledge about the true structure of the Kuiper Belt. We demonstrate how to statistically compare different dynamical model outputs with real TNO discoveries, how to quantify detection biases within a TNO population, how to measure intrinsic population sizes, and how to use upper limits from non-detections. We hope this will provide a framework for dynamical modellers to statistically test the validity of their models.

Nonlinear dynamic simulation of single- and multi-spool core engines

NASA Technical Reports Server (NTRS)

Schobeiri, T.; Lippke, C.; Abouelkheir, M.

1993-01-01

In this paper a new computational method for accurate simulation of the nonlinear dynamic behavior of single- and multi-spool core engines, turbofan engines, and power generation gas turbine engines is presented. In order to perform the simulation, a modularly structured computer code has been developed which includes individual mathematical modules representing various engine components. The generic structure of the code enables the dynamic simulation of arbitrary engine configurations ranging from single-spool thrust generation to multi-spool thrust/power generation engines under adverse dynamic operating conditions. For precise simulation of turbine and compressor components, row-by-row calculation procedures were implemented that account for the specific turbine and compressor cascade and blade geometry and characteristics. The dynamic behavior of the subject engine is calculated by solving a number of systems of partial differential equations, which describe the unsteady behavior of the individual components. In order to ensure the capability, accuracy, robustness, and reliability of the code, comprehensive critical performance assessment and validation tests were performed. As representatives, three different transient cases with single- and multi-spool thrust and power generation engines were simulated. The transient cases range from operating with a prescribed fuel schedule, to extreme load changes, to generator and turbine shut down.

Melt-growth dynamics in CdTe crystals

DOE PAGES

Zhou, X. W.; Ward, D. K.; Wong, B. M.; ...

2012-06-01

We use a new, quantum-mechanics-based bond-order potential (BOP) to reveal melt growth dynamics and fine scale defect formation mechanisms in CdTe crystals. Previous molecular dynamics simulations of semiconductors have shown qualitatively incorrect behavior due to the lack of an interatomic potential capable of predicting both crystalline growth and property trends of many transitional structures encountered during the melt → crystal transformation. Here, we demonstrate successful molecular dynamics simulations of melt growth in CdTe using a BOP that significantly improves over other potentials on property trends of different phases. Our simulations result in a detailed understanding of defect formation during themore » melt growth process. Equally important, we show that the new BOP enables defect formation mechanisms to be studied at a scale level comparable to empirical molecular dynamics simulation methods with a fidelity level approaching quantum-mechanical methods.« less

Dynamic modelling of an adsorption storage tank using a hybrid approach combining computational fluid dynamics and process simulation

USGS Publications Warehouse

Mota, J.P.B.; Esteves, I.A.A.C.; Rostam-Abadi, M.

2004-01-01

A computational fluid dynamics (CFD) software package has been coupled with the dynamic process simulator of an adsorption storage tank for methane fuelled vehicles. The two solvers run as independent processes and handle non-overlapping portions of the computational domain. The codes exchange data on the boundary interface of the two domains to ensure continuity of the solution and of its gradient. A software interface was developed to dynamically suspend and activate each process as necessary, and be responsible for data exchange and process synchronization. This hybrid computational tool has been successfully employed to accurately simulate the discharge of a new tank design and evaluate its performance. The case study presented here shows that CFD and process simulation are highly complementary computational tools, and that there are clear benefits to be gained from a close integration of the two. ?? 2004 Elsevier Ltd. All rights reserved.

ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems.

PubMed

Niethammer, Christoph; Becker, Stefan; Bernreuther, Martin; Buchholz, Martin; Eckhardt, Wolfgang; Heinecke, Alexander; Werth, Stephan; Bungartz, Hans-Joachim; Glass, Colin W; Hasse, Hans; Vrabec, Jadran; Horsch, Martin

2014-10-14

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.

Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics.

PubMed

Chen, Minghan; Li, Fei; Wang, Shuo; Cao, Young

2017-03-14

Stochastic simulation of reaction-diffusion systems presents great challenges for spatiotemporal biological modeling and simulation. One widely used framework for stochastic simulation of reaction-diffusion systems is reaction diffusion master equation (RDME). Previous studies have discovered that for the RDME, when discretization size approaches zero, reaction time for bimolecular reactions in high dimensional domains tends to infinity. In this paper, we demonstrate that in the 1D domain, highly nonlinear reaction dynamics given by Hill function may also have dramatic change when discretization size is smaller than a critical value. Moreover, we discuss methods to avoid this problem: smoothing over space, fixed length smoothing over space and a hybrid method. Our analysis reveals that the switch-like Hill dynamics reduces to a linear function of discretization size when the discretization size is small enough. The three proposed methods could correctly (under certain precision) simulate Hill function dynamics in the microscopic RDME system.

Distributed dynamic simulations of networked control and building performance applications.

PubMed

Yahiaoui, Azzedine

2018-02-01

The use of computer-based automation and control systems for smart sustainable buildings, often so-called Automated Buildings (ABs), has become an effective way to automatically control, optimize, and supervise a wide range of building performance applications over a network while achieving the minimum energy consumption possible, and in doing so generally refers to Building Automation and Control Systems (BACS) architecture. Instead of costly and time-consuming experiments, this paper focuses on using distributed dynamic simulations to analyze the real-time performance of network-based building control systems in ABs and improve the functions of the BACS technology. The paper also presents the development and design of a distributed dynamic simulation environment with the capability of representing the BACS architecture in simulation by run-time coupling two or more different software tools over a network. The application and capability of this new dynamic simulation environment are demonstrated by an experimental design in this paper.

Fragmentation-based QM/MM simulations: length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions.

PubMed

Li, Hui; Li, Wei; Li, Shuhua; Ma, Jing

2008-06-12

Molecular fragmentation quantum mechanics (QM) calculations have been combined with molecular mechanics (MM) to construct the fragmentation QM/MM method for simulations of dilute solutions of macromolecules. We adopt the electrostatics embedding QM/MM model, where the low-cost generalized energy-based fragmentation calculations are employed for the QM part. Conformation energy calculations, geometry optimizations, and Born-Oppenheimer molecular dynamics simulations of poly(ethylene oxide), PEO(n) (n = 6-20), and polyethylene, PE(n) ( n = 9-30), in aqueous solution have been performed within the framework of both fragmentation and conventional QM/MM methods. The intermolecular hydrogen bonding and chain configurations obtained from the fragmentation QM/MM simulations are consistent with the conventional QM/MM method. The length dependence of chain conformations and dynamics of PEO and PE oligomers in aqueous solutions is also investigated through the fragmentation QM/MM molecular dynamics simulations.

Distributed dynamic simulations of networked control and building performance applications

PubMed Central

Yahiaoui, Azzedine

2017-01-01

The use of computer-based automation and control systems for smart sustainable buildings, often so-called Automated Buildings (ABs), has become an effective way to automatically control, optimize, and supervise a wide range of building performance applications over a network while achieving the minimum energy consumption possible, and in doing so generally refers to Building Automation and Control Systems (BACS) architecture. Instead of costly and time-consuming experiments, this paper focuses on using distributed dynamic simulations to analyze the real-time performance of network-based building control systems in ABs and improve the functions of the BACS technology. The paper also presents the development and design of a distributed dynamic simulation environment with the capability of representing the BACS architecture in simulation by run-time coupling two or more different software tools over a network. The application and capability of this new dynamic simulation environment are demonstrated by an experimental design in this paper. PMID:29568135

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

A Framework for Simulating Turbine-Based Combined-Cycle Inlet Mode-Transition

NASA Technical Reports Server (NTRS)

Le, Dzu K.; Vrnak, Daniel R.; Slater, John W.; Hessel, Emil O.

2012-01-01

A simulation framework based on the Memory-Mapped-Files technique was created to operate multiple numerical processes in locked time-steps and send I/O data synchronously across to one-another to simulate system-dynamics. This simulation scheme is currently used to study the complex interactions between inlet flow-dynamics, variable-geometry actuation mechanisms, and flow-controls in the transition from the supersonic to hypersonic conditions and vice-versa. A study of Mode-Transition Control for a high-speed inlet wind-tunnel model with this MMF-based framework is presented to illustrate this scheme and demonstrate its usefulness in simulating supersonic and hypersonic inlet dynamics and controls or other types of complex systems.

Pressure calculation in hybrid particle-field simulations

NASA Astrophysics Data System (ADS)

Milano, Giuseppe; Kawakatsu, Toshihiro

2010-12-01

In the framework of a recently developed scheme for a hybrid particle-field simulation techniques where self-consistent field (SCF) theory and particle models (molecular dynamics) are combined [J. Chem. Phys. 130, 214106 (2009)], we developed a general formulation for the calculation of instantaneous pressure and stress tensor. The expressions have been derived from statistical mechanical definition of the pressure starting from the expression for the free energy functional in the SCF theory. An implementation of the derived formulation suitable for hybrid particle-field molecular dynamics-self-consistent field simulations is described. A series of test simulations on model systems are reported comparing the calculated pressure with those obtained from standard molecular dynamics simulations based on pair potentials.

Simulating forest fuel and fire risk dynamics across landscapes--LANDIS fuel module design

Treesearch

Hong S. He; Bo Z. Shang; Thomas R. Crow; Eric J. Gustafson; Stephen R. Shifley

2004-01-01

Understanding fuel dynamics over large spatial (103-106 ha) and temporal scales (101-103 years) is important in comprehensive wildfire management. We present a modeling approach to simulate fuel and fire risk dynamics as well as impacts of alternative fuel treatments. The...

Dynamic Evaluation of Long-Term Air Quality Model Simulations Over the Northeastern U.S.

EPA Science Inventory

Dynamic model evaluation assesses a modeling system's ability to reproduce changes in air quality induced by changes in meteorology and/or emissions. In this paper, we illustrate various approaches to dynamic mode evaluation utilizing 18 years of air quality simulations perform...

A dynamic model of the human postural control system

NASA Technical Reports Server (NTRS)

Hill, J. C.

1972-01-01

A digital simulation of the pitch axis dynamics of a stick man of figures is described. Difficulties encountered in linearizing the equations of motion are discussed; the conclusion reached is that a completely linear simulation is of such restricted validity that only a nonlinear simulation is of any practical use. Typical simulation results obtained from the full nonlinear model are presented.

A dynamic model of the human postural control system.

NASA Technical Reports Server (NTRS)

Hill, J. C.

1971-01-01

Description of a digital simulation of the pitch axis dynamics of a stick man. The difficulties encountered in linearizing the equations of motion are discussed; the conclusion reached is that a completely linear simulation is of such restricted validity that only a nonlinear simulation is of any practical use. Typical simulation results obtained from the full nonlinear model are illustrated.

Physically Based Modeling and Simulation with Dynamic Spherical Volumetric Simplex Splines

PubMed Central

Tan, Yunhao; Hua, Jing; Qin, Hong

2009-01-01

In this paper, we present a novel computational modeling and simulation framework based on dynamic spherical volumetric simplex splines. The framework can handle the modeling and simulation of genus-zero objects with real physical properties. In this framework, we first develop an accurate and efficient algorithm to reconstruct the high-fidelity digital model of a real-world object with spherical volumetric simplex splines which can represent with accuracy geometric, material, and other properties of the object simultaneously. With the tight coupling of Lagrangian mechanics, the dynamic volumetric simplex splines representing the object can accurately simulate its physical behavior because it can unify the geometric and material properties in the simulation. The visualization can be directly computed from the object’s geometric or physical representation based on the dynamic spherical volumetric simplex splines during simulation without interpolation or resampling. We have applied the framework for biomechanic simulation of brain deformations, such as brain shifting during the surgery and brain injury under blunt impact. We have compared our simulation results with the ground truth obtained through intra-operative magnetic resonance imaging and the real biomechanic experiments. The evaluations demonstrate the excellent performance of our new technique. PMID:20161636

A Process for the Creation of T-MATS Propulsion System Models from NPSS data

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink (Math Works, Inc.) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

A Process for the Creation of T-MATS Propulsion System Models from NPSS Data

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink(Trademark) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

Crystal water dynamics of guanosine dihydrate: analysis of atomic displacement parameters, time profile of hydrogen-bonding probability, and translocation of water by MD simulation.

PubMed

Yoneda, Shigetaka; Sugawara, Yoko; Urabe, Hisako

2005-01-27

The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism.

A Process for the Creation of T-MATS Propulsion System Models from NPSS Data

NASA Technical Reports Server (NTRS)

Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Jonathan S.; Guo, Ten-Huei

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink(Registered TradeMark) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes.

PubMed

Kang, Myungshim; Chakraborty, Kaushik; Loverde, Sharon M

2018-06-25

We report here on long-time all-atomistic molecular dynamics simulations of functional supramolecular nanotubes composed by the self-assembly of peptide-drug amphiphiles (DAs). These DAs have been shown to possess an inherently high drug loading of the hydrophobic anticancer drug camptothecin. We probe the self-assembly mechanism from random with ∼0.4 μs molecular dynamics simulations. Furthermore, we also computationally characterize the interfacial structure, directionality of π-π stacking, and water dynamics within several peptide-drug nanotubes with diameters consistent with the reported experimental nanotube diameter. Insight gained should inform the future design of these novel anticancer drug delivery systems.

The development of an autonomous rendezvous and docking simulation using rapid integration and prototyping technology

NASA Technical Reports Server (NTRS)

Shackelford, John H.; Saugen, John D.; Wurst, Michael J.; Adler, James

1991-01-01

A generic planar 3 degree of freedom simulation was developed that supports hardware in the loop simulations, guidance and control analysis, and can directly generate flight software. This simulation was developed in a small amount of time utilizing rapid prototyping techniques. The approach taken to develop this simulation tool, the benefits seen using this approach to development, and on-going efforts to improve and extend this capability are described. The simulation is composed of 3 major elements: (1) Docker dynamics model, (2) Dockee dynamics model, and (3) Docker Control System. The docker and dockee models are based on simple planar orbital dynamics equations using a spherical earth gravity model. The docker control system is based on a phase plane approach to error correction.

Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet.

PubMed

Rana, Malay Kumar; Chandra, Amalendu

2013-05-28

The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations.

Molecular dynamics in principal component space.

PubMed

Michielssens, Servaas; van Erp, Titus S; Kutzner, Carsten; Ceulemans, Arnout; de Groot, Bert L

2012-07-26

A molecular dynamics algorithm in principal component space is presented. It is demonstrated that sampling can be improved without changing the ensemble by assigning masses to the principal components proportional to the inverse square root of the eigenvalues. The setup of the simulation requires no prior knowledge of the system; a short initial MD simulation to extract the eigenvectors and eigenvalues suffices. Independent measures indicated a 6-7 times faster sampling compared to a regular molecular dynamics simulation.

Mass Conservation of the Unified Continuous and Discontinuous Element-Based Galerkin Methods on Dynamically Adaptive Grids with Application to Atmospheric Simulations

DTIC Science & Technology

2015-09-01

Discontinuous Element-Based Galerkin Methods on Dynamically Adaptive Grids with Application to Atmospheric Simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER...Discontinuous Element-Based Galerkin Methods on Dynamically Adaptive Grids with Application to Atmospheric Simulations. Michal A. Koperaa,∗, Francis X...mass conservation, as it is an important feature for many atmospheric applications . We believe this is a good metric because, for smooth solutions

Coarse-Grained Molecular Dynamics Simulation of Ionic Polymer Networks

DTIC Science & Technology

2008-07-01

AFRL-RX-WP-TP-2009-4198 COARSE-GRAINED MOLECULAR DYNAMICS SIMULATION OF IONIC POLYMER NETWORKS (Postprint) T.E. Dirama, V. Varshney, K.L...GRAINED MOLECULAR DYNAMICS SIMULATION OF IONIC POLYMER NETWORKS (Postprint) 5a. CONTRACT NUMBER FA8650-05-D-5807-0052 5b. GRANT NUMBER 5c...We studied two types of networks which differ only by one containing ionic pairs that amount to 7% of the total number of bonds present. The stress

Prediction of Protein-Peptide Interactions: Application of the XPairIT to Anthrax Lethal Factor and Substrates

DTIC Science & Technology

2013-09-01

hydrogen bonds in Tyrosine-containing peptides. Dalkas et al[7] used docking and molecular dynamics simulations to study a variety of MAPKK-based... simulated using NAMD molecular dynamics and the CHARMM[20] forcefield at 300K and employing the Generalized Born Implicit Solvent (GBIS[21]) with the...which were reported in Section 2. Specifically, after a ~10ns molecular dynamics simulation in TIP3 explicit water, significant motion of domains III

The "Collisions Cube" Molecular Dynamics Simulator.

ERIC Educational Resources Information Center

Nash, John J.; Smith, Paul E.

1995-01-01

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

Civil (French/US) certification of the Coast Guard's HH-65A Dauphin

NASA Technical Reports Server (NTRS)

Hart, J. C.; Besse, J. M.; Mcelreath, K. W.

1982-01-01

Certification programs with particular emphasis on handling qualities requirements are described. A dynamic simulator was designed and constructed to support and verify the dynamic aspects of the avionics system, particularly the Automatic Flight Control System (AFCS). The role of the Dynamic Simulator is discussed.

The co-development of looking dynamics and discrimination performance

PubMed Central

Perone, Sammy; Spencer, John P.

2015-01-01

The study of looking dynamics and discrimination form the backbone of developmental science and are central processes in theories of infant cognition. Looking dynamics and discrimination change dramatically across the first year of life. Surprisingly, developmental changes in looking and discrimination have not been studied together. Recent simulations of a dynamic neural field (DNF) model of infant looking and memory suggest that looking and discrimination do change together over development and arise from a single neurodevelopmental mechanism. We probe this claim by measuring looking dynamics and discrimination along continuous, metrically organized dimensions in 5-, 7, and 10-month-old infants (N = 119). The results showed that looking dynamics and discrimination changed together over development and are linked within individuals. Quantitative simulations of a DNF model provide insights into the processes that underlie developmental change in looking dynamics and discrimination. Simulation results support the view that these changes might arise from a single neurodevelopmental mechanism. PMID:23957821

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

PubMed

Lemkul, Justin A; Roux, Benoît; van der Spoel, David; MacKerell, Alexander D

2015-07-15

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field. © 2015 Wiley Periodicals, Inc.

Physical Principle for Generation of Randomness

NASA Technical Reports Server (NTRS)

Zak, Michail

2009-01-01

A physical principle (more precisely, a principle that incorporates mathematical models used in physics) has been conceived as the basis of a method of generating randomness in Monte Carlo simulations. The principle eliminates the need for conventional random-number generators. The Monte Carlo simulation method is among the most powerful computational methods for solving high-dimensional problems in physics, chemistry, economics, and information processing. The Monte Carlo simulation method is especially effective for solving problems in which computational complexity increases exponentially with dimensionality. The main advantage of the Monte Carlo simulation method over other methods is that the demand on computational resources becomes independent of dimensionality. As augmented by the present principle, the Monte Carlo simulation method becomes an even more powerful computational method that is especially useful for solving problems associated with dynamics of fluids, planning, scheduling, and combinatorial optimization. The present principle is based on coupling of dynamical equations with the corresponding Liouville equation. The randomness is generated by non-Lipschitz instability of dynamics triggered and controlled by feedback from the Liouville equation. (In non-Lipschitz dynamics, the derivatives of solutions of the dynamical equations are not required to be bounded.)

Exploring GPCR-Lipid Interactions by Molecular Dynamics Simulations: Excitements, Challenges, and the Way Forward.

PubMed

Sengupta, Durba; Prasanna, Xavier; Mohole, Madhura; Chattopadhyay, Amitabha

2018-06-07

Gprotein-coupled receptors (GPCRs) are seven transmembrane receptors that mediate a large number of cellular responses and are important drug targets. One of the current challenges in GPCR biology is to analyze the molecular signatures of receptor-lipid interactions and their subsequent effects on GPCR structure, organization, and function. Molecular dynamics simulation studies have been successful in predicting molecular determinants of receptor-lipid interactions. In particular, predicted cholesterol interaction sites appear to correspond well with experimentally determined binding sites and estimated time scales of association. In spite of several success stories, the methodologies in molecular dynamics simulations are still emerging. In this Feature Article, we provide a comprehensive overview of coarse-grain and atomistic molecular dynamics simulations of GPCR-lipid interaction in the context of experimental observations. In addition, we discuss the effect of secondary and tertiary structural constraints in coarse-grain simulations in the context of functional dynamics and structural plasticity of GPCRs. We envision that this comprehensive overview will help resolve differences in computational studies and provide a way forward.

Mussel dynamics model: A hydroinformatics tool for analyzing the effects of different stressors on the dynamics of freshwater mussel communities

USGS Publications Warehouse

Morales, Y.; Weber, L.J.; Mynett, A.E.; Newton, T.J.

2006-01-01

A model for simulating freshwater mussel population dynamics is presented. The model is a hydroinformatics tool that integrates principles from ecology, river hydraulics, fluid mechanics and sediment transport, and applies the individual-based modelling approach for simulating population dynamics. The general model layout, data requirements, and steps of the simulation process are discussed. As an illustration, simulation results from an application in a 10 km reach of the Upper Mississippi River are presented. The model was used to investigate the spatial distribution of mussels and the effects of food competition in native unionid mussel communities, and communities infested by Dreissena polymorpha, the zebra mussel. Simulation results were found to be realistic and coincided with data obtained from the literature. These results indicate that the model can be a useful tool for assessing the potential effects of different stressors on long-term population dynamics, and consequently, may improve the current understanding of cause and effect relationships in freshwater mussel communities. ?? 2006 Elsevier B.V. All rights reserved.

Dynamic Modulation of Human Motor Activity When Observing Actions

PubMed Central

Press, Clare; Cook, Jennifer; Blakemore, Sarah-Jayne; Kilner, James

2012-01-01

Previous studies have demonstrated that when we observe somebody else executing an action many areas of our own motor systems are active. It has been argued that these motor activations are evidence that we motorically simulate observed actions; this motoric simulation may support various functions such as imitation and action understanding. However, whether motoric simulation is indeed the function of motor activations during action observation is controversial, due to inconsistency in findings. Previous studies have demonstrated dynamic modulations in motor activity when we execute actions. Therefore, if we do motorically simulate observed actions, our motor systems should also be modulated dynamically, and in a corresponding fashion, during action observation. Using magnetoencephalography, we recorded the cortical activity of human participants while they observed actions performed by another person. Here, we show that activity in the human motor system is indeed modulated dynamically during action observation. The finding that activity in the motor system is modulated dynamically when observing actions can explain why studies of action observation using functional magnetic resonance imaging have reported conflicting results, and is consistent with the hypothesis that we motorically simulate observed actions. PMID:21414901

ISM simulations: an overview of models

NASA Astrophysics Data System (ADS)

de Avillez, M. A.; Breitschwerdt, D.; Asgekar, A.; Spitoni, E.

2015-03-01

Until recently the dynamical evolution of the interstellar medium (ISM) was simulated using collisional ionization equilibrium (CIE) conditions. However, the ISM is a dynamical system, in which the plasma is naturally driven out of equilibrium due to atomic and dynamic processes operating on different timescales. A step forward in the field comprises a multi-fluid approach taking into account the joint thermal and dynamical evolutions of the ISM gas.

Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.

PubMed Central

Guenot, J.; Kollman, P. A.

1992-01-01

Although aqueous simulations with periodic boundary conditions more accurately describe protein dynamics than in vacuo simulations, these are computationally intensive for most proteins. Trp repressor dynamic simulations with a small water shell surrounding the starting model yield protein trajectories that are markedly improved over gas phase, yet computationally efficient. Explicit water in molecular dynamics simulations maintains surface exposure of protein hydrophilic atoms and burial of hydrophobic atoms by opposing the otherwise asymmetric protein-protein forces. This properly orients protein surface side chains, reduces protein fluctuations, and lowers the overall root mean square deviation from the crystal structure. For simulations with crystallographic waters only, a linear or sigmoidal distance-dependent dielectric yields a much better trajectory than does a constant dielectric model. As more water is added to the starting model, the differences between using distance-dependent and constant dielectric models becomes smaller, although the linear distance-dependent dielectric yields an average structure closer to the crystal structure than does a constant dielectric model. Multiplicative constants greater than one, for the linear distance-dependent dielectric simulations, produced trajectories that are progressively worse in describing trp repressor dynamics. Simulations of bovine pancreatic trypsin were used to ensure that the trp repressor results were not protein dependent and to explore the effect of the nonbonded cutoff on the distance-dependent and constant dielectric simulation models. The nonbonded cutoff markedly affected the constant but not distance-dependent dielectric bovine pancreatic trypsin inhibitor simulations. As with trp repressor, the distance-dependent dielectric model with a shell of water surrounding the protein produced a trajectory in better agreement with the crystal structure than a constant dielectric model, and the physical properties of the trajectory average structure, both with and without a nonbonded cutoff, were comparable. PMID:1304396

Dynamic evaluation of two decades of WRF-CMAQ ozone simulations over the contiguous United States

EPA Science Inventory

Dynamic evaluation of the fully coupled Weather Research and Forecasting (WRF)– Community Multi-scale Air Quality (CMAQ) model ozone simulations over the contiguous United States (CONUS) using two decades of simulations covering the period from 1990 to 2010 is conducted to ...

Dynamic evaluation of two decades of WRF-CMAQ ozone simulations over the contiguous United States

EPA Science Inventory

Dynamic evaluation of the fully coupled Weather Research and Forecasting (WRF)– Community Multi-scale Air Quality (CMAQ) model ozone simulations over the contiguous United States (CONUS) using two decades of simulations covering the period from 1990 to 2010 is conducted to assess...

Bringing consistency to simulation of population models--Poisson simulation as a bridge between micro and macro simulation.

PubMed

Gustafsson, Leif; Sternad, Mikael

2007-10-01

Population models concern collections of discrete entities such as atoms, cells, humans, animals, etc., where the focus is on the number of entities in a population. Because of the complexity of such models, simulation is usually needed to reproduce their complete dynamic and stochastic behaviour. Two main types of simulation models are used for different purposes, namely micro-simulation models, where each individual is described with its particular attributes and behaviour, and macro-simulation models based on stochastic differential equations, where the population is described in aggregated terms by the number of individuals in different states. Consistency between micro- and macro-models is a crucial but often neglected aspect. This paper demonstrates how the Poisson Simulation technique can be used to produce a population macro-model consistent with the corresponding micro-model. This is accomplished by defining Poisson Simulation in strictly mathematical terms as a series of Poisson processes that generate sequences of Poisson distributions with dynamically varying parameters. The method can be applied to any population model. It provides the unique stochastic and dynamic macro-model consistent with a correct micro-model. The paper also presents a general macro form for stochastic and dynamic population models. In an appendix Poisson Simulation is compared with Markov Simulation showing a number of advantages. Especially aggregation into state variables and aggregation of many events per time-step makes Poisson Simulation orders of magnitude faster than Markov Simulation. Furthermore, you can build and execute much larger and more complicated models with Poisson Simulation than is possible with the Markov approach.

Pseudo-dynamic source characterization accounting for rough-fault effects

NASA Astrophysics Data System (ADS)

Galis, Martin; Thingbaijam, Kiran K. S.; Mai, P. Martin

2016-04-01

Broadband ground-motion simulations, ideally for frequencies up to ~10Hz or higher, are important for earthquake engineering; for example, seismic hazard analysis for critical facilities. An issue with such simulations is realistic generation of radiated wave-field in the desired frequency range. Numerical simulations of dynamic ruptures propagating on rough faults suggest that fault roughness is necessary for realistic high-frequency radiation. However, simulations of dynamic ruptures are too expensive for routine applications. Therefore, simplified synthetic kinematic models are often used. They are usually based on rigorous statistical analysis of rupture models inferred by inversions of seismic and/or geodetic data. However, due to limited resolution of the inversions, these models are valid only for low-frequency range. In addition to the slip, parameters such as rupture-onset time, rise time and source time functions are needed for complete spatiotemporal characterization of the earthquake rupture. But these parameters are poorly resolved in the source inversions. To obtain a physically consistent quantification of these parameters, we simulate and analyze spontaneous dynamic ruptures on rough faults. First, by analyzing the impact of fault roughness on the rupture and seismic radiation, we develop equivalent planar-fault kinematic analogues of the dynamic ruptures. Next, we investigate the spatial interdependencies between the source parameters to allow consistent modeling that emulates the observed behavior of dynamic ruptures capturing the rough-fault effects. Based on these analyses, we formulate a framework for pseudo-dynamic source model, physically consistent with the dynamic ruptures on rough faults.

Accounting for system dynamics in reserve design.

PubMed

Leroux, Shawn J; Schmiegelow, Fiona K A; Cumming, Steve G; Lessard, Robert B; Nagy, John

2007-10-01

Systematic conservation plans have only recently considered the dynamic nature of ecosystems. Methods have been developed to incorporate climate change, population dynamics, and uncertainty in reserve design, but few studies have examined how to account for natural disturbance. Considering natural disturbance in reserve design may be especially important for the world's remaining intact areas, which still experience active natural disturbance regimes. We developed a spatially explicit, dynamic simulation model, CONSERV, which simulates patch dynamics and fire, and used it to evaluate the efficacy of hypothetical reserve networks in northern Canada. We designed six networks based on conventional reserve design methods, with different conservation targets for woodland caribou habitat, high-quality wetlands, vegetation, water bodies, and relative connectedness. We input the six reserve networks into CONSERV and tracked the ability of each to maintain initial conservation targets through time under an active natural disturbance regime. None of the reserve networks maintained all initial targets, and some over-represented certain features, suggesting that both effectiveness and efficiency of reserve design could be improved through use of spatially explicit dynamic simulation during the planning process. Spatial simulation models of landscape dynamics are commonly used in natural resource management, but we provide the first illustration of their potential use for reserve design. Spatial simulation models could be used iteratively to evaluate competing reserve designs and select targets that have a higher likelihood of being maintained through time. Such models could be combined with dynamic planning techniques to develop a general theory for reserve design in an uncertain world.

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

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

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived frommore » fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.« less

Divergence compensation for hardware-in-the-loop simulation of stiffness-varying discrete contact in space

NASA Astrophysics Data System (ADS)

Qi, Chenkun; Zhao, Xianchao; Gao, Feng; Ren, Anye; Hu, Yan

2016-11-01

The hardware-in-the-loop (HIL) contact simulation for flying objects in space is challenging due to the divergence caused by the time delay. In this study, a divergence compensation approach is proposed for the stiffness-varying discrete contact. The dynamic response delay of the motion simulator and the force measurement delay are considered. For the force measurement delay, a phase lead based force compensation approach is used. For the dynamic response delay of the motion simulator, a response error based force compensation approach is used, where the compensation force is obtained from the real-time identified contact stiffness and real-time measured position response error. The dynamic response model of the motion simulator is not required. The simulations and experiments show that the simulation divergence can be compensated effectively and satisfactorily by using the proposed approach.

Gaining insight into the physics of dynamic atomic force microscopy in complex environments using the VEDA simulator

NASA Astrophysics Data System (ADS)

Kiracofe, Daniel; Melcher, John; Raman, Arvind

2012-01-01

Dynamic atomic force microscopy (dAFM) continues to grow in popularity among scientists in many different fields, and research on new methods and operating modes continues to expand the resolution, capabilities, and types of samples that can be studied. But many promising increases in capability are accompanied by increases in complexity. Indeed, interpreting modern dAFM data can be challenging, especially on complicated material systems, or in liquid environments where the behavior is often contrary to what is known in air or vacuum environments. Mathematical simulations have proven to be an effective tool in providing physical insight into these non-intuitive systems. In this article we describe recent developments in the VEDA (virtual environment for dynamic AFM) simulator, which is a suite of freely available, open-source simulation tools that are delivered through the cloud computing cyber-infrastructure of nanoHUB (www.nanohub.org). Here we describe three major developments. First, simulations in liquid environments are improved by enhancements in the modeling of cantilever dynamics, excitation methods, and solvation shell forces. Second, VEDA is now able to simulate many new advanced modes of operation (bimodal, phase-modulation, frequency-modulation, etc.). Finally, nineteen different tip-sample models are available to simulate the surface physics of a wide variety different material systems including capillary, specific adhesion, van der Waals, electrostatic, viscoelasticity, and hydration forces. These features are demonstrated through example simulations and validated against experimental data, in order to provide insight into practical problems in dynamic AFM.

Gaining insight into the physics of dynamic atomic force microscopy in complex environments using the VEDA simulator.

PubMed

Kiracofe, Daniel; Melcher, John; Raman, Arvind

2012-01-01

Dynamic atomic force microscopy (dAFM) continues to grow in popularity among scientists in many different fields, and research on new methods and operating modes continues to expand the resolution, capabilities, and types of samples that can be studied. But many promising increases in capability are accompanied by increases in complexity. Indeed, interpreting modern dAFM data can be challenging, especially on complicated material systems, or in liquid environments where the behavior is often contrary to what is known in air or vacuum environments. Mathematical simulations have proven to be an effective tool in providing physical insight into these non-intuitive systems. In this article we describe recent developments in the VEDA (virtual environment for dynamic AFM) simulator, which is a suite of freely available, open-source simulation tools that are delivered through the cloud computing cyber-infrastructure of nanoHUB (www.nanohub.org). Here we describe three major developments. First, simulations in liquid environments are improved by enhancements in the modeling of cantilever dynamics, excitation methods, and solvation shell forces. Second, VEDA is now able to simulate many new advanced modes of operation (bimodal, phase-modulation, frequency-modulation, etc.). Finally, nineteen different tip-sample models are available to simulate the surface physics of a wide variety different material systems including capillary, specific adhesion, van der Waals, electrostatic, viscoelasticity, and hydration forces. These features are demonstrated through example simulations and validated against experimental data, in order to provide insight into practical problems in dynamic AFM.

Integrating macro and micro scale approaches in the agent-based modeling of residential dynamics

NASA Astrophysics Data System (ADS)

Saeedi, Sara

2018-06-01

With the advancement of computational modeling and simulation (M&S) methods as well as data collection technologies, urban dynamics modeling substantially improved over the last several decades. The complex urban dynamics processes are most effectively modeled not at the macro-scale, but following a bottom-up approach, by simulating the decisions of individual entities, or residents. Agent-based modeling (ABM) provides the key to a dynamic M&S framework that is able to integrate socioeconomic with environmental models, and to operate at both micro and macro geographical scales. In this study, a multi-agent system is proposed to simulate residential dynamics by considering spatiotemporal land use changes. In the proposed ABM, macro-scale land use change prediction is modeled by Artificial Neural Network (ANN) and deployed as the agent environment and micro-scale residential dynamics behaviors autonomously implemented by household agents. These two levels of simulation interacted and jointly promoted urbanization process in an urban area of Tehran city in Iran. The model simulates the behavior of individual households in finding ideal locations to dwell. The household agents are divided into three main groups based on their income rank and they are further classified into different categories based on a number of attributes. These attributes determine the households' preferences for finding new dwellings and change with time. The ABM environment is represented by a land-use map in which the properties of the land parcels change dynamically over the simulation time. The outputs of this model are a set of maps showing the pattern of different groups of households in the city. These patterns can be used by city planners to find optimum locations for building new residential units or adding new services to the city. The simulation results show that combining macro- and micro-level simulation can give full play to the potential of the ABM to understand the driving mechanism of urbanization and provide decision-making support for urban management.

Fast Dynamic Simulation-Based Small Signal Stability Assessment and Control

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

Acharya, Naresh; Baone, Chaitanya; Veda, Santosh

2014-12-31

Power grid planning and operation decisions are made based on simulation of the dynamic behavior of the system. Enabling substantial energy savings while increasing the reliability of the aging North American power grid through improved utilization of existing transmission assets hinges on the adoption of wide-area measurement systems (WAMS) for power system stabilization. However, adoption of WAMS alone will not suffice if the power system is to reach its full entitlement in stability and reliability. It is necessary to enhance predictability with "faster than real-time" dynamic simulations that will enable the dynamic stability margins, proactive real-time control, and improve gridmore » resiliency to fast time-scale phenomena such as cascading network failures. Present-day dynamic simulations are performed only during offline planning studies, considering only worst case conditions such as summer peak, winter peak days, etc. With widespread deployment of renewable generation, controllable loads, energy storage devices and plug-in hybrid electric vehicles expected in the near future and greater integration of cyber infrastructure (communications, computation and control), monitoring and controlling the dynamic performance of the grid in real-time would become increasingly important. The state-of-the-art dynamic simulation tools have limited computational speed and are not suitable for real-time applications, given the large set of contingency conditions to be evaluated. These tools are optimized for best performance of single-processor computers, but the simulation is still several times slower than real-time due to its computational complexity. With recent significant advances in numerical methods and computational hardware, the expectations have been rising towards more efficient and faster techniques to be implemented in power system simulators. This is a natural expectation, given that the core solution algorithms of most commercial simulators were developed decades ago, when High Performance Computing (HPC) resources were not commonly available.« less

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

DOE PAGES

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

2015-11-23

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

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent.

PubMed

Doshi, Urmi; Hamelberg, Donald

2014-04-03

Molecular dynamics simulations can provide valuable atomistic insights into biomolecular function. However, the accuracy of molecular simulations on general-purpose computers depends on the time scale of the events of interest. Advanced simulation methods, such as accelerated molecular dynamics, have shown tremendous promise in sampling the conformational dynamics of biomolecules, where standard molecular dynamics simulations are nonergodic. Here we present a sampling method based on accelerated molecular dynamics in which rotatable dihedral angles and nonbonded interactions are boosted separately. This method (RaMD-db) is a different implementation of the dual-boost accelerated molecular dynamics, introduced earlier. The advantage is that this method speeds up sampling of the conformational space of biomolecules in explicit solvent, as the degrees of freedom most relevant for conformational transitions are accelerated. We tested RaMD-db on one of the most difficult sampling problems - protein folding. Starting from fully extended polypeptide chains, two fast folding α-helical proteins (Trpcage and the double mutant of C-terminal fragment of Villin headpiece) and a designed β-hairpin (Chignolin) were completely folded to their native structures in very short simulation time. Multiple folding/unfolding transitions could be observed in a single trajectory. Our results show that RaMD-db is a promisingly fast and efficient sampling method for conformational transitions in explicit solvent. RaMD-db thus opens new avenues for understanding biomolecular self-assembly and functional dynamics occurring on long time and length scales.

Improved global simulation of groundwater-ecosystem interactions via tight coupling of a dynamic global ecosystem model and a global hydrological model

NASA Astrophysics Data System (ADS)

Braakhekke, Maarten; Rebel, Karin; Dekker, Stefan; Smith, Benjamin; Sutanudjaja, Edwin; van Beek, Rens; van Kampenhout, Leo; Wassen, Martin

2017-04-01

In up to 30% of the global land surface ecosystems are potentially influenced by the presence of a shallow groundwater table. In these regions upward water flux by capillary rise increases soil moisture availability in the root zone, which has a strong effect on evapotranspiration, vegetation dynamics, and fluxes of carbon and nitrogen. Most global hydrological models and several land surface models simulate groundwater table dynamics and their effects on land surface processes. However, these models typically have relatively simplistic representation of vegetation and do not consider changes in vegetation type and structure. Dynamic global vegetation models (DGVMs), describe land surface from an ecological perspective, combining detailed description of vegetation dynamics and structure, and biogeochemical processes and are thus more appropriate to simulate the ecological and biogeochemical effects of groundwater interactions. However, currently virtually all DGVMs ignore these effects, assuming that water tables are too deep to affect soil moisture in the root zone. We have implemented a tight coupling between the dynamic global ecosystem model LPJ-GUESS and the global hydrological model PCR-GLOBWB, which explicitly simulates groundwater dynamics. This coupled model allows us to explicitly account for groundwater effects on terrestrial ecosystem processes at global scale. Results of global simulations indicate that groundwater strongly influences fluxes of water, carbon and nitrogen, in many regions, adding up to a considerable effect at the global scale.

Generation of Simulated Tracking Data for LADEE Operational Readiness Testing

NASA Technical Reports Server (NTRS)

Woodburn, James; Policastri, Lisa; Owens, Brandon

2015-01-01

Operational Readiness Tests were an important part of the pre-launch preparation for the LADEE mission. The generation of simulated tracking data to stress the Flight Dynamics System and the Flight Dynamics Team was important for satisfying the testing goal of demonstrating that the software and the team were ready to fly the operational mission. The simulated tracking was generated in a manner to incorporate the effects of errors in the baseline dynamical model, errors in maneuver execution and phenomenology associated with various tracking system based components. The ability of the mission team to overcome these challenges in a realistic flight dynamics scenario indicated that the team and flight dynamics system were ready to fly the LADEE mission. Lunar Atmosphere and Dust Environment.

Dynamic analysis of astronaut motions in microgravity: Applications for Extravehicular Activity (EVA)

NASA Technical Reports Server (NTRS)

Newman, Dava J.

1995-01-01

Simulations of astronaut motions during extravehicular activity (EVA) tasks were performed using computational multibody dynamics methods. The application of computational dynamic simulation to EVA was prompted by the realization that physical microgravity simulators have inherent limitations: viscosity in neutral buoyancy tanks; friction in air bearing floors; short duration for parabolic aircraft; and inertia and friction in suspension mechanisms. These limitations can mask critical dynamic effects that later cause problems during actual EVA's performed in space. Methods of formulating dynamic equations of motion for multibody systems are discussed with emphasis on Kane's method, which forms the basis of the simulations presented herein. Formulation of the equations of motion for a two degree of freedom arm is presented as an explicit example. The four basic steps in creating the computational simulations were: system description, in which the geometry, mass properties, and interconnection of system bodies are input to the computer; equation formulation based on the system description; inverse kinematics, in which the angles, velocities, and accelerations of joints are calculated for prescribed motion of the endpoint (hand) of the arm; and inverse dynamics, in which joint torques are calculated for a prescribed motion. A graphical animation and data plotting program, EVADS (EVA Dynamics Simulation), was developed and used to analyze the results of the simulations that were performed on a Silicon Graphics Indigo2 computer. EVA tasks involving manipulation of the Spartan 204 free flying astronomy payload, as performed during Space Shuttle mission STS-63 (February 1995), served as the subject for two dynamic simulations. An EVA crewmember was modeled as a seven segment system with an eighth segment representing the massive payload attached to the hand. For both simulations, the initial configuration of the lower body (trunk, upper leg, and lower leg) was a neutral microgravity posture. In the first simulation, the payload was manipulated around a circular trajectory of 0.15 m radius in 10 seconds. It was found that the wrist joint theoretically exceeded its ulnal deviation limit by as much as 49. 8 deg and was required to exert torques as high as 26 N-m to accomplish the task, well in excess of the wrist physiological limit of 12 N-m. The largest torque in the first simulation, 52 N-m, occurred in the ankle joint. To avoid these problems, the second simulation placed the arm in a more comfortable initial position and the radius and speed of the circular trajectory were reduced by half. As a result, the joint angles and torques were reduced to values well within their physiological limits. In particular, the maximum wrist torque for the second simulation was only 3 N-m and the maximum ankle torque was only 6 N-m.

Dynamics of the GB3 loop regions from MD simulation: how much of it is real?

PubMed

Li, Tong; Jing, Qingqing; Yao, Lishan

2011-04-07

A total of 1.1 μs of molecular dynamics (MD) simulations were performed to study the structure and dynamics of protein GB3. The simulation motional amplitude of the loop regions is generally overestimated in comparison with the experimental backbone N-H order parameters S(2). Two-state behavior is observed for several residues in these regions, with the minor state population in the range of 3-13%. Further inspection suggests that the (φ, ψ) dihedral angles of the minor states deviate from the GB3 experimental values, implying the existence of nonnative states. After fitting the MD trajectories of these residues to the NMR RDCs, the minor state populations are significantly reduced by at least 80%, suggesting that MD simulations are strongly biased toward the minor states, thus overestimating the dynamics of the loop regions. The optimized trajectories produce intra, sequential H(N)-H(α) RDCs and intra (3)J(HNHα) that are not included in the trajectories fitting for these residues that are closer to the experimental data. Unlike GB3, 0.55 μs MD simulations of protein ubiquitin do not show distinctive minor states, and the derived NMR order parameters are better converged. Our findings indicate that the artifacts of the simulations depend on the specific system studied and that one should be cautious interpreting the enhanced dihedral dynamics from long MD simulations.

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

PubMed Central

Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations.

PubMed

Ahlstrom, Logan S; Vorontsov, Ivan I; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

PubMed Central

Caulfield, Thomas R.; Devkota, Batsal; Rollins, Geoffrey C.

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16. PMID:21716650

Dynamic modeling method for infrared smoke based on enhanced discrete phase model

NASA Astrophysics Data System (ADS)

Zhang, Zhendong; Yang, Chunling; Zhang, Yan; Zhu, Hongbo

2018-03-01

The dynamic modeling of infrared (IR) smoke plays an important role in IR scene simulation systems and its accuracy directly influences the system veracity. However, current IR smoke models cannot provide high veracity, because certain physical characteristics are frequently ignored in fluid simulation; simplifying the discrete phase as a continuous phase and ignoring the IR decoy missile-body spinning. To address this defect, this paper proposes a dynamic modeling method for IR smoke, based on an enhanced discrete phase model (DPM). A mathematical simulation model based on an enhanced DPM is built and a dynamic computing fluid mesh is generated. The dynamic model of IR smoke is then established using an extended equivalent-blackbody-molecule model. Experiments demonstrate that this model realizes a dynamic method for modeling IR smoke with higher veracity.

Force and Moment Approach for Achievable Dynamics Using Nonlinear Dynamic Inversion

NASA Technical Reports Server (NTRS)

Ostroff, Aaron J.; Bacon, Barton J.

1999-01-01

This paper describes a general form of nonlinear dynamic inversion control for use in a generic nonlinear simulation to evaluate candidate augmented aircraft dynamics. The implementation is specifically tailored to the task of quickly assessing an aircraft's control power requirements and defining the achievable dynamic set. The achievable set is evaluated while undergoing complex mission maneuvers, and perfect tracking will be accomplished when the desired dynamics are achievable. Variables are extracted directly from the simulation model each iteration, so robustness is not an issue. Included in this paper is a description of the implementation of the forces and moments from simulation variables, the calculation of control effectiveness coefficients, methods for implementing different types of aerodynamic and thrust vectoring controls, adjustments for control effector failures, and the allocation approach used. A few examples illustrate the perfect tracking results obtained.

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.

III-Nitride, SiC and Diamond Materials for Electronic Devices. Symposium Held April 8-12 1996, San Francisco, California, U.S.A. Volume 423.

DTIC Science & Technology

1996-12-01

gallium, nitrogen and gallium nitride structures. Thus it can be shown to be transferable and efficient for predictive molecular -dynamic simulations on...potentials and forces for the molecular dynamics simulations are derived by means of a density-functional based nonorthogonal tight-binding (DF-TB) scheme...LDA). Molecular -dynamics simulations for determining the different reconstructions of the SiC surface use the slab method (two-dimensional periodic

Molecular dynamics simulation of β₂-microglobulin in denaturing and stabilizing conditions.

PubMed

Fogolari, Federico; Corazza, Alessandra; Varini, Nicola; Rotter, Matteo; Gumral, Devrim; Codutti, Luca; Rennella, Enrico; Viglino, Paolo; Bellotti, Vittorio; Esposito, Gennaro

2011-03-01

β₂-Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of β₂-microglobulin structure, dynamics, and thermodynamics in solution, at atomic detail, along the pathway leading to fibril formation is difficult because the onset of disorder and aggregation prevents signal resolution in Nuclear Magnetic Resonance experiments. Moreover, it is difficult to characterize conformers in exchange equilibrium. To gain insight (at atomic level) on processes for which experimental information is available at molecular or supramolecular level, molecular dynamics simulations have been widely used in the last decade. Here, we use molecular dynamics to address three key aspects of β₂-microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of β₂-microglobulin in trifluoroethanol and in conditions mimicking low pH are used to study the behavior of the protein in environmental conditions that are able to trigger amyloid formation; (2) adaptive biasing force molecular dynamics simulation is used to force cis-trans isomerization at Proline 32 and to calculate the relative free energy in the folded and unfolded state. The native-like trans-conformer (known as intermediate 2 and determining the slow phase of refolding), is simulated for 10 ns, detailing the possible link between cis-trans isomerization and conformational disorder; (3) molecular dynamics simulation of highly concentrated doxycycline (a molecule able to suppress fibril formation) in the presence of β₂-microglobulin provides details of the binding modes of the drug and a rationale for its effect. Copyright © 2010 Wiley-Liss, Inc.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations.

PubMed

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric

2016-10-21

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na + , K + , and Cl - ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

Protein dynamics and enzyme catalysis: insights from simulations.

PubMed

McGeagh, John D; Ranaghan, Kara E; Mulholland, Adrian J

2011-08-01

The role of protein dynamics in enzyme catalysis is one of the most active and controversial areas in enzymology today. Some researchers claim that protein dynamics are at the heart of enzyme catalytic efficiency, while others state that dynamics make no significant contribution to catalysis. What is the biochemist - or student - to make of the ferocious arguments in this area? Protein dynamics are complex and fascinating, as molecular dynamics simulations and experiments have shown. The essential question is: do these complex motions have functional significance? In particular, how do they affect or relate to chemical reactions within enzymes, and how are chemical and conformational changes coupled together? Biomolecular simulations can analyse enzyme reactions and dynamics in atomic detail, beyond that achievable in experiments: accurate atomistic modelling has an essential part to play in clarifying these issues. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches. Copyright © 2010 Elsevier B.V. All rights reserved.

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

Architectural Improvements and New Processing Tools for the Open XAL Online Model

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

Allen, Christopher K; Pelaia II, Tom; Freed, Jonathan M

The online model is the component of Open XAL providing accelerator modeling, simulation, and dynamic synchronization to live hardware. Significant architectural changes and feature additions have been recently made in two separate areas: 1) the managing and processing of simulation data, and 2) the modeling of RF cavities. Simulation data and data processing have been completely decoupled. A single class manages all simulation data while standard tools were developed for processing the simulation results. RF accelerating cavities are now modeled as composite structures where parameter and dynamics computations are distributed. The beam and hardware models both maintain their relative phasemore » information, which allows for dynamic phase slip and elapsed time computation.« less

Direct Quantum Dynamics Using Grid-Based Wave Function Propagation and Machine-Learned Potential Energy Surfaces.

PubMed

Richings, Gareth W; Habershon, Scott

2017-09-12

We describe a method for performing nuclear quantum dynamics calculations using standard, grid-based algorithms, including the multiconfiguration time-dependent Hartree (MCTDH) method, where the potential energy surface (PES) is calculated "on-the-fly". The method of Gaussian process regression (GPR) is used to construct a global representation of the PES using values of the energy at points distributed in molecular configuration space during the course of the wavepacket propagation. We demonstrate this direct dynamics approach for both an analytical PES function describing 3-dimensional proton transfer dynamics in malonaldehyde and for 2- and 6-dimensional quantum dynamics simulations of proton transfer in salicylaldimine. In the case of salicylaldimine we also perform calculations in which the PES is constructed using Hartree-Fock calculations through an interface to an ab initio electronic structure code. In all cases, the results of the quantum dynamics simulations are in excellent agreement with previous simulations of both systems yet do not require prior fitting of a PES at any stage. Our approach (implemented in a development version of the Quantics package) opens a route to performing accurate quantum dynamics simulations via wave function propagation of many-dimensional molecular systems in a direct and efficient manner.

Molecular Dynamics Simulations and XAFS (MD-XAFS)

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

Schenter, Gregory K.; Fulton, John L.

2017-01-20

MD-XAFS (Molecular Dynamics X-ray Adsorption Fine Structure) makes the connection between simulation techniques that generate an ensemble of molecular configurations and the direct signal observed from X-ray measurement.

Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations.

PubMed

Mori, Yoshiharu; Okamoto, Yuko

2013-02-01

A simulated tempering method, which is referred to as simulated-tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated tempering were performed to study the intramolecular proton transfer reaction of malonaldehyde in an aqueous solution. Conformational sampling in reaction coordinate space can be easily enhanced with this method, and the free energy along a reaction coordinate can be calculated accurately. Moreover, the simulated-tempering umbrella sampling provides trajectory data more efficiently than the conventional umbrella sampling method.

Simulation of cooperating robot manipulators on a mobile platform

NASA Technical Reports Server (NTRS)

Murphy, Steve H.; Wen, John T.; Saridis, George N.

1990-01-01

The dynamic equations of motion for two manipulators holding a common object on a freely moving mobile platform are developed. The full dynamic interactions from arms to platform and arm-tip to arm-tip are included in the formulation. The development of the closed chain dynamics allows for the use of any solution for the open topological tree of base and manipulator links. In particular, because the system has 18 degrees of freedom, recursive solutions for the dynamic simulation become more promising for efficient calculations of the motion. Simulation of the system is accomplished through a MATLAB program, and the response is visualized graphically using the SILMA Cimstation.

Peculiarities of Vibration Characteristics of Amorphous Ices

NASA Astrophysics Data System (ADS)

Gets, Kirill V.; Subbotin, Oleg S.; Belosludov, Vladimir R.

2012-03-01

Dynamic properties of low (LDA), high (HDA) and very high (VHDA) density amorphous ices were investigated within the approach based on Lattice Dynamics simulations. In this approach, we assume that the short-range molecular order mainly determines the dynamic and thermodynamic properties of amorphous ices. Simulation cell of 512 water molecules with periodical boundary conditions and disordering allows us to study dynamical properties and dispersion curves in the Brillouin zone of pseudo-crystal. Existence of collective phenomena in amorphous ices which is usual for crystals but anomalous for disordered phase was confirmed in our simulations. Molecule amplitudes of delocalized (collective) as well as localized vibrations have been considered.

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.

Longitudinal train dynamics: an overview

NASA Astrophysics Data System (ADS)

Wu, Qing; Spiryagin, Maksym; Cole, Colin

2016-12-01

This paper discusses the evolution of longitudinal train dynamics (LTD) simulations, which covers numerical solvers, vehicle connection systems, air brake systems, wagon dumper systems and locomotives, resistance forces and gravitational components, vehicle in-train instabilities, and computing schemes. A number of potential research topics are suggested, such as modelling of friction, polymer, and transition characteristics for vehicle connection simulations, studies of wagon dumping operations, proper modelling of vehicle in-train instabilities, and computing schemes for LTD simulations. Evidence shows that LTD simulations have evolved with computing capabilities. Currently, advanced component models that directly describe the working principles of the operation of air brake systems, vehicle connection systems, and traction systems are available. Parallel computing is a good solution to combine and simulate all these advanced models. Parallel computing can also be used to conduct three-dimensional long train dynamics simulations.

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.

A mathematical simulation model of the CH-47B helicopter, volume 2

NASA Technical Reports Server (NTRS)

Weber, J. M.; Liu, T. Y.; Chung, W.

1984-01-01

A nonlinear simulation model of the CH-47B helicopter, was adapted for use in a simulation facility. The model represents the specific configuration of the variable stability CH-47B helicopter. Modeling of the helicopter uses a total force approach in six rigid body degrees of freedom. Rotor dynamics are simulated using the Wheatley-Bailey equations, steady state flapping dynamics and included in the model of the option for simulation of external suspension, slung load equations of motion. Validation of the model was accomplished by static and dynamic data from the original Boeing Vertol mathematical model and flight test data. The model is appropriate for use in real time piloted simulation and is implemented on the ARC Sigma IX computer where it may be operated with a digital cycle time of 0.03 sec.

The response of vegetation distribution, ecosystem productivity, and fire in California to future climate scenarios simulated by the MC1 dynamic vegetation dynamic.

Treesearch

James M. Lenihan; Dominique Bachelet; Raymond Drapek; Ronald P. Neilson

2006-01-01

The objective of this study was to dynamically simulate the response of vegetation distribution, carbon, and fire to three scenarios of future climate change for California using the MAPSS-CENTURY (MCI) dynamic general vegetation model. Under all three scenarios, Alpine/Subalpine Forest cover declined with increased growing season length and warmth, and increases in...

Analysis, modeling, and simulation (AMS) testbed development and evaluation to support dynamic mobility applications (DMA) and active transportation and demand management (ATDM) programs — evaluation summary for ATDM program.

DOT National Transportation Integrated Search

2017-07-04

The primary objective of this project is to develop multiple simulation testbeds/transportation models to evaluate the impacts of Dynamic Mobility Application (DMA) connected vehicle applications and Active Transportation and Dynamic management (ATDM...

Short-Range Order and Collective Dynamics of DMPC Bilayers: A Comparison between Molecular Dynamics Simulations, X-Ray, and Neutron Scattering Experiments

PubMed Central

Hub, Jochen S.; Salditt, Tim; Rheinstädter, Maikel C.; de Groot, Bert L.

2007-01-01

We present an extensive comparison of short-range order and short wavelength dynamics of a hydrated phospholipid bilayer derived by molecular dynamics simulations, elastic x-ray, and inelastic neutron scattering experiments. The quantities that are compared between simulation and experiment include static and dynamic structure factors, reciprocal space mappings, and electron density profiles. We show that the simultaneous use of molecular dynamics and diffraction data can help to extract real space properties like the area per lipid and the lipid chain ordering from experimental data. In addition, we assert that the interchain distance can be computed to high accuracy from the interchain correlation peak of the structure factor. Moreover, it is found that the position of the interchain correlation peak is not affected by the area per lipid, while its correlation length decreases linearly with the area per lipid. This finding allows us to relate a property of the structure factor quantitatively to the area per lipid. Finally, the short wavelength dynamics obtained from the simulations and from inelastic neutron scattering are analyzed and compared. The conventional interpretation in terms of the three-effective-eigenmode model is found to be only partly suitable to describe the complex fluid dynamics of lipid chains. PMID:17631531

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

PubMed

Jamroz, Michal; Orozco, Modesto; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-08

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.

SSEM: A model for simulating runoff and erosion of saline-sodic soil slopes under coastal reclamation

NASA Astrophysics Data System (ADS)

Liu, Dongdong; She, Dongli

2018-06-01

Current physically based erosion models do not carefully consider the dynamic variations of soil properties during rainfall and are unable to simulate saline-sodic soil slope erosion processes. The aim of this work was to build upon a complete model framework, SSEM, to simulate runoff and erosion processes for saline-sodic soils by coupling dynamic saturated hydraulic conductivity Ks and soil erodibility Kτ. Sixty rainfall simulation rainfall experiments (2 soil textures × 5 sodicity levels × 2 slope gradients × 3 duplicates) provided data for model calibration and validation. SSEM worked very well for simulating the runoff and erosion processes of saline-sodic silty clay. The runoff and erosion processes of saline-sodic silt loam were more complex than those of non-saline soils or soils with higher clay contents; thus, SSEM did not perform very well for some validation events. We further examined the model performances of four concepts: Dynamic Ks and Kτ (Case 1, SSEM), Dynamic Ks and Constant Kτ (Case 2), Constant Ks and Dynamic Kτ (Case 3) and Constant Ks and Constant Kτ (Case 4). The results demonstrated that the model, which considers dynamic variations in soil saturated hydraulic conductivity and soil erodibility, can provide more reasonable runoff and erosion prediction results for saline-sodic soils.

Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks.

PubMed

Cazade, Pierre-André; Berezovska, Ganna; Meuwly, Markus

2015-05-01

The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled. All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics. Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites. Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion. Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation

NASA Astrophysics Data System (ADS)

Hudson, Brian D.; George, Ashley R.; Ford, Martyn G.; Livingstone, David J.

1992-04-01

Molecular dynamics simulations have been performed on a number of conformationally flexible pyrethroid insecticides. The results indicate that molecular dynamics is a suitable tool for conformational searching of small molecules given suitable simulation parameters. The structures derived from the simulations are compared with the static conformation used in a previous study. Various physicochemical parameters have been calculated for a set of conformations selected from the simulations using multivariate analysis. The averaged values of the parameters over the selected set (and the factors derived from them) are compared with the single conformation values used in the previous study.

Emulation of rocket trajectory based on a six degree of freedom model

NASA Astrophysics Data System (ADS)

Zhang, Wenpeng; Li, Fan; Wu, Zhong; Li, Rong

2008-10-01

In this paper, a 6-DOF motion mathematical model is discussed. It is consisted of body dynamics and kinematics block, aero dynamics block and atmosphere block. Based on Simulink, the whole rocket trajectory mathematical model is developed. In this model, dynamic system simulation becomes easy and visual. The method of modularization design gives more convenience to transplant. At last, relevant data is given to be validated by Monte Carlo means. Simulation results show that the flight trajectory of the rocket can be simulated preferably by means of this model, and it also supplies a necessary simulating tool for the development of control system.

Finite-element approach to Brownian dynamics of polymers.

PubMed

Cyron, Christian J; Wall, Wolfgang A

2009-12-01

In the last decades simulation tools for Brownian dynamics of polymers have attracted more and more interest. Such simulation tools have been applied to a large variety of problems and accelerated the scientific progress significantly. However, the currently most frequently used explicit bead models exhibit severe limitations, especially with respect to time step size, the necessity of artificial constraints and the lack of a sound mathematical foundation. Here we present a framework for simulations of Brownian polymer dynamics based on the finite-element method. This approach allows simulating a wide range of physical phenomena at a highly attractive computational cost on the basis of a far-developed mathematical background.

ML-Space: Hybrid Spatial Gillespie and Particle Simulation of Multi-Level Rule-Based Models in Cell Biology.

PubMed

Bittig, Arne T; Uhrmacher, Adelinde M

2017-01-01

Spatio-temporal dynamics of cellular processes can be simulated at different levels of detail, from (deterministic) partial differential equations via the spatial Stochastic Simulation algorithm to tracking Brownian trajectories of individual particles. We present a spatial simulation approach for multi-level rule-based models, which includes dynamically hierarchically nested cellular compartments and entities. Our approach ML-Space combines discrete compartmental dynamics, stochastic spatial approaches in discrete space, and particles moving in continuous space. The rule-based specification language of ML-Space supports concise and compact descriptions of models and to adapt the spatial resolution of models easily.

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.

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.

Simulation Analysis of Helicopter Ground Resonance Nonlinear Dynamics

NASA Astrophysics Data System (ADS)

Zhu, Yan; Lu, Yu-hui; Ling, Ai-min

2017-07-01

In order to accurately predict the dynamic instability of helicopter ground resonance, a modeling and simulation method of helicopter ground resonance considering nonlinear dynamic characteristics of components (rotor lead-lag damper, landing gear wheel and absorber) is presented. The numerical integral method is used to calculate the transient responses of the body and rotor, simulating some disturbance. To obtain quantitative instabilities, Fast Fourier Transform (FFT) is conducted to estimate the modal frequencies, and the mobile rectangular window method is employed in the predictions of the modal damping in terms of the response time history. Simulation results show that ground resonance simulation test can exactly lead up the blade lead-lag regressing mode frequency, and the modal damping obtained according to attenuation curves are close to the test results. The simulation test results are in accordance with the actual accident situation, and prove the correctness of the simulation method. This analysis method used for ground resonance simulation test can give out the results according with real helicopter engineering tests.

Dynamic Hybrid Simulation of the Lunar Wake During ARTEMIS Crossing

NASA Astrophysics Data System (ADS)

Wiehle, S.; Plaschke, F.; Angelopoulos, V.; Auster, H.; Glassmeier, K.; Kriegel, H.; Motschmann, U. M.; Mueller, J.

2010-12-01

The interaction of the highly dynamic solar wind with the Moon is simulated with the A.I.K.E.F. (Adaptive Ion Kinetic Electron Fluid) code for the ARTEMIS P1 flyby on February 13, 2010. The A.I.K.E.F. hybrid plasma simulation code is the improved version of the Braunschweig code. It is able to automatically increase simulation grid resolution in areas of interest during runtime, which greatly increases resolution as well as performance. As the Moon has no intrinsic magnetic field and no ionosphere, the solar wind particles are absorbed at its surface, resulting in the formation of the lunar wake at the nightside. The solar wind magnetic field is basically convected through the Moon and the wake is slowly filled up with solar wind particles. However, this interaction is strongly influenced by the highly dynamic solar wind during the flyby. This is considered by a dynamic variation of the upstream conditions in the simulation using OMNI solar wind measurement data. By this method, a very good agreement between simulation and observations is achieved. The simulations show that the stationary structure of the lunar wake constitutes a tableau vivant in space representing the well-known Friedrichs diagram for MHD waves.

Solar Potential Analysis and Integration of the Time-Dependent Simulation Results for Semantic 3d City Models Using Dynamizers

NASA Astrophysics Data System (ADS)

Chaturvedi, K.; Willenborg, B.; Sindram, M.; Kolbe, T. H.

2017-10-01

Semantic 3D city models play an important role in solving complex real-world problems and are being adopted by many cities around the world. A wide range of application and simulation scenarios directly benefit from the adoption of international standards such as CityGML. However, most of the simulations involve properties, whose values vary with respect to time, and the current generation semantic 3D city models do not support time-dependent properties explicitly. In this paper, the details of solar potential simulations are provided operating on the CityGML standard, assessing and estimating solar energy production for the roofs and facades of the 3D building objects in different ways. Furthermore, the paper demonstrates how the time-dependent simulation results are better-represented inline within 3D city models utilizing the so-called Dynamizer concept. This concept not only allows representing the simulation results in standardized ways, but also delivers a method to enhance static city models by such dynamic property values making the city models truly dynamic. The dynamizer concept has been implemented as an Application Domain Extension of the CityGML standard within the OGC Future City Pilot Phase 1. The results are given in this paper.

Dynamical diagnostics of the SST annual cycle in the eastern equatorial Pacific: Part II analysis of CMIP5 simulations

NASA Astrophysics Data System (ADS)

Chen, Ying-Ying; Jin, Fei-Fei

2017-12-01

In this study, a simple coupled framework established in Part I is utilized to investigate inter-model diversity in simulating the equatorial Pacific SST annual cycle (SSTAC). It demonstrates that the simulated amplitude and phase characteristics of SSTAC in models are controlled by two internal dynamical factors (the damping rate and phase speed) and two external forcing factors (the strength of the annual and semi-annual harmonic forcing). These four diagnostic factors are further condensed into a dynamical response factor and a forcing factor to derive theoretical solutions of amplitude and phase of SSTAC. The theoretical solutions are in remarkable agreement with observations and CMIP5 simulations. The great diversity in the simulated SSTACs is related to the spreads in these dynamic and forcing factors. Most models tend to simulate a weak SSTAC, due to their weak damping rate and annual harmonic forcing. The latter is due to bias in the meridional asymmetry of the annual mean state of the tropical Pacific, represented by the weak cross-equatorial winds in the cold tongue region.

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations.

PubMed

Sinko, William; de Oliveira, César Augusto F; Pierce, Levi C T; McCammon, J Andrew

2012-01-10

Molecular dynamics (MD) is one of the most common tools in computational chemistry. Recently, our group has employed accelerated molecular dynamics (aMD) to improve the conformational sampling over conventional molecular dynamics techniques. In the original aMD implementation, sampling is greatly improved by raising energy wells below a predefined energy level. Recently, our group presented an alternative aMD implementation where simulations are accelerated by lowering energy barriers of the potential energy surface. When coupled with thermodynamic integration simulations, this implementation showed very promising results. However, when applied to large systems, such as proteins, the simulation tends to be biased to high energy regions of the potential landscape. The reason for this behavior lies in the boost equation used since the highest energy barriers are dramatically more affected than the lower ones. To address this issue, in this work, we present a new boost equation that prevents oversampling of unfavorable high energy conformational states. The new boost potential provides not only better recovery of statistics throughout the simulation but also enhanced sampling of statistically relevant regions in explicit solvent MD simulations.

Genetic Algorithms and Their Application to the Protein Folding Problem

DTIC Science & Technology

1993-12-01

and symbolic methods, random methods such as Monte Carlo simulation and simulated annealing, distance geometry, and molecular dynamics. Many of these...calculated energies with those obtained using the molecular simulation software package called CHARMm. 10 9) Test both the simple and parallel simpie genetic...homology-based, and simplification techniques. 3.21 Molecular Dynamics. Perhaps the most natural approach is to actually simulate the folding process. This

Virtual Habitat -a Dynamic Simulation of Closed Life Support Systems -Overall Status and Outlook

NASA Astrophysics Data System (ADS)

Zhukov, Anton; Schnaitmann, Jonas; Mecsaci, Ahmad; Bickel, Thomas; Markus Czupalla, M. Sc.

In order to optimize Life Support Systems (LSS) on a system level, stability questions and closure grade must be investigated. To do so the exploration group of the Technical University of Munich (TUM) is developing the "Virtual Habitat" (V-HAB) dynamic LSS simulation software. The main advantages of the dynamic simulation of LSS within V-HAB are the possibilities to compose different LSS configurations from the LSS subsystems and conduct dynamic simulation of it to test its stability in different mission scenarios inclusive emergency events and define the closure grade of the LSS. Additional the optimization of LSS based on different criteria will be possible. The Virtual Habitat simulation tool consists of four main modules: • Closed Environment Module (CEM) -monitoring of compounds in a closed environment • Crew Module (CM) -dynamic human simulation • P/C Systems Module (PCSM) -dynamic P/C subsystems • Plant Module (PM) -dynamic plant simulation Since the first idea and version, the V-HAB simulation has been significantly updated increasing its capabilities and maturity significantly. The updates which shall be introduced concern all modules of V-HAB. In particular: Significant progress has been made in development of the human model. In addition to the exist-ing human sub-models three newly developed ones (thermal regulation, digestion and schedule controller) have been introduced and shall be presented. Regarding the Plant Module a wheat plant model has been integrated in the V-HAB and is being correlated against test data. Ad-ditionally a first version of the algae bioreactor model has been developed and integrated. In terms of the P/C System module, an innovative approach for the P/C subsystem modelling has been developed and applied. The capabilities and features of the improved V-HAB models and the overall functionality of the V-HAB are demonstrated in form of meaningful test cases. In addition to the presentation of the results, the correlation strategy for the Virtual Habitat simulation shall be introduced assessing the models current confidence level and giving an outlook on the future correlation strategy.

The SCEC/USGS dynamic earthquake rupture code verification exercise

USGS Publications Warehouse

Harris, R.A.; Barall, M.; Archuleta, R.; Dunham, E.; Aagaard, Brad T.; Ampuero, J.-P.; Bhat, H.; Cruz-Atienza, Victor M.; Dalguer, L.; Dawson, P.; Day, S.; Duan, B.; Ely, G.; Kaneko, Y.; Kase, Y.; Lapusta, N.; Liu, Yajing; Ma, S.; Oglesby, D.; Olsen, K.; Pitarka, A.; Song, S.; Templeton, E.

2009-01-01

Numerical simulations of earthquake rupture dynamics are now common, yet it has been difficult to test the validity of these simulations because there have been few field observations and no analytic solutions with which to compare the results. This paper describes the Southern California Earthquake Center/U.S. Geological Survey (SCEC/USGS) Dynamic Earthquake Rupture Code Verification Exercise, where codes that simulate spontaneous rupture dynamics in three dimensions are evaluated and the results produced by these codes are compared using Web-based tools. This is the first time that a broad and rigorous examination of numerous spontaneous rupture codes has been performed—a significant advance in this science. The automated process developed to attain this achievement provides for a future where testing of codes is easily accomplished.Scientists who use computer simulations to understand earthquakes utilize a range of techniques. Most of these assume that earthquakes are caused by slip at depth on faults in the Earth, but hereafter the strategies vary. Among the methods used in earthquake mechanics studies are kinematic approaches and dynamic approaches.The kinematic approach uses a computer code that prescribes the spatial and temporal evolution of slip on the causative fault (or faults). These types of simulations are very helpful, especially since they can be used in seismic data inversions to relate the ground motions recorded in the field to slip on the fault(s) at depth. However, these kinematic solutions generally provide no insight into the physics driving the fault slip or information about why the involved fault(s) slipped that much (or that little). In other words, these kinematic solutions may lack information about the physical dynamics of earthquake rupture that will be most helpful in forecasting future events.To help address this issue, some researchers use computer codes to numerically simulate earthquakes and construct dynamic, spontaneous rupture (hereafter called “spontaneous rupture”) solutions. For these types of numerical simulations, rather than prescribing the slip function at each location on the fault(s), just the friction constitutive properties and initial stress conditions are prescribed. The subsequent stresses and fault slip spontaneously evolve over time as part of the elasto-dynamic solution. Therefore, spontaneous rupture computer simulations of earthquakes allow us to include everything that we know, or think that we know, about earthquake dynamics and to test these ideas against earthquake observations.

NetFlow Dynamics

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

Corbet Jr., Thomas F; Beyeler, Walter E; Vanwestrienen, Dirk

NetFlow Dynamics is a web-accessible analysis environment for simulating dynamic flows of materials on model networks. Performing a simulation requires both the NetFlow Dynamics application and a network model which is a description of the structure of the nodes and edges of a network including the flow capacity of each edge and the storage capacity of each node, and the sources and sinks of the material flowing on the network. NetFlow Dynamics consists of databases for storing network models, algorithms to calculate flows on networks, and a GIS-based graphical interface for performing simulations and viewing simulation results. Simulated flows aremore » dynamic in the sense that flows on each edge of the network and inventories at each node change with time and can be out of equilibrium with boundary conditions. Any number of network models could be simulated using Net Flow Dynamics. To date, the models simulated have been models of petroleum infrastructure. The main model has been the National Transportation Fuels Model (NTFM), a network of U.S. oil fields, transmission pipelines, rail lines, refineries, tank farms, and distribution terminals. NetFlow Dynamics supports two different flow algorithms, the Gradient Flow algorithm and the Inventory Control algorithm, that were developed specifically for the NetFlow Dynamics application. The intent is to add additional algorithms in the future as needed. The ability to select from multiple algorithms is desirable because a single algorithm never covers all analysis needs. The current algorithms use a demand-driven capacity-constrained formulation which means that the algorithms strive to use all available capacity and stored inventory to meet desired flows to sinks, subject to the capacity constraints of each network component. The current flow algorithms are best suited for problems in which a material flows on a capacity-constrained network representing a supply chain in which the material supplied can be stored at each node of the network. In the petroleum models, the flowing materials are crude oil and refined products that can be stored at tank farms, refineries, or terminals (i.e. the nodes of the network). Examples of other network models that could be simulated are currency flowing in a financial network, agricultural products moving to market, or natural gas flowing on a pipeline network.« less

A size-composition resolved aerosol model for simulating the dynamics of externally mixed particles: SCRAM (v 1.0)

NASA Astrophysics Data System (ADS)

Zhu, S.; Sartelet, K. N.; Seigneur, C.

2015-06-01

The Size-Composition Resolved Aerosol Model (SCRAM) for simulating the dynamics of externally mixed atmospheric particles is presented. This new model classifies aerosols by both composition and size, based on a comprehensive combination of all chemical species and their mass-fraction sections. All three main processes involved in aerosol dynamics (coagulation, condensation/evaporation and nucleation) are included. The model is first validated by comparison with a reference solution and with results of simulations using internally mixed particles. The degree of mixing of particles is investigated in a box model simulation using data representative of air pollution in Greater Paris. The relative influence on the mixing state of the different aerosol processes (condensation/evaporation, coagulation) and of the algorithm used to model condensation/evaporation (bulk equilibrium, dynamic) is studied.

Comparison of human driver dynamics in simulators with complex and simple visual displays and in an automobile on the road

NASA Technical Reports Server (NTRS)

Mcruer, D. T.; Klein, R. H.

1975-01-01

As part of a comprehensive program exploring driver/vehicle system response in lateral steering tasks, driver/vehicle system describing functions and other dynamic data have been gathered in several milieu. These include a simple fixed base simulator with an elementary roadway delineation only display; a fixed base statically operating automobile with a terrain model based, wide angle projection system display; and a full scale moving base automobile operating on the road. Dynamic data with the two fixed base simulators compared favorably, implying that the impoverished visual scene, lack of engine noise, and simplified steering wheel feel characteristics in the simple simulator did not induce significant driver dynamic behavior variations. The fixed base vs. moving base comparisons showed substantially greater crossover frequencies and phase margins on the road course.

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

PubMed

Bottaro, Sandro; Bussi, Giovanni; Kennedy, Scott D; Turner, Douglas H; Lindorff-Larsen, Kresten

2018-05-01

RNA molecules are key players in numerous cellular processes and are characterized by a complex relationship between structure, dynamics, and function. Despite their apparent simplicity, RNA oligonucleotides are very flexible molecules, and understanding their internal dynamics is particularly challenging using experimental data alone. We show how to reconstruct the conformational ensemble of four RNA tetranucleotides by combining atomistic molecular dynamics simulations with nuclear magnetic resonance spectroscopy data. The goal is achieved by reweighting simulations using a maximum entropy/Bayesian approach. In this way, we overcome problems of current simulation methods, as well as in interpreting ensemble- and time-averaged experimental data. We determine the populations of different conformational states by considering several nuclear magnetic resonance parameters and point toward properties that are not captured by state-of-the-art molecular force fields. Although our approach is applied on a set of model systems, it is fully general and may be used to study the conformational dynamics of flexible biomolecules and to detect inaccuracies in molecular dynamics force fields.

Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange.

PubMed

Kubitzki, Marcus B; de Groot, Bert L

2007-06-15

Today's standard molecular dynamics simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large number of degrees of freedom involved. Aiming at increased sampling efficiency, we present a novel simulation method combining the ideas of essential dynamics and REX. Unlike standard REX, in each replica only a selection of essential collective modes of a subsystem of interest (essential subspace) is coupled to a higher temperature, with the remainder of the system staying at a reference temperature, T(0). This selective excitation along with the replica framework permits efficient approximate ensemble-preserving conformational sampling and allows much larger temperature differences between replicas, thereby considerably enhancing sampling efficiency. Ensemble properties and sampling performance of the method are discussed using dialanine and guanylin test systems, with multi-microsecond molecular dynamics simulations of these test systems serving as references.

Molecular dynamics simulations for mechanical properties of borophene: parameterization of valence force field model and Stillinger-Weber potential

PubMed Central

Zhou, Yu-Ping; Jiang, Jin-Wu

2017-01-01

While most existing theoretical studies on the borophene are based on first-principles calculations, the present work presents molecular dynamics simulations for the lattice dynamical and mechanical properties in borophene. The obtained mechanical quantities are in good agreement with previous first-principles calculations. The key ingredients for these molecular dynamics simulations are the two efficient empirical potentials developed in the present work for the interaction of borophene with low-energy triangular structure. The first one is the valence force field model, which is developed with the assistance of the phonon dispersion of borophene. The valence force field model is a linear potential, so it is rather efficient for the calculation of linear quantities in borophene. The second one is the Stillinger-Weber potential, whose parameters are derived based on the valence force field model. The Stillinger-Weber potential is applicable in molecular dynamics simulations of nonlinear physical or mechanical quantities in borophene. PMID:28349983

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.

PubMed

Karczyńska, Agnieszka S; Czaplewski, Cezary; Krupa, Paweł; Mozolewska, Magdalena A; Joo, Keehyoung; Lee, Jooyoung; Liwo, Adam

2017-12-05

Molecular simulations restrained to single or multiple templates are commonly used in protein-structure modeling. However, the restraints introduce additional barriers, thus impairing the ergodicity of simulations, which can affect the quality of the resulting models. In this work, the effect of restraint types and simulation schemes on ergodicity and model quality was investigated by performing template-restrained canonical molecular dynamics (MD), multiplexed replica-exchange molecular dynamics, and Hamiltonian replica exchange molecular dynamics (HREMD) simulations with the coarse-grained UNRES force field on nine selected proteins, with pseudo-harmonic log-Gaussian (unbounded) or Lorentzian (bounded) restraint functions. The best ergodicity was exhibited by HREMD. It has been found that non-ergodicity does not affect model quality if good templates are used to generate restraints. However, when poor-quality restraints not covering the entire protein are used, the improved ergodicity of HREMD can lead to significantly improved protein models. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

α - synuclein under the magnifying glass. Insights from atomistic and coarse-grain simulations

NASA Astrophysics Data System (ADS)

Ilie, Ioana M.; Nayar, Divya; den Otter, Wouter K.; van der Vegt, Nico F. A.; Briels, Wim J.; University of Twente Collaboration; University of Darmstadt Collaboration

Neurodegenerative diseases are linked to the accumulation of misfolded intrinsically disordered proteins in the brain. Here, we use both all-atom and coarse-grain simulations to explore the intricate dynamics and the aggregation of α-synuclein, the protein implicated in Parkinson's disease. We explore the free energy landscapes of α-synuclein by using Molecular Dynamics simulations and extract information on the structure of the protein as well as on its binding affinities. Next, to study the aggregation, we proceed with representing α-synuclein as a chain of deformable particles that can adapt their geometry, binding affinities and can rearrange into different disordered and ordered structures. We use Brownian Dynamics to simulate the translational and rotational motions of the particles, as well as their interaction properties. The simulations show valuable insight into the internal dynamics of α-synuclein and the formation of ordered and disordered aggregates. In addition, the study is extended to investigate the attachment and folding of a protein to a fiber.

Full Quantum Dynamics Simulation of a Realistic Molecular System Using the Adaptive Time-Dependent Density Matrix Renormalization Group Method.

PubMed

Yao, Yao; Sun, Ke-Wei; Luo, Zhen; Ma, Haibo

2018-01-18

The accurate theoretical interpretation of ultrafast time-resolved spectroscopy experiments relies on full quantum dynamics simulations for the investigated system, which is nevertheless computationally prohibitive for realistic molecular systems with a large number of electronic and/or vibrational degrees of freedom. In this work, we propose a unitary transformation approach for realistic vibronic Hamiltonians, which can be coped with using the adaptive time-dependent density matrix renormalization group (t-DMRG) method to efficiently evolve the nonadiabatic dynamics of a large molecular system. We demonstrate the accuracy and efficiency of this approach with an example of simulating the exciton dissociation process within an oligothiophene/fullerene heterojunction, indicating that t-DMRG can be a promising method for full quantum dynamics simulation in large chemical systems. Moreover, it is also shown that the proper vibronic features in the ultrafast electronic process can be obtained by simulating the two-dimensional (2D) electronic spectrum by virtue of the high computational efficiency of the t-DMRG method.

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms☆

PubMed Central

Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

2016-01-01

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov. PMID:26766517

Improvements in flight table dynamic transparency for hardware-in-the-loop facilities

NASA Astrophysics Data System (ADS)

DeMore, Louis A.; Mackin, Rob; Swamp, Michael; Rusterholtz, Roger

2000-07-01

Flight tables are a 'necessary evil' in the Hardware-In-The- Loop (HWIL) simulation. Adding the actual or prototypic flight hardware to the loop, in order to increase the realism of the simulation, forces us to add motion simulation to the process. Flight table motion bases bring unwanted dynamics, non- linearities, transport delays, etc to an already difficult problem sometimes requiring the simulation engineer to compromise the results. We desire that the flight tables be 'dynamically transparent' to the simulation scenario. This paper presents a State Variable Feedback (SVF) control system architecture with feed-forward techniques that improves the flight table's dynamic transparency by significantly reducing the table's low frequency phase lag. We offer some actual results with existing flight tables that demonstrate the improved transparency. These results come from a demonstration conducted on a flight table in the KHILS laboratory at Eglin AFB and during a refurbishment of a flight table for the Boeing Company of St. Charles, Missouri.

Collective Langevin dynamics of conformational motions in proteins

NASA Astrophysics Data System (ADS)

Lange, Oliver F.; Grubmüller, Helmut

2006-06-01

Functionally relevant slow conformational motions of proteins are, at present, in most cases inaccessible to molecular dynamics (MD) simulations. The main reason is that the major part of the computational effort is spend for the accurate description of a huge number of high frequency motions of the protein and the surrounding solvent. The accumulated influence of these fluctuations is crucial for a correct treatment of the conformational dynamics; however, their details can be considered irrelevant for most purposes. To accurately describe long time protein dynamics we here propose a reduced dimension approach, collective Langevin dynamics (CLD), which evolves the dynamics of the system within a small subspace of relevant collective degrees of freedom. The dynamics within the low-dimensional conformational subspace is evolved via a generalized Langevin equation which accounts for memory effects via memory kernels also extracted from short explicit MD simulations. To determine the memory kernel with differing levels of regularization, we propose and evaluate two methods. As a first test, CLD is applied to describe the conformational motion of the peptide neurotensin. A drastic dimension reduction is achieved by considering one single curved conformational coordinate. CLD yielded accurate thermodynamical and dynamical behaviors. In particular, the rate of transitions between two conformational states agreed well with a rate obtained from a 150ns reference molecular dynamics simulation, despite the fact that the time scale of the transition (˜50ns) was much longer than the 1ns molecular dynamics simulation from which the memory kernel was extracted.

Dynamic and thermodynamic crossover scenarios in the Kob-Andersen mixture: Insights from multi-CPU and multi-GPU simulations.

PubMed

Coslovich, Daniele; Ozawa, Misaki; Kob, Walter

2018-05-17

The physical behavior of glass-forming liquids presents complex features of both dynamic and thermodynamic nature. Some studies indicate the presence of thermodynamic anomalies and of crossovers in the dynamic properties, but their origin and degree of universality is difficult to assess. Moreover, conventional simulations are barely able to cover the range of temperatures at which these crossovers usually occur. To address these issues, we simulate the Kob-Andersen Lennard-Jones mixture using efficient protocols based on multi-CPU and multi-GPU parallel tempering. Our setup enables us to probe the thermodynamics and dynamics of the liquid at equilibrium well below the critical temperature of the mode-coupling theory, [Formula: see text]. We find that below [Formula: see text] the analysis is hampered by partial crystallization of the metastable liquid, which nucleates extended regions populated by large particles arranged in an fcc structure. By filtering out crystalline samples, we reveal that the specific heat grows in a regular manner down to [Formula: see text] . Possible thermodynamic anomalies suggested by previous studies can thus occur only in a region of the phase diagram where the system is highly metastable. Using the equilibrium configurations obtained from the parallel tempering simulations, we perform molecular dynamics and Monte Carlo simulations to probe the equilibrium dynamics down to [Formula: see text]. A temperature-derivative analysis of the relaxation time and diffusion data allows us to assess different dynamic scenarios around [Formula: see text]. Hints of a dynamic crossover come from analysis of the four-point dynamic susceptibility. Finally, we discuss possible future numerical strategies to clarify the nature of crossover phenomena in glass-forming liquids.

VEDA: a web-based virtual environment for dynamic atomic force microscopy.

PubMed

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Invited Article: VEDA: A web-based virtual environment for dynamic atomic force microscopy

NASA Astrophysics Data System (ADS)

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Dynamic Communicability Predicts Infectiousness

NASA Astrophysics Data System (ADS)

Mantzaris, Alexander V.; Higham, Desmond J.

Using real, time-dependent social interaction data, we look at correlations between some recently proposed dynamic centrality measures and summaries from large-scale epidemic simulations. The evolving network arises from email exchanges. The centrality measures, which are relatively inexpensive to compute, assign rankings to individual nodes based on their ability to broadcast information over the dynamic topology. We compare these with node rankings based on infectiousness that arise when a full stochastic SI simulation is performed over the dynamic network. More precisely, we look at the proportion of the network that a node is able to infect over a fixed time period, and the length of time that it takes for a node to infect half the network. We find that the dynamic centrality measures are an excellent, and inexpensive, proxy for the full simulation-based measures.

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

NASA Astrophysics Data System (ADS)

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-01

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics.

PubMed

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-14

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

Computational plasticity algorithm for particle dynamics simulations

NASA Astrophysics Data System (ADS)

Krabbenhoft, K.; Lyamin, A. V.; Vignes, C.

2018-01-01

The problem of particle dynamics simulation is interpreted in the framework of computational plasticity leading to an algorithm which is mathematically indistinguishable from the common implicit scheme widely used in the finite element analysis of elastoplastic boundary value problems. This algorithm provides somewhat of a unification of two particle methods, the discrete element method and the contact dynamics method, which usually are thought of as being quite disparate. In particular, it is shown that the former appears as the special case where the time stepping is explicit while the use of implicit time stepping leads to the kind of schemes usually labelled contact dynamics methods. The framing of particle dynamics simulation within computational plasticity paves the way for new approaches similar (or identical) to those frequently employed in nonlinear finite element analysis. These include mixed implicit-explicit time stepping, dynamic relaxation and domain decomposition schemes.

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.

Hamiltonian quantum simulation with bounded-strength controls

NASA Astrophysics Data System (ADS)

Bookatz, Adam D.; Wocjan, Pawel; Viola, Lorenza

2014-04-01

We propose dynamical control schemes for Hamiltonian simulation in many-body quantum systems that avoid instantaneous control operations and rely solely on realistic bounded-strength control Hamiltonians. Each simulation protocol consists of periodic repetitions of a basic control block, constructed as a modification of an ‘Eulerian decoupling cycle,’ that would otherwise implement a trivial (zero) target Hamiltonian. For an open quantum system coupled to an uncontrollable environment, our approach may be employed to engineer an effective evolution that simulates a target Hamiltonian on the system while suppressing unwanted decoherence to the leading order, thereby allowing for dynamically corrected simulation. We present illustrative applications to both closed- and open-system simulation settings, with emphasis on simulation of non-local (two-body) Hamiltonians using only local (one-body) controls. In particular, we provide simulation schemes applicable to Heisenberg-coupled spin chains exposed to general linear decoherence, and show how to simulate Kitaev's honeycomb lattice Hamiltonian starting from Ising-coupled qubits, as potentially relevant to the dynamical generation of a topologically protected quantum memory. Additional implications for quantum information processing are discussed.

Simulating the effects of the southern pine beetle on regional dynamics 60 years into the future

Treesearch

Jennifer K. Costanza; Jiri Hulcr; Frank H. Koch; Todd Earnhardt; Alexa J. McKerrow; Rob R. Dunn; Jaime A. Collazo

2012-01-01

We developed a spatially explicit model that simulated future southern pine beetle (Dendroctonus frontalis, SPB) dynamics and pine forest management for a real landscape over 60 years to inform regional forest management. The SPB has a considerable effect on forest dynamics in the Southeastern United States, especially in loblolly pine (...

Perceptions of the Effectiveness of System Dynamics-Based Interactive Learning Environments: An Empirical Study

ERIC Educational Resources Information Center

Qudrat-Ullah, Hassan

2010-01-01

The use of simulations in general and of system dynamics simulation based interactive learning environments (SDILEs) in particular is well recognized as an effective way of improving users' decision making and learning in complex, dynamic tasks. However, the effectiveness of SDILEs in classrooms has rarely been evaluated. This article describes…

A large-signal dynamic simulation for the series resonant converter

NASA Technical Reports Server (NTRS)

King, R. J.; Stuart, T. A.

1983-01-01

A simple nonlinear discrete-time dynamic model for the series resonant dc-dc converter is derived using approximations appropriate to most power converters. This model is useful for the dynamic simulation of a series resonant converter using only a desktop calculator. The model is compared with a laboratory converter for a large transient event.

Relaxation dynamics of internal segments of DNA chains in nanochannels

NASA Astrophysics Data System (ADS)

Jain, Aashish; Muralidhar, Abhiram; Dorfman, Kevin; Dorfman Group Team

We will present relaxation dynamics of internal segments of a DNA chain confined in nanochannel. The results have direct application in genome mapping technology, where long DNA molecules containing sequence-specific fluorescent probes are passed through an array of nanochannels to linearize them, and then the distances between these probes (the so-called ``DNA barcode'') are measured. The relaxation dynamics of internal segments set the experimental error due to dynamic fluctuations. We developed a multi-scale simulation algorithm, combining a Pruned-Enriched Rosenbluth Method (PERM) simulation of a discrete wormlike chain model with hard spheres with Brownian dynamics (BD) simulations of a bead-spring chain. Realistic parameters such as the bead friction coefficient and spring force law parameters are obtained from PERM simulations and then mapped onto the bead-spring model. The BD simulations are carried out to obtain the extension autocorrelation functions of various segments, which furnish their relaxation times. Interestingly, we find that (i) corner segments relax faster than the center segments and (ii) relaxation times of corner segments do not depend on the contour length of DNA chain, whereas the relaxation times of center segments increase linearly with DNA chain size.

Control Parameters Optimization Based on Co-Simulation of a Mechatronic System for an UA-Based Two-Axis Inertially Stabilized Platform.

PubMed

Zhou, Xiangyang; Zhao, Beilei; Gong, Guohao

2015-08-14

This paper presents a method based on co-simulation of a mechatronic system to optimize the control parameters of a two-axis inertially stabilized platform system (ISP) applied in an unmanned airship (UA), by which high control performance and reliability of the ISP system are achieved. First, a three-dimensional structural model of the ISP is built by using the three-dimensional parametric CAD software SOLIDWORKS(®); then, to analyze the system's kinematic and dynamic characteristics under operating conditions, dynamics modeling is conducted by using the multi-body dynamics software ADAMS™, thus the main dynamic parameters such as displacement, velocity, acceleration and reaction curve are obtained, respectively, through simulation analysis. Then, those dynamic parameters were input into the established MATLAB(®) SIMULINK(®) controller to simulate and test the performance of the control system. By these means, the ISP control parameters are optimized. To verify the methods, experiments were carried out by applying the optimized parameters to the control system of a two-axis ISP. The results show that the co-simulation by using virtual prototyping (VP) is effective to obtain optimized ISP control parameters, eventually leading to high ISP control performance.

Control Parameters Optimization Based on Co-Simulation of a Mechatronic System for an UA-Based Two-Axis Inertially Stabilized Platform

PubMed Central

Zhou, Xiangyang; Zhao, Beilei; Gong, Guohao

2015-01-01

This paper presents a method based on co-simulation of a mechatronic system to optimize the control parameters of a two-axis inertially stabilized platform system (ISP) applied in an unmanned airship (UA), by which high control performance and reliability of the ISP system are achieved. First, a three-dimensional structural model of the ISP is built by using the three-dimensional parametric CAD software SOLIDWORKS®; then, to analyze the system’s kinematic and dynamic characteristics under operating conditions, dynamics modeling is conducted by using the multi-body dynamics software ADAMS™, thus the main dynamic parameters such as displacement, velocity, acceleration and reaction curve are obtained, respectively, through simulation analysis. Then, those dynamic parameters were input into the established MATLAB® SIMULINK® controller to simulate and test the performance of the control system. By these means, the ISP control parameters are optimized. To verify the methods, experiments were carried out by applying the optimized parameters to the control system of a two-axis ISP. The results show that the co-simulation by using virtual prototyping (VP) is effective to obtain optimized ISP control parameters, eventually leading to high ISP control performance. PMID:26287210

Reaching extended length-scales with temperature-accelerated dynamics

NASA Astrophysics Data System (ADS)

Amar, Jacques G.; Shim, Yunsic

2013-03-01

In temperature-accelerated dynamics (TAD) a high-temperature molecular dynamics (MD) simulation is used to accelerate the search for the next low-temperature activated event. While TAD has been quite successful in extending the time-scales of simulations of non-equilibrium processes, due to the fact that the computational work scales approximately as the cube of the number of atoms, until recently only simulations of relatively small systems have been carried out. Recently, we have shown that by combining spatial decomposition with our synchronous sublattice algorithm, significantly improved scaling is possible. However, in this approach the size of activated events is limited by the processor size while the dynamics is not exact. Here we discuss progress in developing an alternate approach in which high-temperature parallel MD along with localized saddle-point (LSAD) calculations, are used to carry out TAD simulations without restricting the size of activated events while keeping the dynamics ``exact'' within the context of harmonic transition-state theory. In tests of our LSAD method applied to Ag/Ag(100) annealing and Cu/Cu(100) growth simulations we find significantly improved scaling of TAD, while maintaining a negligibly small error in the energy barriers. Supported by NSF DMR-0907399.

A new airborne laser rangefinder dynamic target simulator for non-stationary environment

NASA Astrophysics Data System (ADS)

Ma, Pengge; Pang, Dongdong; Yi, Yang

2017-11-01

For the non-stationary environment simulation in laser range finder product testing, a new dynamic target simulation system is studied. First of all, the three-pulsed laser ranging principle, laser target signal composition and mathematical representation are introduced. Then, the actual nonstationary working environment of laser range finder is analyzed, and points out that the real sunshine background light clutter and target shielding effect in laser echo become the main influencing factors. After that, the dynamic laser target signal simulation method is given. Eventlly, the implementation of automatic test system based on arbitrary waveform generator is described. Practical application shows that the new echo signal automatic test system can simulate the real laser ranging environment of laser range finder, and is suitable for performance test of products.

CABS-flex: Server for fast simulation of protein structure fluctuations.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-07-01

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics--a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions.

Dynamical features and electric field strengths of double layers driven by currents. [in auroras

NASA Technical Reports Server (NTRS)

Singh, N.; Thiemann, H.; Schunk, R. W.

1985-01-01

In recent years, a number of papers have been concerned with 'ion-acoustic' double layers. In the present investigation, results from numerical simulations are presented to show that the shapes and forms of current-driven double layers evolve dynamically with the fluctuations in the current through the plasma. It is shown that double layers with a potential dip can form even without the excitation of ion-acoustic modes. Double layers in two-and one-half-dimensional simulations are discussed, taking into account the simulation technique, the spatial and temporal features of plasma, and the dynamical behavior of the parallel potential distribution. Attention is also given to double layers in one-dimensional simulations, and electrical field strengths predicted by two-and one-half-dimensional simulations.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

Testing the World with Simulations.

ERIC Educational Resources Information Center

Roberts, Nancy

1983-01-01

Explains the three main concepts of the system dynamics approach to model building (dynamics, feedback, and systems) and the basic steps to problem solving by simulation applicable to all educational levels. Some DYNAMO commands are briefly described. (EAO)

Molecular Dynamics Simulations to Clarify the Concentration Dependency of Protein Aggregation

NASA Astrophysics Data System (ADS)

Nishikawa, Naohiro; Sakae, Yoshitake; Okamoto, Yuko

We examined the concentration dependency of amyloid protein aggregation by using several molecular dynamics simulations, which were performed with different concentrations for each system. For these simulations, we used a fragment of amyloid-β, which is believed to be the cause of Alzheimer's disease, as our simulation system. We found that high concentration of amyloid peptides promotes the formation of β-structures which is the origin of amyloid fibrils.

CFD-Based Design of Turbopump Inlet Duct for Reduced Dynamic Loads

NASA Technical Reports Server (NTRS)

Rothermel, Jeffry; Dorney, Suzanne M.; Dorney, Daniel J.

2003-01-01

Numerical simulations have been completed for a variety of designs for a 90 deg elbow duct. The objective is to identify a design that minimizes the dynamic load entering a LOX turbopump located at the elbow exit. Designs simulated to date indicate that simpler duct geometries result in lower losses. Benchmark simulations have verified that the compressible flow codes used in this study are applicable to these incompressible flow simulations.

CFD-based Design of LOX Pump Inlet Duct for Reduced Dynamic Loads

NASA Technical Reports Server (NTRS)

Rothermel, Jeffry; Dorney, Daniel J.; Dorney, Suzanne M.

2003-01-01

Numerical simulations have been completed for a variety of designs for a 90 deg elbow duct. The objective is to identify a design that minimizes the dynamic load entering a LOX turbopump located at the elbow exit. Designs simulated to date indicate that simpler duct geometries result in lower losses. Benchmark simulations have verified that the compressible flow code used in this study is applicable to these incompressible flow simulations.

Longitudinal train dynamics model for a rail transit simulation system

DOE PAGES

Wang, Jinghui; Rakha, Hesham A.

2018-01-01

The paper develops a longitudinal train dynamics model in support of microscopic railway transportation simulation. The model can be calibrated without any mechanical data making it ideal for implementation in transportation simulators. The calibration and validation work is based on data collected from the Portland light rail train fleet. The calibration procedure is mathematically formulated as a constrained non-linear optimization problem. The validity of the model is assessed by comparing instantaneous model predictions against field observations, and also evaluated in the domains of acceleration/deceleration versus speed and acceleration/deceleration versus distance. A test is conducted to investigate the adequacy of themore » model in simulation implementation. The results demonstrate that the proposed model can adequately capture instantaneous train dynamics, and provides good performance in the simulation test. Thus, the model provides a simple theoretical foundation for microscopic simulators and will significantly support the planning, management and control of railway transportation systems.« less

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.

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms

PubMed Central

Stone, John E.; Hynninen, Antti-Pekka; Phillips, James C.; Schulten, Klaus

2017-01-01

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms. PMID:29202130

Self-Organization of Metal Nanoparticles in Light: Electrodynamics-Molecular Dynamics Simulations and Optical Binding Experiments.

PubMed

McCormack, Patrick; Han, Fei; Yan, Zijie

2018-02-01

Light-driven self-organization of metal nanoparticles (NPs) can lead to unique optical matter systems, yet simulation of such self-organization (i.e., optical binding) is a complex computational problem that increases nonlinearly with system size. Here we show that a combined electrodynamics-molecular dynamics simulation technique can simulate the trajectories and predict stable configurations of silver NPs in optical fields. The simulated dynamic equilibrium of a two-NP system matches the probability density of oscillations for two optically bound NPs obtained experimentally. The predicted stable configurations for up to eight NPs are further compared to experimental observations of silver NP clusters formed by optical binding in a Bessel beam. All configurations are confirmed to form in real systems, including pentagonal clusters with five-fold symmetry. Our combined simulations and experiments have revealed a diverse optical matter system formed by anisotropic optical binding interactions, providing a new strategy to discover artificial materials.

Longitudinal train dynamics model for a rail transit simulation system

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

Wang, Jinghui; Rakha, Hesham A.

The paper develops a longitudinal train dynamics model in support of microscopic railway transportation simulation. The model can be calibrated without any mechanical data making it ideal for implementation in transportation simulators. The calibration and validation work is based on data collected from the Portland light rail train fleet. The calibration procedure is mathematically formulated as a constrained non-linear optimization problem. The validity of the model is assessed by comparing instantaneous model predictions against field observations, and also evaluated in the domains of acceleration/deceleration versus speed and acceleration/deceleration versus distance. A test is conducted to investigate the adequacy of themore » model in simulation implementation. The results demonstrate that the proposed model can adequately capture instantaneous train dynamics, and provides good performance in the simulation test. Thus, the model provides a simple theoretical foundation for microscopic simulators and will significantly support the planning, management and control of railway transportation systems.« less

T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges

PubMed Central

2010-01-01

Atomistic Molecular Dynamics provides powerful and flexible tools for the prediction and analysis of molecular and macromolecular systems. Specifically, it provides a means by which we can measure theoretically that which cannot be measured experimentally: the dynamic time-evolution of complex systems comprising atoms and molecules. It is particularly suitable for the simulation and analysis of the otherwise inaccessible details of MHC-peptide interaction and, on a larger scale, the simulation of the immune synapse. Progress has been relatively tentative yet the emergence of truly high-performance computing and the development of coarse-grained simulation now offers us the hope of accurately predicting thermodynamic parameters and of simulating not merely a handful of proteins but larger, longer simulations comprising thousands of protein molecules and the cellular scale structures they form. We exemplify this within the context of immunoinformatics. PMID:21067546

Parallel Simulation of Subsonic Fluid Dynamics on a Cluster of Workstations.

DTIC Science & Technology

1994-11-01

inside wind musical instruments. Typical simulations achieve $80\\%$ parallel efficiency (speedup/processors) using 20 HP-Apollo workstations. Detailed...TERMS AI, MIT, Artificial Intelligence, Distributed Computing, Workstation Cluster, Network, Fluid Dynamics, Musical Instruments 17. SECURITY...for example, the flow of air inside wind musical instruments. Typical simulations achieve 80% parallel efficiency (speedup/processors) using 20 HP

Enhanced sampling techniques in molecular dynamics simulations of biological systems.

PubMed

Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

2015-05-01

Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

Nonlinear absorption dynamics using field-induced surface hopping: zinc porphyrin in water.

PubMed

Röhr, Merle I S; Petersen, Jens; Wohlgemuth, Matthias; Bonačić-Koutecký, Vlasta; Mitrić, Roland

2013-05-10

We wish to present the application of our field-induced surface-hopping (FISH) method to simulate nonlinear absorption dynamics induced by strong nonresonant laser fields. We provide a systematic comparison of the FISH approach with exact quantum dynamics simulations on a multistate model system and demonstrate that FISH allows for accurate simulations of nonlinear excitation processes including multiphoton electronic transitions. In particular, two different approaches for simulating two-photon transitions are compared. The first approach is essentially exact and involves the solution of the time-dependent Schrödinger equation in an extended manifold of excited states, while in the second one only transiently populated nonessential states are replaced by an effective quadratic coupling term, and dynamics is performed in a considerably smaller manifold of states. We illustrate the applicability of our method to complex molecular systems by simulating the linear and nonlinear laser-driven dynamics in zinc (Zn) porphyrin in the gas phase and in water. For this purpose, the FISH approach is connected with the quantum mechanical-molecular mechanical approach (QM/MM) which is generally applicable to large classes of complex systems. Our findings that multiphoton absorption and dynamics increase the population of higher excited states of Zn porphyrin in the nonlinear regime, in particular in solution, provides a means for manipulating excited-state properties, such as transient absorption dynamics and electronic relaxation. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three-dimensional curved grid finite-difference modelling for non-planar rupture dynamics

NASA Astrophysics Data System (ADS)

Zhang, Zhenguo; Zhang, Wei; Chen, Xiaofei

2014-11-01

In this study, we present a new method for simulating the 3-D dynamic rupture process occurring on a non-planar fault. The method is based on the curved-grid finite-difference method (CG-FDM) proposed by Zhang & Chen and Zhang et al. to simulate the propagation of seismic waves in media with arbitrary irregular surface topography. While keeping the advantages of conventional FDM, that is computational efficiency and easy implementation, the CG-FDM also is flexible in modelling the complex fault model by using general curvilinear grids, and thus is able to model the rupture dynamics of a fault with complex geometry, such as oblique dipping fault, non-planar fault, fault with step-over, fault branching, even if irregular topography exists. The accuracy and robustness of this new method have been validated by comparing with the previous results of Day et al., and benchmarks for rupture dynamics simulations. Finally, two simulations of rupture dynamics with complex fault geometry, that is a non-planar fault and a fault rupturing a free surface with topography, are presented. A very interesting phenomenon was observed that topography can weaken the tendency for supershear transition to occur when rupture breaks out at a free surface. Undoubtedly, this new method provides an effective, at least an alternative, tool to simulate the rupture dynamics of a complex non-planar fault, and can be applied to model the rupture dynamics of a real earthquake with complex geometry.

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

PubMed

Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

2004-07-15

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

Biomechanics and muscle coordination of human walking. Part I: introduction to concepts, power transfer, dynamics and simulations.

PubMed

Zajac, Felix E; Neptune, Richard R; Kautz, Steven A

2002-12-01

Current understanding of how muscles coordinate walking in humans is derived from analyses of body motion, ground reaction force and EMG measurements. This is Part I of a two-part review that emphasizes how muscle-driven dynamics-based simulations assist in the understanding of individual muscle function in walking, especially the causal relationships between muscle force generation and walking kinematics and kinetics. Part I reviews the strengths and limitations of Newton-Euler inverse dynamics and dynamical simulations, including the ability of each to find the contributions of individual muscles to the acceleration/deceleration of the body segments. We caution against using the concept of biarticular muscles transferring power from one joint to another to infer muscle coordination principles because energy flow among segments, even the adjacent segments associated with the joints, cannot be inferred from computation of joint powers and segmental angular velocities alone. Rather, we encourage the use of dynamical simulations to perform muscle-induced segmental acceleration and power analyses. Such analyses have shown that the exchange of segmental energy caused by the forces or accelerations induced by a muscle can be fundamentally invariant to whether the muscle is shortening, lengthening, or neither. How simulation analyses lead to understanding the coordination of seated pedaling, rather than walking, is discussed in this first part because the dynamics of pedaling are much simpler, allowing important concepts to be revealed. We elucidate how energy produced by muscles is delivered to the crank through the synergistic action of other non-energy producing muscles; specifically, that a major function performed by a muscle arises from the instantaneous segmental accelerations and redistribution of segmental energy throughout the body caused by its force generation. Part II reviews how dynamical simulations provide insight into muscle coordination of walking.

Direct comparison of elastic incoherent neutron scattering experiments with molecular dynamics simulations of DMPC phase transitions.

PubMed

Aoun, Bachir; Pellegrini, Eric; Trapp, Marcus; Natali, Francesca; Cantù, Laura; Brocca, Paola; Gerelli, Yuri; Demé, Bruno; Marek Koza, Michael; Johnson, Mark; Peters, Judith

2016-04-01

Neutron scattering techniques have been employed to investigate 1,2-dimyristoyl-sn -glycero-3-phosphocholine (DMPC) membranes in the form of multilamellar vesicles (MLVs) and deposited, stacked multilamellar-bilayers (MLBs), covering transitions from the gel to the liquid phase. Neutron diffraction was used to characterise the samples in terms of transition temperatures, whereas elastic incoherent neutron scattering (EINS) demonstrates that the dynamics on the sub-macromolecular length-scale and pico- to nano-second time-scale are correlated with the structural transitions through a discontinuity in the observed elastic intensities and the derived mean square displacements. Molecular dynamics simulations have been performed in parallel focussing on the length-, time- and temperature-scales of the neutron experiments. They correctly reproduce the structural features of the main gel-liquid phase transition. Particular emphasis is placed on the dynamical amplitudes derived from experiment and simulations. Two methods are used to analyse the experimental data and mean square displacements. They agree within a factor of 2 irrespective of the probed time-scale, i.e. the instrument utilized. Mean square displacements computed from simulations show a comparable level of agreement with the experimental values, albeit, the best match with the two methods varies for the two instruments. Consequently, experiments and simulations together give a consistent picture of the structural and dynamical aspects of the main lipid transition and provide a basis for future, theoretical modelling of dynamics and phase behaviour in membranes. The need for more detailed analytical models is pointed out by the remaining variation of the dynamical amplitudes derived in two different ways from experiments on the one hand and simulations on the other.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

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

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Micromagnetic computer simulations of spin waves in nanometre-scale patterned magnetic elements

NASA Astrophysics Data System (ADS)

Kim, Sang-Koog

2010-07-01

Current needs for further advances in the nanotechnologies of information-storage and -processing devices have attracted a great deal of interest in spin (magnetization) dynamics in nanometre-scale patterned magnetic elements. For instance, the unique dynamic characteristics of non-uniform magnetic microstructures such as various types of domain walls, magnetic vortices and antivortices, as well as spin wave dynamics in laterally restricted thin-film geometries, have been at the centre of extensive and intensive researches. Understanding the fundamentals of their unique spin structure as well as their robust and novel dynamic properties allows us to implement new functionalities into existing or future devices. Although experimental tools and theoretical approaches are effective means of understanding the fundamentals of spin dynamics and of gaining new insights into them, the limitations of those same tools and approaches have left gaps of unresolved questions in the pertinent physics. As an alternative, however, micromagnetic modelling and numerical simulation has recently emerged as a powerful tool for the study of a variety of phenomena related to spin dynamics of nanometre-scale magnetic elements. In this review paper, I summarize the recent results of simulations of the excitation and propagation and other novel wave characteristics of spin waves, highlighting how the micromagnetic computer simulation approach contributes to an understanding of spin dynamics of nanomagnetism and considering some of the merits of numerical simulation studies. Many examples of micromagnetic modelling for numerical calculations, employing various dimensions and shapes of patterned magnetic elements, are given. The current limitations of continuum micromagnetic modelling and of simulations based on the Landau-Lifshitz-Gilbert equation of motion of magnetization are also discussed, along with further research directions for spin-wave studies.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE PAGES

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...

2016-10-17

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations.

PubMed

Ollila, O H Samuli; Heikkinen, Harri A; Iwaï, Hideo

2018-06-14

Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.

Use of measurement theory for operationalization and quantification of psychological constructs in systems dynamics modelling

NASA Astrophysics Data System (ADS)

Fitkov-Norris, Elena; Yeghiazarian, Ara

2016-11-01

The analytical tools available to social scientists have traditionally been adapted from tools originally designed for analysis of natural science phenomena. This article discusses the applicability of systems dynamics - a qualitative based modelling approach, as a possible analysis and simulation tool that bridges the gap between social and natural sciences. After a brief overview of the systems dynamics modelling methodology, the advantages as well as limiting factors of systems dynamics to the potential applications in the field of social sciences and human interactions are discussed. The issues arise with regards to operationalization and quantification of latent constructs at the simulation building stage of the systems dynamics methodology and measurement theory is proposed as a ready and waiting solution to the problem of dynamic model calibration, with a view of improving simulation model reliability and validity and encouraging the development of standardised, modular system dynamics models that can be used in social science research.

Large eddy simulation of spanwise rotating turbulent channel flow with dynamic variants of eddy viscosity model

NASA Astrophysics Data System (ADS)

Jiang, Zhou; Xia, Zhenhua; Shi, Yipeng; Chen, Shiyi

2018-04-01

A fully developed spanwise rotating turbulent channel flow has been numerically investigated utilizing large-eddy simulation. Our focus is to assess the performances of the dynamic variants of eddy viscosity models, including dynamic Vreman's model (DVM), dynamic wall adapting local eddy viscosity (DWALE) model, dynamic σ (Dσ ) model, and the dynamic volumetric strain-stretching (DVSS) model, in this canonical flow. The results with dynamic Smagorinsky model (DSM) and direct numerical simulations (DNS) are used as references. Our results show that the DVM has a wrong asymptotic behavior in the near wall region, while the other three models can correctly predict it. In the high rotation case, the DWALE can get reliable mean velocity profile, but the turbulence intensities in the wall-normal and spanwise directions show clear deviations from DNS data. DVSS exhibits poor predictions on both the mean velocity profile and turbulence intensities. In all three cases, Dσ performs the best.

An iterative method for hydrodynamic interactions in Brownian dynamics simulations of polymer dynamics

NASA Astrophysics Data System (ADS)

Miao, Linling; Young, Charles D.; Sing, Charles E.

2017-07-01

Brownian Dynamics (BD) simulations are a standard tool for understanding the dynamics of polymers in and out of equilibrium. Quantitative comparison can be made to rheological measurements of dilute polymer solutions, as well as direct visual observations of fluorescently labeled DNA. The primary computational challenge with BD is the expensive calculation of hydrodynamic interactions (HI), which are necessary to capture physically realistic dynamics. The full HI calculation, performed via a Cholesky decomposition every time step, scales with the length of the polymer as O(N3). This limits the calculation to a few hundred simulated particles. A number of approximations in the literature can lower this scaling to O(N2 - N2.25), and explicit solvent methods scale as O(N); however both incur a significant constant per-time step computational cost. Despite this progress, there remains a need for new or alternative methods of calculating hydrodynamic interactions; large polymer chains or semidilute polymer solutions remain computationally expensive. In this paper, we introduce an alternative method for calculating approximate hydrodynamic interactions. Our method relies on an iterative scheme to establish self-consistency between a hydrodynamic matrix that is averaged over simulation and the hydrodynamic matrix used to run the simulation. Comparison to standard BD simulation and polymer theory results demonstrates that this method quantitatively captures both equilibrium and steady-state dynamics after only a few iterations. The use of an averaged hydrodynamic matrix allows the computationally expensive Brownian noise calculation to be performed infrequently, so that it is no longer the bottleneck of the simulation calculations. We also investigate limitations of this conformational averaging approach in ring polymers.

The Effects of Longitudinal Control-System Dynamics on Pilot Opinion and Response Characteristics as Determined from Flight Tests and from Ground Simulator Studies

NASA Technical Reports Server (NTRS)

Sadoff, Melvin

1958-01-01

The results of a fixed-base simulator study of the effects of variable longitudinal control-system dynamics on pilot opinion are presented and compared with flight-test data. The control-system variables considered in this investigation included stick force per g, time constant, and dead-band, or stabilizer breakout force. In general, the fairly good correlation between flight and simulator results for two pilots demonstrates the validity of fixed-base simulator studies which are designed to complement and supplement flight studies and serve as a guide in control-system preliminary design. However, in the investigation of certain problem areas (e.g., sensitive control-system configurations associated with pilot- induced oscillations in flight), fixed-base simulator results did not predict the occurrence of an instability, although the pilots noted the system was extremely sensitive and unsatisfactory. If it is desired to predict pilot-induced-oscillation tendencies, tests in moving-base simulators may be required. It was found possible to represent the human pilot by a linear pilot analog for the tracking task assumed in the present study. The criterion used to adjust the pilot analog was the root-mean-square tracking error of one of the human pilots on the fixed-base simulator. Matching the tracking error of the pilot analog to that of the human pilot gave an approximation to the variation of human-pilot behavior over a range of control-system dynamics. Results of the pilot-analog study indicated that both for optimized control-system dynamics (for poor airplane dynamics) and for a region of good airplane dynamics, the pilot response characteristics are approximately the same.

Prediction of glass transition temperature of freeze-dried formulations by molecular dynamics simulation.

PubMed

Yoshioka, Sumie; Aso, Yukio; Kojima, Shigeo

2003-06-01

To examine whether the glass transition temperature (Tg) of freeze-dried formulations containing polymer excipients can be accurately predicted by molecular dynamics simulation using software currently available on the market. Molecular dynamics simulations were carried out for isomaltodecaose, a fragment of dextran, and alpha-glucose, the repeated unit of dextran. in the presence or absence of water molecules. Estimated values of Tg were compared with experimental values obtained by differential scanning calorimetry (DSC). Isothermal-isobaric molecular dynamics simulations (NPTMD) and isothermal molecular dynamics simulations at a constant volume (NVTMD) were carried out using the software package DISCOVER (Material Studio) with the Polymer Consortium Force Field. Mean-squared displacement and radial distribution function were calculated. NVTMD using the values of density obtained by NPTMD provided the diffusivity of glucose-ring oxygen and water oxygen in amorphous alpha-glucose and isomaltodecaose, which exhibited a discontinuity in temperature dependence due to glass transition. Tg was estimated to be approximately 400K and 500K for pure amorphous a-glucose and isomaltodecaose, respectively, and in the presence of one water molecule per glucose unit, Tg was 340K and 360K, respectively. Estimated Tg values were higher than experimentally determined values because of the very fast cooling rates in the simulations. However, decreases in Tg on hydration and increases in Tg associated with larger fragment size could be demonstrated. The results indicate that molecular dynamics simulation is a useful method for investigating the effects of hydration and molecular weight on the Tg of lyophilized formulations containing polymer excipients. although the relationship between cooling rates and Tg must first be elucidated to predict Tg vales observed by DSC measurement. January 16.

Validating clustering of molecular dynamics simulations using polymer models.

PubMed

Phillips, Joshua L; Colvin, Michael E; Newsam, Shawn

2011-11-14

Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the first to utilize model polymers to rigorously test the utility of clustering algorithms for studying biopolymers.

Validating clustering of molecular dynamics simulations using polymer models

PubMed Central

2011-01-01

Background Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the first to utilize model polymers to rigorously test the utility of clustering algorithms for studying biopolymers. PMID:22082218

Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

PubMed Central

Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em

2015-01-01

We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers. PMID:26156459

Coupling fast fluid dynamics and multizone airflow models in Modelica Buildings library to simulate the dynamics of HVAC systems

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

Tian, Wei; Sevilla, Thomas Alonso; Zuo, Wangda

Historically, multizone models are widely used in building airflow and energy performance simulations due to their fast computing speed. However, multizone models assume that the air in a room is well mixed, consequently limiting their application. In specific rooms where this assumption fails, the use of computational fluid dynamics (CFD) models may be an alternative option. Previous research has mainly focused on coupling CFD models and multizone models to study airflow in large spaces. While significant, most of these analyses did not consider the coupled simulation of the building airflow with the building's Heating, Ventilation, and Air-Conditioning (HVAC) systems. Thismore » paper tries to fill the gap by integrating the models for HVAC systems with coupled multizone and CFD simulations for airflows, using the Modelica simul ation platform. To improve the computational efficiency, we incorporated a simplified CFD model named fast fluid dynamics (FFD). We first introduce the data synchronization strategy and implementation in Modelica. Then, we verify the implementation using two case studies involving an isothermal and a non-isothermal flow by comparing model simulations to experiment data. Afterward, we study another three cases that are deemed more realistic. This is done by attaching a variable air volume (VAV) terminal box and a VAV system to previous flows to assess the capability of the models in studying the dynamic control of HVAC systems. Finally, we discuss further research needs on the coupled simulation using the models.« less

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.

Simulations of the plasma dynamics in high-current ion diodes

NASA Astrophysics Data System (ADS)

Boine-Frankenheim, O.; Pointon, T. D.; Mehlhorn, T. A.

Our time-implicit fluid/Particle-In-Cell (PIC) code DYNAID [1]is applied to problems relevant for applied- B ion diode operation. We present simulations of the laser ion source, which will soon be employed on the SABRE accelerator at SNL, and of the dynamics of the anode source plasma in the applied electric and magnetic fields. DYNAID is still a test-bed for a higher-dimensional simulation code. Nevertheless, the code can already give new theoretical insight into the dynamics of plasmas in pulsed power devices.

TRACKING SIMULATIONS NEAR HALF-INTEGER RESONANCE AT PEP-II

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

Nosochkov, Yuri

2003-05-13

Beam-beam simulations predict that PEP-II luminosity can be increased by operating the horizontal betatron tune near and above a half-integer resonance. However, effects of the resonance and its synchrotron sidebands significantly enhance betatron and chromatic perturbations which tend to reduce dynamic aperture. In the study, chromatic variation of horizontal tune near the resonance was minimized by optimizing local sextupoles in the Interaction Region. Dynamic aperture was calculated using tracking simulations in LEGO code. Dependence of dynamic aperture on the residual orbit, dispersion and {beta} distortion after correction was investigated.

Numerical simulations of the charged-particle flow dynamics for sources with a curved emission surface

NASA Astrophysics Data System (ADS)

Altsybeyev, V. V.

2016-12-01

The implementation of numerical methods for studying the dynamics of particle flows produced by pulsed sources is discussed. A particle tracking method with so-called gun iteration for simulations of beam dynamics is used. For the space charge limited emission problem, we suggest a Gauss law emission model for precise current-density calculation in the case of a curvilinear emitter. The results of numerical simulations of particle-flow formation for cylindrical bipolar diode and for diode with elliptical emitter are presented.

Substructured multibody molecular dynamics.

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

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James

2006-11-01

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

Non-linear quantum-classical scheme to simulate non-equilibrium strongly correlated fermionic many-body dynamics

PubMed Central

Kreula, J. M.; Clark, S. R.; Jaksch, D.

2016-01-01

We propose a non-linear, hybrid quantum-classical scheme for simulating non-equilibrium dynamics of strongly correlated fermions described by the Hubbard model in a Bethe lattice in the thermodynamic limit. Our scheme implements non-equilibrium dynamical mean field theory (DMFT) and uses a digital quantum simulator to solve a quantum impurity problem whose parameters are iterated to self-consistency via a classically computed feedback loop where quantum gate errors can be partly accounted for. We analyse the performance of the scheme in an example case. PMID:27609673

N-MODY: A Code for Collisionless N-body Simulations in Modified Newtonian Dynamics

NASA Astrophysics Data System (ADS)

Londrillo, Pasquale; Nipoti, Carlo

2011-02-01

N-MODY is a parallel particle-mesh code for collisionless N-body simulations in modified Newtonian dynamics (MOND). N-MODY is based on a numerical potential solver in spherical coordinates that solves the non-linear MOND field equation, and is ideally suited to simulate isolated stellar systems. N-MODY can be used also to compute the MOND potential of arbitrary static density distributions. A few applications of N-MODY indicate that some astrophysically relevant dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter.

Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations

DOE PAGES

Chen, Ying; Bylaska, Eric J.; Weare, John H.

2017-03-31

Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite (α-Fe(OOH). Ab-initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Here, several exchange correlation functionals were employed (PBE96, PBE96+Grimme, and PBE0) in the simulations of a (3 x 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a=30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick).

Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations

PubMed Central

Marino, Kristen A.; Filizola, Marta

2017-01-01

An increasing number of G protein-coupled receptor (GPCR) crystal structures provide important—albeit static—pictures of how small molecules or peptides interact with their receptors. These high-resolution structures represent a tremendous opportunity to apply molecular dynamics (MD) simulations to capture atomic-level dynamical information that is not easy to obtain experimentally. Understanding ligand binding and unbinding processes, as well as the related responses of the receptor, is crucial to the design of better drugs targeting GPCRs. Here, we discuss possible ways to study the dynamics involved in the binding of small molecules to GPCRs, using long timescale MD simulations or metadynamics-based approaches. PMID:29188572

Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations

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

Chen, Ying; Bylaska, Eric J.; Weare, John H.

Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite (α-Fe(OOH). Ab-initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Here, several exchange correlation functionals were employed (PBE96, PBE96+Grimme, and PBE0) in the simulations of a (3 x 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a=30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick).

Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations.

PubMed

Marino, Kristen A; Filizola, Marta

2018-01-01

An increasing number of G protein-coupled receptor (GPCR) crystal structures provide important-albeit static-pictures of how small molecules or peptides interact with their receptors. These high-resolution structures represent a tremendous opportunity to apply molecular dynamics (MD) simulations to capture atomic-level dynamical information that is not easy to obtain experimentally. Understanding ligand binding and unbinding processes, as well as the related responses of the receptor, is crucial to the design of better drugs targeting GPCRs. Here, we discuss possible ways to study the dynamics involved in the binding of small molecules to GPCRs, using long timescale MD simulations or metadynamics-based approaches.

Study of the effect of static/dynamic Coulomb friction variation at the tape-head interface of a spacecraft tape recorder by non-linear time response simulation

NASA Technical Reports Server (NTRS)

Mukhopadhyay, A. K.

1978-01-01

A description is presented of six simulation cases investigating the effect of the variation of static-dynamic Coulomb friction on servo system stability/performance. The upper and lower levels of dynamic Coulomb friction which allowed operation within requirements were determined roughly to be three times and 50% respectively of nominal values considered in a table. A useful application for the nonlinear time response simulation is the sensitivity analysis of final hardware design with respect to such system parameters as cannot be varied realistically or easily in the actual hardware. Parameters of the static/dynamic Coulomb friction fall in this category.

Dynamic and fluid-structure interaction simulations of bioprosthetic heart valves using parametric design with T-splines and Fung-type material models

NASA Astrophysics Data System (ADS)

Hsu, Ming-Chen; Kamensky, David; Xu, Fei; Kiendl, Josef; Wang, Chenglong; Wu, Michael C. H.; Mineroff, Joshua; Reali, Alessandro; Bazilevs, Yuri; Sacks, Michael S.

2015-06-01

This paper builds on a recently developed immersogeometric fluid-structure interaction (FSI) methodology for bioprosthetic heart valve (BHV) modeling and simulation. It enhances the proposed framework in the areas of geometry design and constitutive modeling. With these enhancements, BHV FSI simulations may be performed with greater levels of automation, robustness and physical realism. In addition, the paper presents a comparison between FSI analysis and standalone structural dynamics simulation driven by prescribed transvalvular pressure, the latter being a more common modeling choice for this class of problems. The FSI computation achieved better physiological realism in predicting the valve leaflet deformation than its standalone structural dynamics counterpart.

Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations.

PubMed

Sakuraba, Shun; Asai, Kiyoshi; Kameda, Tomoshi

2015-11-05

The dimerization free energies of RNA-RNA duplexes are fundamental values that represent the structural stability of RNA complexes. We report a comparative analysis of RNA-RNA duplex dimerization free-energy changes upon mutations, estimated from a molecular dynamics simulation and experiments. A linear regression for nine pairs of double-stranded RNA sequences, six base pairs each, yielded a mean absolute deviation of 0.55 kcal/mol and an R(2) value of 0.97, indicating quantitative agreement between simulations and experimental data. The observed accuracy indicates that the molecular dynamics simulation with the current molecular force field is capable of estimating the thermodynamic properties of RNA molecules.

Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory

NASA Astrophysics Data System (ADS)

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-01

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory.

PubMed

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-13

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

Molecular Dynamics of Dense Fluids: Simulation-Theory Symbiosis

NASA Astrophysics Data System (ADS)

Yip, Sidney

35 years ago Berni J. Alder showed the Boltzmann-Enskog kinetic theory failed to adequately account for the viscosity of fluids near solid density as determined by molecular dynamics simulation. This work, along with other notable simulation findings, provided great stimulus to the statistical mechanical studies of transport phenomena, particularly in dealing with collective effects in the time correlation functions of liquids. An extended theoretical challenge that remains partially resolved at best is the shear viscosity of supercooled liquids. How can one give a unified explanation of the so-called fragile and strong characteristic temperature behavior, with implications for the dynamics of glass transition? In this tribute on the occasion of his 90th birthday symposium, we recount a recent study where simulation, combined with heuristic (transition-state) and first principles (linear response) theories, identifies the molecular mechanisms governing glassy-state relaxation. Such an interplay between simulation and theory is progress from the early days; instead of simulation challenging theory, now simulation and theory complement each other.

Dynamic Simulation of a Wave Rotor Topped Turboshaft Engine

NASA Technical Reports Server (NTRS)

Greendyke, R. B.; Paxson, D. E.; Schobeiri, M. T.

1997-01-01

The dynamic behavior of a wave rotor topped turboshaft engine is examined using a numerical simulation. The simulation utilizes an explicit, one-dimensional, multi-passage, CFD based wave rotor code in combination with an implicit, one-dimensional, component level dynamic engine simulation code. Transient responses to rapid fuel flow rate changes and compressor inlet pressure changes are simulated and compared with those of a similarly sized, untopped, turboshaft engine. Results indicate that the wave rotor topped engine responds in a stable, and rapid manner. Furthermore, during certain transient operations, the wave rotor actually tends to enhance engine stability. In particular, there is no tendency toward surge in the compressor of the wave rotor topped engine during rapid acceleration. In fact, the compressor actually moves slightly away from the surge line during this transient. This behavior is precisely the opposite to that of an untopped engine. The simulation is described. Issues associated with integrating CFD and component level codes are discussed. Results from several transient simulations are presented and discussed.

Evaluation of Subgrid-Scale Models for Large Eddy Simulation of Compressible Flows

NASA Technical Reports Server (NTRS)

Blaisdell, Gregory A.

1996-01-01

The objective of this project was to evaluate and develop subgrid-scale (SGS) turbulence models for large eddy simulations (LES) of compressible flows. During the first phase of the project results from LES using the dynamic SGS model were compared to those of direct numerical simulations (DNS) of compressible homogeneous turbulence. The second phase of the project involved implementing the dynamic SGS model in a NASA code for simulating supersonic flow over a flat-plate. The model has been successfully coded and a series of simulations has been completed. One of the major findings of the work is that numerical errors associated with the finite differencing scheme used in the code can overwhelm the SGS model and adversely affect the LES results. Attached to this overview are three submitted papers: 'Evaluation of the Dynamic Model for Simulations of Compressible Decaying Isotropic Turbulence'; 'The effect of the formulation of nonlinear terms on aliasing errors in spectral methods'; and 'Large-Eddy Simulation of a Spatially Evolving Compressible Boundary Layer Flow'.

Human Sensibility Ergonomics Approach to Vehicle Simulator Based on Dynamics

NASA Astrophysics Data System (ADS)

Son, Kwon; Choi, Kyung-Hyun; Yoon, Ji-Sup

Simulators have been used to evaluate drivers' reactions to various transportation products. Most research, however, has concentrated on their technical performance. This paper considers driver's motion perception on a vehicle simulator through the analysis of human sensibility ergonomics. A sensibility ergonomic method is proposed in order to improve the reliability of vehicle simulators. A simulator in a passenger vehicle consists of three main modules such as vehicle dynamics, virtual environment, and motion representation modules. To evaluate drivers' feedback, human perceptions are categorized into a set verbal expressions collected and investigated to find the most appropriate ones for translation and angular accelerations of the simulator. The cut-off frequency of the washout filter in the representation module is selected as one sensibility factor. Sensibility experiments were carried out to find a correlation between the expressions and the cut-off frequency of the filter. This study suggests a methodology to obtain an ergonomic database that can be applied to the sensibility evaluation of dynamic simulators.

GRODY - GAMMA RAY OBSERVATORY DYNAMICS SIMULATOR IN ADA

NASA Technical Reports Server (NTRS)

Stark, M.

1994-01-01

Analysts use a dynamics simulator to test the attitude control system algorithms used by a satellite. The simulator must simulate the hardware, dynamics, and environment of the particular spacecraft and provide user services which enable the analyst to conduct experiments. Researchers at Goddard's Flight Dynamics Division developed GRODY alongside GROSS (GSC-13147), a FORTRAN simulator which performs the same functions, in a case study to assess the feasibility and effectiveness of the Ada programming language for flight dynamics software development. They used popular object-oriented design techniques to link the simulator's design with its function. GRODY is designed for analysts familiar with spacecraft attitude analysis. The program supports maneuver planning as well as analytical testing and evaluation of the attitude determination and control system used on board the Gamma Ray Observatory (GRO) satellite. GRODY simulates the GRO on-board computer and Control Processor Electronics. The analyst/user sets up and controls the simulation. GRODY allows the analyst to check and update parameter values and ground commands, obtain simulation status displays, interrupt the simulation, analyze previous runs, and obtain printed output of simulation runs. The video terminal screen display allows visibility of command sequences, full-screen display and modification of parameters using input fields, and verification of all input data. Data input available for modification includes alignment and performance parameters for all attitude hardware, simulation control parameters which determine simulation scheduling and simulator output, initial conditions, and on-board computer commands. GRODY generates eight types of output: simulation results data set, analysis report, parameter report, simulation report, status display, plots, diagnostic output (which helps the user trace any problems that have occurred during a simulation), and a permanent log of all runs and errors. The analyst can send results output in graphical or tabular form to a terminal, disk, or hardcopy device, and can choose to have any or all items plotted against time or against each other. Goddard researchers developed GRODY on a VAX 8600 running VMS version 4.0. For near real time performance, GRODY requires a VAX at least as powerful as a model 8600 running VMS 4.0 or a later version. To use GRODY, the VAX needs an Ada Compilation System (ACS), Code Management System (CMS), and 1200K memory. GRODY is written in Ada and FORTRAN.

Solvation and Dynamics of Sodium and Potassium in Ethylene Carbonate from ab Initio Molecular Dynamics Simulations

DOE PAGES

Pham, Tuan Anh; Kweon, Kyoung E.; Samanta, Amit; ...

2017-09-18

The development of sodium and potassium batteries offers a promising way to meet the scaling and cost challenges of energy storage. However, compared to Li +, several intrinsic properties of Na + and K +, including their solvation and dynamics in typical organic electrolytes utilized in battery applications, are less well-understood. Here in this paper, we report a systematic investigation of Na + and K + in ethylene carbonate (EC) using first-principles molecular dynamics simulations. Our simulations reveal significant differences in the solvation structure and dynamical properties of Na + and K + compared to Li +. We find that,more » in contrast to Li + which exhibits a well-defined first solvation shell, the larger Na+ and K+ ions show more disordered and flexible solvation structures. These differences in solvation were found to significantly influence the ion dynamics, leading to larger diffusion coefficients of Na + and K + compared to Li +. Our simulations also reveal a clear and interesting analog in the behavior of the ions in EC and aqueous environments, particularly in the specific ion effects on the solvent dynamics. Lastly, this work provides fundamental understanding of the intrinsic properties of Na + and K + in organic electrolytes, which may ultimately influence the intercalation mechanism at the electrode–electrolyte interface and therefore battery performance, lifetime, and safety.« less

Static and dynamic light scattering by red blood cells: A numerical study.

PubMed

Mauer, Johannes; Peltomäki, Matti; Poblete, Simón; Gompper, Gerhard; Fedosov, Dmitry A

2017-01-01

Light scattering is a well-established experimental technique, which gains more and more popularity in the biological field because it offers the means for non-invasive imaging and detection. However, the interpretation of light-scattering signals remains challenging due to the complexity of most biological systems. Here, we investigate static and dynamic scattering properties of red blood cells (RBCs) using two mesoscopic hydrodynamics simulation methods-multi-particle collision dynamics and dissipative particle dynamics. Light scattering is studied for various membrane shear elasticities, bending rigidities, and RBC shapes (e.g., biconcave and stomatocyte). Simulation results from the two simulation methods show good agreement, and demonstrate that the static light scattering of a diffusing RBC is not very sensitive to the changes in membrane properties and moderate alterations in cell shapes. We also compute dynamic light scattering of a diffusing RBC, from which dynamic properties of RBCs such as diffusion coefficients can be accessed. In contrast to static light scattering, the dynamic measurements can be employed to differentiate between the biconcave and stomatocytic RBC shapes and generally allow the differentiation based on the membrane properties. Our simulation results can be used for better understanding of light scattering by RBCs and the development of new non-invasive methods for blood-flow monitoring.

Static and dynamic light scattering by red blood cells: A numerical study

PubMed Central

Mauer, Johannes; Peltomäki, Matti; Poblete, Simón; Gompper, Gerhard

2017-01-01

Light scattering is a well-established experimental technique, which gains more and more popularity in the biological field because it offers the means for non-invasive imaging and detection. However, the interpretation of light-scattering signals remains challenging due to the complexity of most biological systems. Here, we investigate static and dynamic scattering properties of red blood cells (RBCs) using two mesoscopic hydrodynamics simulation methods—multi-particle collision dynamics and dissipative particle dynamics. Light scattering is studied for various membrane shear elasticities, bending rigidities, and RBC shapes (e.g., biconcave and stomatocyte). Simulation results from the two simulation methods show good agreement, and demonstrate that the static light scattering of a diffusing RBC is not very sensitive to the changes in membrane properties and moderate alterations in cell shapes. We also compute dynamic light scattering of a diffusing RBC, from which dynamic properties of RBCs such as diffusion coefficients can be accessed. In contrast to static light scattering, the dynamic measurements can be employed to differentiate between the biconcave and stomatocytic RBC shapes and generally allow the differentiation based on the membrane properties. Our simulation results can be used for better understanding of light scattering by RBCs and the development of new non-invasive methods for blood-flow monitoring. PMID:28472125

Molecular Dynamics Simulations of Orai Reveal How the Third Transmembrane Segment Contributes to Hydration and Ca2+ Selectivity in Calcium Release-Activated Calcium Channels.

PubMed

Alavizargar, Azadeh; Berti, Claudio; Ejtehadi, Mohammad Reza; Furini, Simone

2018-04-26

Calcium release-activated calcium (CRAC) channels open upon depletion of Ca 2+ from the endoplasmic reticulum, and when open, they are permeable to a selective flux of calcium ions. The atomic structure of Orai, the pore domain of CRAC channels, from Drosophila melanogaster has revealed many details about conduction and selectivity in this family of ion channels. However, it is still unclear how residues on the third transmembrane helix can affect the conduction properties of the channel. Here, molecular dynamics and Brownian dynamics simulations were employed to analyze how a conserved glutamate residue on the third transmembrane helix (E262) contributes to selectivity. The comparison between the wild-type and mutated channels revealed a severe impact of the mutation on the hydration pattern of the pore domain and on the dynamics of residues K270, and Brownian dynamics simulations proved that the altered configuration of residues K270 in the mutated channel impairs selectivity to Ca 2+ over Na + . The crevices of water molecules, revealed by molecular dynamics simulations, are perfectly located to contribute to the dynamics of the hydrophobic gate and the basic gate, suggesting a possible role in channel opening and in selectivity function.

N-body simulations in modified Newtonian dynamics

NASA Astrophysics Data System (ADS)

Nipoti, C.; Londrillo, P.; Ciotti, L.

We describe some results obtained with N-MODY, a code for N-body simulations of collisionless stellar systems in modified Newtonian dynamics (MOND). We found that a few fundamental dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter. In particular, violent relaxation, phase mixing and galaxy merging take significantly longer in MOND than in Newtonian gravity, while dynamical friction is more effective in a MOND system than in an equivalent Newtonian system with dark matter.

Development of High Fidelity Mobility Simulation of an Autonomous Vehicle in an Off-Road Scenario Using Integrated Sensor, Controller, and Multi-Body Dynamics

DTIC Science & Technology

2011-08-04

AND MULTI-BODY DYNAMICS Jayakumar , Smith, Ross, Jategaonkar, Konarzewski 4 August 2011 UNCLASSIFIED: Distribution Statement A. Approved for public...Autonomous Vehicle in an Off-Road Scenario Using Integrated Sensor, Controller, and Multi-Body Dynamics 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM...Cannot neglect vehicle dynamics 4 August 2011 3 UNCLASSIFIED Importance of Simulation Fidelity • Performance evaluation requires entire system

On finding the analytic dependencies of the external field potential on the control function when optimizing the beam dynamics

NASA Astrophysics Data System (ADS)

Ovsyannikov, A. D.; Kozynchenko, S. A.; Kozynchenko, V. A.

2017-12-01

When developing a particle accelerator for generating the high-precision beams, the injection system design is of importance, because it largely determines the output characteristics of the beam. At the present paper we consider the injection systems consisting of electrodes with given potentials. The design of such systems requires carrying out simulation of beam dynamics in the electrostatic fields. For external field simulation we use the new approach, proposed by A.D. Ovsyannikov, which is based on analytical approximations, or finite difference method, taking into account the real geometry of the injection system. The software designed for solving the problems of beam dynamics simulation and optimization in the injection system for non-relativistic beams has been developed. Both beam dynamics and electric field simulations in the injection system which use analytical approach and finite difference method have been made and the results presented in this paper.

Structural and dynamical properties of the V(3+) ion in dilute aqueous solution: An ab initio QM/MM molecular dynamics simulation.

PubMed

Kritayakornupong, Chinapong

2009-12-01

A hybrid ab initio QM/MM molecular dynamics simulation at the Hartree-Fock level has been performed to investigate structural and dynamical parameters of the V(3+) ion in dilute aqueous solution. A distorted octahedral structure with the average V(3+)-O distance of 1.99 A is evaluated from the QM/MM simulation, which is in good agreement with the X-ray data. Several structural parameters such as angular distribution functions, theta- and tilt-angle distributions have been determined to obtain the full description of the hydration structure of the hydrated V(3+). The Jahn-Teller distortions of the V(3+) ion are pronounced in the QM/MM simulation. The mean residence time of 14.5 ps is estimated for the ligand exchange processes in the second hydration shell. (c) 2009 Wiley Periodicals, Inc.

Stabilization of Model Membrane Systems by Disaccharides. Quasielastic Neutron Scattering Experiments and Atomistic Simulations

NASA Astrophysics Data System (ADS)

Doxastakis, Emmanouil; Garcia Sakai, Victoria; Ohtake, Satoshi; Maranas, Janna K.; de Pablo, Juan J.

2006-03-01

Trehalose, a disaccharide of glucose, is often used for the stabilization of cell membranes in the absence of water. This work studies the effects of trehalose on model membrane systems as they undergo a melting transition using a combination of experimental methods and atomistic molecular simulations. Quasielastic neutron scattering experiments on selectively deuterated samples provide the incoherent dynamic structure over a wide time range. Elastic scans probing the lipid tail dynamics display clear evidence of a main melting transition that is significantly lowered in the presence of trehalose. Lipid headgroup mobility is considerably restricted at high temperatures and directly associated with the dynamics of the sugar in the mixture. Molecular simulations provide a detailed overview of the dynamics and their spatial and time dependence. The combined simulation and experimental methodology offers a unique, molecular view of the physics of systems commonly employed in cryopreservation and lyophilization processes.

Integration of Multiple Data Sources to Simulate the Dynamics of Land Systems

PubMed Central

Deng, Xiangzheng; Su, Hongbo; Zhan, Jinyan

2008-01-01

In this paper we present and develop a new model, which we have called Dynamics of Land Systems (DLS). The DLS model is capable of integrating multiple data sources to simulate the dynamics of a land system. Three main modules are incorporated in DLS: a spatial regression module, to explore the relationship between land uses and influencing factors, a scenario analysis module of the land uses of a region during the simulation period and a spatial disaggregation module, to allocate land use changes from a regional level to disaggregated grid cells. A case study on Taips County in North China is incorporated in this paper to test the functionality of DLS. The simulation results under the baseline, economic priority and environmental scenarios help to understand the land system dynamics and project near future land-use trajectories of a region, in order to focus management decisions on land uses and land use planning. PMID:27879726